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Webb J, Zhao M, Campbell AH, Paul NA, Cummins SF, Eamens AL. The microRNA Pathway of Macroalgae: Its Similarities and Differences to the Plant and Animal microRNA Pathways. Genes (Basel) 2025; 16:442. [PMID: 40282402 PMCID: PMC12026948 DOI: 10.3390/genes16040442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2025] [Revised: 03/31/2025] [Accepted: 04/05/2025] [Indexed: 04/29/2025] Open
Abstract
In plants and animals, the microRNA (miRNA) class of small regulatory RNA plays an essential role in controlling gene expression in all aspects of development, to respond to environmental stress, or to defend against pathogen attack. This well-established master regulatory role for miRNAs has led to each protein-mediated step of both the plant and animal miRNA pathways being thoroughly characterized. Furthermore, this degree of characterization has led to the development of a suite of miRNA-based technologies for gene expression manipulation for fundamental research or for use in industrial or medical applications. In direct contrast, molecular research on the miRNA pathway of macroalgae, specifically seaweeds (marine macroalgae), remains in its infancy. However, the molecular research conducted to date on the seaweed miRNA pathway has shown that it shares functional features specific to either the plant or animal miRNA pathway. In addition, of the small number of seaweed species where miRNA data is available, little sequence conservation of individual miRNAs exists. These preliminary findings show the pressing need for substantive research into the seaweed miRNA pathway to advance our current understanding of this essential gene expression regulatory process. Such research will also generate the knowledge required to develop novel miRNA-based technologies for use in seaweeds. In this review, we compare and contrast the seaweed miRNA pathway to those well-characterized pathways of plants and animals and outline the low degree of miRNA sequence conservation across the polyphyletic group known as the seaweeds.
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Affiliation(s)
- Jessica Webb
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Min Zhao
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Alexandra H. Campbell
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Nicholas A. Paul
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Scott F. Cummins
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Andrew L. Eamens
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia (M.Z.); (A.H.C.); (N.A.P.); (S.F.C.)
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Zhang M, Cheng W, Yuan X, Wang J, Cheng T, Zhang Q. Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume. FRONTIERS IN PLANT SCIENCE 2022; 13:931454. [PMID: 35937373 PMCID: PMC9355595 DOI: 10.3389/fpls.2022.931454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/30/2022] [Indexed: 05/08/2023]
Abstract
MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.
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Zhang J, Shi J, Yuan C, Liu X, Du G, Fan R, Zhang B. MicroRNA Expression Profile Analysis of Chlamydomonas reinhardtii during Lipid Accumulation Process under Nitrogen Deprivation Stresses. Bioengineering (Basel) 2021; 9:bioengineering9010006. [PMID: 35049715 PMCID: PMC8773410 DOI: 10.3390/bioengineering9010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
Lipid accumulation in various microalgae has been found induced by nitrogen deprivation, and it controls many different genes expression. Yet, the underlying molecular mechanisms still remain largely unknown. MicroRNA (miRNAs) play a critical role in post-transcriptional gene regulation. In this study, miRNAs were hypothesized involved in lipid accumulation by nitrogen deprivation. A deep-sequencing platform was used to explore miRNAs-mediated responses induced by nitrogen deprivation in Chlamydomonas reinhardtii. The eukaryotic orthologous groups of proteins (KOG) function in the predicted target genes of miRNA with response to nitrogen deprivation were mainly involved in signal transduction mechanisms, including transcription, lipid transport, and metabolism. A total of 109 miRNA were predicted, including 79 known miRNA and 30 novel miRNA. A total of 29 miRNAs showed significantly differential expressions after nitrogen deprivation, and most of them were upregulated. A total of 10 miRNAs and their targeting genes might involve in lipid transport and metabolism biological process. This study first investigates nitrogen deprivation-regulated miRNAs in microalgae and broadens perspectives on miRNAs importance in microalgae lipid accumulation via nitrogen deprivation. This study provides theoretical guidance for the application of microalgae in bio-oil engineering production.
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Affiliation(s)
- Jingxian Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chenyang Yuan
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiangcen Liu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guilin Du
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruimei Fan
- Sino-UK Joint Laboratory for Brain Function and Injury and Department of Physiology and Neurobiology, Xinxiang Medical University, Xinxiang 453003, China
- Correspondence: (R.F.); (B.Z.)
| | - Baoguo Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (R.F.); (B.Z.)
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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Paul S, Bravo Vázquez LA, Márquez Nafarrate M, Gutiérrez Reséndiz AI, Srivastava A, Sharma A. The regulatory activities of microRNAs in non-vascular plants: a mini review. PLANTA 2021; 254:57. [PMID: 34424349 DOI: 10.1007/s00425-021-03707-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/14/2021] [Indexed: 05/21/2023]
Abstract
MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
| | - Luis Alberto Bravo Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Marilyn Márquez Nafarrate
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Av. Eugenio Garza Sada, No. 2501 Tecnologico, CP 64849, Monterrey, Mexico
| | - Ana Isabel Gutiérrez Reséndiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
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Yan G, Zhang J, Jiang M, Gao X, Yang H, Li L. Identification of Known and Novel MicroRNAs in Raspberry Organs Through High-Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2020; 11:728. [PMID: 32582255 PMCID: PMC7284492 DOI: 10.3389/fpls.2020.00728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/06/2020] [Indexed: 05/23/2023]
Abstract
MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in plants by negatively affecting gene expression. Studies on the identification of miRNAs and their functions in various plant species and organs have significantly contributed to plant development research. In the current study, we utilized high-throughput sequencing to detect the miRNAs in the root, stem, and leaf tissues of raspberry (Rubus idaeus). A total of more than 35 million small RNA reads ranging in size from 18 to 35 nucleotides were obtained, with 147 known miRNAs and 542 novel miRNAs identified among the three organs. Sequence verification and the relative expression profiles of the six known miRNAs were investigated by stem-loop quantitative real-time PCR. Furthermore, the potential target genes of the known and novel miRNAs were predicted and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Enrichment analysis of the GO-associated biological processes and molecular functions revealed that these target genes were potentially involved in a wide range of metabolic pathways and developmental processes. Moreover, the miRNA target prediction revealed that most of the targets predicted as transcription factor-coding genes are involved in cellular and metabolic processes. This report is the first to identify miRNAs in raspberry. The detected miRNAs were analyzed by cluster analysis according to their expression, which revealed that these conservative miRNAs are necessary for plant functioning. The results add novel miRNAs to the raspberry transcriptome, providing a useful resource for the further elucidation of the functional roles of miRNAs in raspberry growth and development.
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Affiliation(s)
- Gengxuan Yan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Jie Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Meng Jiang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xince Gao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Hongyi Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lili Li
- Institute of Forestry Science of Heilongjiang Province, Harbin, China
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Shao J, Wang L, Liu Y, Qi Q, Wang B, Lu S, Liu C. Identification of milRNAs and their target genes in Ganoderma lucidum by high-throughput sequencing and degradome analysis. Fungal Genet Biol 2020; 136:103313. [DOI: 10.1016/j.fgb.2019.103313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/09/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022]
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Wang Y, Peng M, Wang W, Chen Y, He Z, Cao J, Lin Z, Yang Z, Gong M, Yin Y. Verification of miRNAs in ginseng decoction by high-throughput sequencing and quantitative real-time PCR. Heliyon 2019; 5:e01418. [PMID: 30984884 PMCID: PMC6446053 DOI: 10.1016/j.heliyon.2019.e01418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/13/2019] [Accepted: 03/21/2019] [Indexed: 12/24/2022] Open
Abstract
Panax ginseng C. A. Meyer is a precious traditional Chinese medicine that has been clinically used for over thousands of years. In general, ginseng needs to be prepared to ginseng decoction before taking it. MicroRNAs are a class of small (18–24 nt), single-stranded molecules that regulate gene expression at the post-transcriptional level. Considering that ginseng miRNAs may be bioactive compounds, we used Illumina high-throughput sequencing and quantitative real-time PCR (qRT-PCR) to validate the existence of miRNAs in fresh ginseng decoction which have been boiled at high temperature. Our previous studies have demonstrated that there are several miRNAs in fresh ginseng. The roots of fresh Panax ginseng were prepared according to routine methods, from which miRNAs were extracted and sequenced. A total of 43 miRNAs were identified from water decoction by Illumina high-throughput sequencing, belonging to 71 miRNA families. The target genes of these miRNAs were predicted by sequencing, and were annotated by GO, KEGG and Nr databases. The functions of these target genes mainly included plant hormone signal transduction, transcription regulation, macromolecular metabolism and auxin signaling. Nine highly expressed miRNAs (miR159, miR167, miR396, miR166, miR168, miR156, miR165, miR162 and miR394) were verified by qRT-PCR, and the results of Illumina high-throughput sequencing and qRT-PCR were consistent. Results from this study indicate that miRNAs remained stable in P. ginseng after high-temperature boiling. Additionally, Illumina high-throughput sequencing was superior in the acquisition of higher amount of small RNAs.
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Affiliation(s)
- Yingfang Wang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Engineering & Technology Research Center of Topical Precise Drug Delivery System, Guangzhou 510006, china
- Corresponding author.
| | - Mengyuan Peng
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjuan Wang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yanlin Chen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhihua He
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jingjing Cao
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhiyun Lin
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zemin Yang
- School of Basic Courses, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Mengjuan Gong
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yongqin Yin
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
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Chen F, Zhang J, Chen J, Li X, Dong W, Hu J, Lin M, Liu Y, Li G, Wang Z, Zhang L. realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5055577. [PMID: 30020436 PMCID: PMC6051438 DOI: 10.1093/database/bay072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 06/15/2018] [Indexed: 11/28/2022]
Abstract
With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development. Database URL: http://realdb.algaegenome.org/
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Affiliation(s)
- Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiawei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junhao Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Xiaojiang Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Dong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jian Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meigui Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guowei Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China.,College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Xue WH, Fan ZR, Li LF, Lu JL, Ma BJ, Kan QC, Zhao J. Construction of an oesophageal cancer-specific ceRNA network based on miRNA, lncRNA, and mRNA expression data. World J Gastroenterol 2018; 24:23-34. [PMID: 29358879 PMCID: PMC5757122 DOI: 10.3748/wjg.v24.i1.23] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/07/2017] [Accepted: 11/27/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To explore the expression profiles of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and mRNAs in oesophageal squamous cell carcinoma (ESCC) in order to construct an oesophageal cancer-specific competing endogenous RNA (ceRNA) network.
METHODS In this work, the expression data of miRNAs, lncRNAs, and mRNAs in ESCC were obtained. An oesophageal cancer-specific ceRNA network was then constructed and investigated.
RESULTS CeRNAs have the ability to reduce the targeting activity of miRNAs, leading to the de-repression of specific mRNAs with common miRNA response elements. CeRNA interactions have a critical effect in gene regulation and cancer development.
CONCLUSION This study suggests a novel perspective on potential oesophageal cancer mechanisms as well as novel pathways for modulating ceRNA networks for treating cancers.
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MESH Headings
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/pathology
- Cluster Analysis
- Computational Biology
- Databases, Genetic
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/metabolism
- Esophageal Neoplasms/mortality
- Esophageal Neoplasms/pathology
- Esophageal Squamous Cell Carcinoma
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- MicroRNAs/genetics
- MicroRNAs/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
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Affiliation(s)
- Wen-Hua Xue
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Zhi-Rui Fan
- Cancer Centre, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Li-Feng Li
- Cancer Centre, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Jing-Li Lu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Bing-Jun Ma
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Quan-Cheng Kan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Jie Zhao
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
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Li Q, Deng C, Xia Y, Kong L, Zhang H, Zhang S, Wang J. Identification of novel miRNAs and miRNA expression profiling in embryogenic tissues of Picea balfouriana treated by 6-benzylaminopurine. PLoS One 2017; 12:e0176112. [PMID: 28486552 PMCID: PMC5423612 DOI: 10.1371/journal.pone.0176112] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
Here, we compared miRNA expression profiles in embryonic cell cultures of the conifer Picea balfouriana following application of the synthetic cytokinin 6-benzylaminopurine (6-BAP). We used next-generation sequencing to analyze three libraries of small RNAs from the treated embryogenic cell cultures and generated 24,000,000 raw reads from each of the libraries. Over 70 differentially regulated micro RNA (miRNA) families (≥2 fold change in expression) were identified between pairs of treatments. A quantitative analysis showed that miR3633 and miR1026 were upregulated in tissues with the highest embryogenic ability. These two miRNAs were predicted to target genes encoding receptor-like protein kinase and GAMYB transcription factors, respectively. In one library, miR1160, miR5638, miR1315, and miR5225 were downregulated. These four miRNAs were predicted to target genes encoding APETALA2, calmodulin-binding protein, and calcium-dependent protein kinase transcription factors. The expression patterns of the miRNAs and their targets were negatively correlated. Approximately 181 potentially novel P. balfouriana miRNAs were predicted from the three libraries, and seven were validated during the quantitative analysis. This study is the first report of differential miRNA regulation in tissues treated with 6-BAP during somatic embryogenesis. The differentially expressed miRNAs will be of value for investigating the mechanisms of embryogenic processes that are responsive to 6-BAP in P. balfouriana.
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Affiliation(s)
- Qingfen Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Cheng Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yan Xia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lisheng Kong
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- * E-mail:
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Gomes F, Watanabe L, Nozawa S, Oliveira L, Cardoso J, Vianez J, Nunes M, Schneider H, Sampaio I. Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. Genomics 2017; 109:67-74. [PMID: 28192178 DOI: 10.1016/j.ygeno.2017.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 01/20/2023]
Abstract
Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the "biological processes" domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools.
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Affiliation(s)
- Fátima Gomes
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Luciana Watanabe
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Sérgio Nozawa
- Dow AgroSciences, Av Antonio Diederichsen, 400, - Ribeirão Preto, SP 14020-250, Brazil.
| | - Layanna Oliveira
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Jedson Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil; Postgraduate Program in Virology (PPGV), Evandro Chagas Institute, Ministry of Health, Ananindeua, PA 67030-000, Brazil.
| | - João Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Márcio Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Horacio Schneider
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Iracilda Sampaio
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
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Ordóñez-Baquera PL, González-Rodríguez E, Aguado-Santacruz GA, Rascón-Cruz Q, Conesa A, Moreno-Brito V, Echavarria R, Dominguez-Viveros J. Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis. Comput Biol Chem 2017; 66:26-35. [DOI: 10.1016/j.compbiolchem.2016.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/04/2016] [Accepted: 11/04/2016] [Indexed: 11/26/2022]
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15
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Zhou R, Wang Q, Jiang F, Cao X, Sun M, Liu M, Wu Z. Identification of miRNAs and their targets in wild tomato at moderately and acutely elevated temperatures by high-throughput sequencing and degradome analysis. Sci Rep 2016; 6:33777. [PMID: 27653374 PMCID: PMC5031959 DOI: 10.1038/srep33777] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/02/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are 19-24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. Here, three small-RNA libraries and three degradome libraries were constructed from the leaves of the heat-tolerant tomato at normal, moderately and acutely elevated temperatures (26/18 °C, 33/33 °C and 40/40 °C, respectively). Following high-throughput sequencing, 662 conserved and 97 novel miRNAs were identified in total with 469 conserved and 91 novel miRNAs shared in the three small-RNA libraries. Of these miRNAs, 96 and 150 miRNAs were responsive to the moderately and acutely elevated temperature, respectively. Following degradome sequencing, 349 sequences were identified as targets of 138 conserved miRNAs, and 13 sequences were identified as targets of eight novel miRNAs. The expression levels of seven miRNAs and six target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in tomatoes at elevated temperatures.
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Affiliation(s)
- Rong Zhou
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, China
- Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Zhongling Street No. 50, Nanjing, 210014, China
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu province, Jiangsu, Nanjing, China
| | - Qian Wang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095, China
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095, China
| | - Xue Cao
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095, China
| | - Mintao Sun
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095, China
| | - Min Liu
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095, China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in East China, Ministry of Agriculture, Nanjing, 210095, China
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Wu Y, Guo J, Cai Y, Gong X, Xiong X, Qi W, Pang Q, Wang X, Wang Y. Genome-wide identification and characterization of Eutrema salsugineum microRNAs for salt tolerance. PHYSIOLOGIA PLANTARUM 2016; 157:453-68. [PMID: 26806325 DOI: 10.1111/ppl.12419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 11/12/2015] [Accepted: 12/10/2015] [Indexed: 05/23/2023]
Abstract
Eutrema salsugineum, a close relative of Arabidopsis thaliana, is a valuable halophytic model plant that has extreme tolerance to salinity. As posttranscriptional gene regulators, microRNAs (miRNAs) control gene expression and a variety of biological processes, including plant-stress responses. To identify salt-stress responsive miRNAs in E. salsugineum and reveal their possible roles in the adaptive response to salt stress, we chose the Solexa sequencing platform to screen the miRNAs in 4-week-old E. salsugineum seedlings under salt treatment. A total of 82 conserved miRNAs belonging to 27 miRNA families and 17 novel miRNAs were identified and 11 conserved miRNA families and 4 novel miRNAs showed a significant response to salt stress. To investigate the possible biological roles of miRNAs, 1060 potential targets were predicted. Moreover, 35 gene ontology (GO) categories and 1 pathway, including a few terms that were directly and indirectly related to salt stress, were significantly enriched in the salt-stress-responsive miRNAs targets. The relative expression analysis of six target genes was analyzed using quantitative real-time polymerase chain reaction (PCR) and showed a negative correlation with their corresponding miRNAs. Many stress regulatory and phytohormone regulatory cis-regulatory elements were widely present in the promoter region of the salt-responsive miRNA precursors. This study describes the large-scale characterization of E. salsugineum miRNAs and provides a useful resource for further understanding of miRNA functions in the regulation of the E. salsugineum salt-stress response.
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Affiliation(s)
- Ying Wu
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jing Guo
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Yimei Cai
- CAS Key Laboratory of Genome Sciences and Information, BeGenomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Xiaolin Gong
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Xuemei Xiong
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Wenwen Qi
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, BeGenomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yang Wang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China
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Zhang X, Gamarra J, Castro S, Carrasco E, Hernandez A, Mock T, Hadaegh AR, Read BA. Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi. PLoS One 2016; 11:e0154279. [PMID: 27101007 PMCID: PMC4839659 DOI: 10.1371/journal.pone.0154279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/11/2016] [Indexed: 12/31/2022] Open
Abstract
Small RNAs (smRNAs) control a variety of cellular processes by silencing target genes at the transcriptional or post-transcription level. While extensively studied in plants, relatively little is known about smRNAs and their targets in marine phytoplankton, such as Emiliania huxleyi (E. huxleyi). Deep sequencing was performed of smRNAs extracted at different time points as E. huxleyi cells transition from logarithmic to stationary phase growth in batch culture. Computational analyses predicted 18 E. huxleyi specific miRNAs. The 18 miRNA candidates and their precursors vary in length (18–24 nt and 71–252 nt, respectively), genome copy number (3–1,459), and the number of genes targeted (2–107). Stem-loop real time reverse transcriptase (RT) PCR was used to validate miRNA expression which varied by nearly three orders of magnitude when growth slows and cells enter stationary phase. Stem-loop RT PCR was also used to examine the expression profiles of miRNA in calcifying and non-calcifying cultures, and a small subset was found to be differentially expressed when nutrients become limiting and calcification is enhanced. In addition to miRNAs, endogenous small RNAs such as ra-siRNAs, ta-siRNAs, nat-siRNAs, and piwiRNAs were predicted along with the machinery for the biogenesis and processing of si-RNAs. This study is the first genome-wide investigation smRNAs pathways in E. huxleyi. Results provide new insights into the importance of smRNAs in regulating aspects of physiological growth and adaptation in marine phytoplankton and further challenge the notion that smRNAs evolved with multicellularity, expanding our perspective of these ancient regulatory pathways.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Jaime Gamarra
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Steven Castro
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Estela Carrasco
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Aaron Hernandez
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, United Kingdom
| | - Ahmad R. Hadaegh
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Betsy A. Read
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
- * E-mail:
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Sun H, Zhou Z, Dong Y, Yang A, Jiang J, Chen Z, Guan X, Wang B, Gao S, Jiang B. Expression analysis of microRNAs related to the skin ulceration syndrome of sea cucumber Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2016; 49:205-212. [PMID: 26723265 DOI: 10.1016/j.fsi.2015.12.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/20/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in many biological processes. To investigate the miRNAs related to skin ulceration syndrome (SUS) of Apostichopus japonicus, small RNA libraries of body wall, intestine, respiratory tree and coelomocytes from healthy and diseased A. japonicus were sequenced on Illumina Hiseq 2000 platform. A total of 247 conserved and 10 novel miRNAs were identified across all libraries. After pair-wise comparisons, 215 miRNAs in body wall, 36 in intestine, 2 in respiratory tree and 38 in coelomocytes showed significant expression differences. Further analyses were conducted on some tissue-specific differentially expressed miRNAs: miR-8 and miR-486-5p in body wall, miR-200-3p, let-7-5p and miR-125 in intestine, miR-278a-3p and bantam in respiratory, miR-10a and miR-184 in coelomocytes. Notably, these miRNAs in some species were reported to function in various physiological or pathological processes associated with immune regulations. Using stem-loop quantitative real time PCR, six representative miRNAs in four tissues were selected to validate the sequencing results. The Pearson's correlation coefficient (R) of the six miRNAs ranged from 0.777 to 0.948, which confirmed the consistency and accuracy between these two approaches. This study provides comprehensive expression and regulation patterns of functional miRNAs in different tissues and gives insights into the tissue-specific immune response mechanisms in SUS-infected A. japonicus.
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Affiliation(s)
- Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zhong Chen
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bai Wang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shan Gao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
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Guo R, Chen X, Lin Y, Xu X, Thu MK, Lai Z. Identification of Novel and Conserved miRNAs in Leaves of In vitro Grown Citrus reticulata "Lugan" Plantlets by Solexa Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 6:1212. [PMID: 26779240 PMCID: PMC4705231 DOI: 10.3389/fpls.2015.01212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/16/2015] [Indexed: 05/23/2023]
Abstract
MicroRNAs (miRNAs) play essential roles in plant development, but the roles in the in vitro plant development are unknown. Leaves of ponkan plantlets derived from mature embryos at in vitro culture conditions were used to sequence small RNA fraction via Solexa sequencing, and the miRNAs expression was analyzed. The results showed that there were 3,065,625 unique sequences in ponkan, of which 0.79% were miRNAs. The RNA sequences with lengths of 18-25 nt derived from the library were analyzed, leading to the identification of 224 known miRNAs, of which the most abundant were miR157, miR156, and miR166. Three hundred and fifty-eight novel miRNA candidates were also identified, and the number of reads of ponkan novel miRNAs varied from 5 to 168,273. The expression of the most known miRNAs obtained was at low levels, which varied from 5 to 4,946,356. To better understand the role of miRNAs during the preservation of ponkan in vitro plantlet, the expression patterns of cre-miR156a/159b/160a/166a/167a/168a/171/398b were validated by quantitative real-time PCR (qPCR). The results showed that not only the development-associated miRNAs, e.g., cre-miR156/159/166/396, expressed highly at the early preservation period in the in vitro ponkan plantlet leaves but also the stress-related miRNAs, e.g., cre-miR171 and cre-miR398b, expressed highly at the same time. The expression levels of most tested miRNAs were found to decrease after 6 months and the amounts of these miRNAs were kept at low levels at 18 months. After analyzing the expression level of their targets during the reservation of the ponkan in vitro plantlet, development-associated cre-ARF6 and stress-related cre-CSD modules exhibited negative correlation with miR167 and miR398, respectively, indicating an involvement of the miRNAs in the in vitro development of ponkan and function in the conservation of ponkan germplasm.
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Affiliation(s)
- Rongfang Guo
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xiaodong Chen
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yuling Lin
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xuhan Xu
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institut de la Recherche Interdisciplinaire de ToulouseToulouse, France
| | - Min Kyaw Thu
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhongxiong Lai
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
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Jian H, Wang J, Wang T, Wei L, Li J, Liu L. Identification of Rapeseed MicroRNAs Involved in Early Stage Seed Germination under Salt and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2016; 7:658. [PMID: 27242859 PMCID: PMC4865509 DOI: 10.3389/fpls.2016.00658] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/29/2016] [Indexed: 05/18/2023]
Abstract
Drought and salinity are severe and wide-ranging abiotic stresses that substantially affect crop germination, development and productivity, and seed germination is the first critical step in plant growth and development. To comprehensively investigate small-RNA targets and improve our understanding of miRNA-mediated post-transcriptional regulation networks during Brassica napus seed imbibition under drought and salt stresses, we constructed three small-RNA libraries from B. napus variety ZS11 embryos exposed to salt (200 mM NaCl, denoted "S"), drought (200 g L(-1) PEG-6000, denoted "D"), and distilled water (denoted "CK") during imbibition and sequenced them using an Illumina Genome Analyzer. A total of 11,528,557, 12,080,081, and 12,315,608 raw reads were obtained from the CK, D, and S libraries, respectively. Further analysis identified 85 known miRNAs belonging to 31 miRNA families and 882 novel miRNAs among the three libraries. Comparison of the D and CK libraries revealed significant down-regulation of six miRNA families, miR156, miR169, miR860, miR399, miR171, and miR395, whereas only miR172 was significantly up-regulated. In contrast, comparison of the S library with the CK library showed significant down-regulation of only two miRNA families: miRNA393 and miRNA399. Putative targets for 336, 376, and 340 novel miRNAs were successfully predicted in the CK, D, and S libraries, respectively, and 271 miRNA families and 20 target gene families [including disease resistance protein (DIRP), drought-responsive family protein (DRRP), early responsive to dehydration stress protein (ERD), stress-responsive alpha-beta barrel domain protein (SRAP), and salt tolerance homolog2 (STH2)] were confirmed as being core miRNAs and genes involved in the seed imbibition response to salt and drought stresses. The sequencing results were partially validated by quantitative RT-PCR for both conserved and novel miRNAs as well as the predicted target genes. Our data suggest that diverse and complex miRNAs are involved in seed imbibition, indicating that miRNAs are involved in plant hormone regulation, and may play important roles during seed germination under salt- or drought-stress conditions.
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Bukhari SAH, Shang S, Zhang M, Zheng W, Zhang G, Wang TZ, Shamsi IH, Wu F. Genome-wide identification of chromium stress-responsive micro RNAs and their target genes in tobacco (Nicotiana tabacum) roots. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:2573-82. [PMID: 26053264 DOI: 10.1002/etc.3097] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 04/07/2015] [Accepted: 05/31/2015] [Indexed: 05/29/2023]
Abstract
Tobacco easily accumulates certain heavy metals in leaves and thus poses a potential threat to human health. To systematically dissect Cr-responsive microRNAs (miRNAs) and their targets at the global level, 4 small RNA libraries were constructed from the roots of Cr-treated (Cr) and Cr-free (control) for 2 contrasting tobacco genotypes,Yunyan2 (Cr-sensitive) and Guiyan1 (Cr-tolerant). Using high-throughput-sequencing-technology, the authors identified 53 conserved and 29 novel miRNA families. Comparative genomic analysis of 41 conserved Cr-responsive miRNA families revealed that 11 miRNA families showed up-regulation in Guiyan1 but unaltered in Yunyan2, and 17 miRNA families were up-regulated only in Yunyan2 under Cr stress. Only 1 family, miR6149, was down-regulated in Yunyan2 but remained unchanged in Guiyan1. Of the 29 novel miRNA families, 14 expressed differently in the 2 genotypes under Cr stress. Based on a high-throughput degradome sequencing homology search, potential targets were predicted for the 41 conserved and 14 novel Cr-responsive miRNA families. Clusters of Orthologous Groups functional category analysis revealed that some of these predicted target transcripts of miRNAs are responsive to biotic and abiotic stresses. Furthermore, the expression patterns of many Cr-responsive miRNAs were validated by stem-loop real-time transcription polymerase chain reaction. The results of the present study provide valuable information and a framework for understanding the function of miRNAs in Cr tolerance.
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Affiliation(s)
- Syed Asad Hussain Bukhari
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Shenghua Shang
- Guizhou Tobacco Science Institute, Guiyang, People's Republic of China
| | - Mian Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Weite Zheng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Ting-Zhang Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Imran Haider Shamsi
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
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22
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Yusuf NHM, Ong WD, Redwan RM, Latip MA, Kumar SV. Discovery of precursor and mature microRNAs and their putative gene targets using high-throughput sequencing in pineapple (Ananas comosus var. comosus). Gene 2015; 571:71-80. [DOI: 10.1016/j.gene.2015.06.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/05/2015] [Accepted: 06/19/2015] [Indexed: 01/01/2023]
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Geng H, Sui Z, Zhang S, Du Q, Ren Y, Liu Y, Kong F, Zhong J, Ma Q. Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis. PLoS One 2015; 10:e0138709. [PMID: 26398216 PMCID: PMC4580472 DOI: 10.1371/journal.pone.0138709] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 09/02/2015] [Indexed: 12/19/2022] Open
Abstract
Micro-ribonucleic acids (miRNAs) are a large group of endogenous, tiny, non-coding RNAs consisting of 19–25 nucleotides that regulate gene expression at either the transcriptional or post-transcriptional level by mediating gene silencing in eukaryotes. They are considered to be important regulators that affect growth, development, and response to various stresses in plants. Alexandrium catenella is an important marine toxic phytoplankton species that can cause harmful algal blooms (HABs). To date, identification and function analysis of miRNAs in A. catenella remain largely unexamined. In this study, high-throughput sequencing was performed on A. catenella to identify and quantitatively profile the repertoire of small RNAs from two different growth phases. A total of 38,092,056 and 32,969,156 raw reads were obtained from the two small RNA libraries, respectively. In total, 88 mature miRNAs belonging to 32 miRNA families were identified. Significant differences were found in the member number, expression level of various families, and expression abundance of each member within a family. A total of 15 potentially novel miRNAs were identified. Comparative profiling showed that 12 known miRNAs exhibited differential expression between the lag phase and the logarithmic phase. Real-time quantitative RT-PCR (qPCR) was performed to confirm the expression of two differentially expressed miRNAs that were one up-regulated novel miRNA (aca-miR-3p-456915), and one down-regulated conserved miRNA (tae-miR159a). The expression trend of the qPCR assay was generally consistent with the deep sequencing result. Target predictions of the 12 differentially expressed miRNAs resulted in 1813target genes. Gene ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) annotations revealed that some miRNAs were associated with growth and developmental processes of the alga. These results provide insights into the roles that miRNAs play in the growth of A. catenella, and they provide the basis for further studies of the molecular mechanisms that underlie bloom growth in red tides species.
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Affiliation(s)
- Huili Geng
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
- * E-mail:
| | - Shu Zhang
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qingwei Du
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yuanyuan Ren
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yuan Liu
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jie Zhong
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qingxia Ma
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao, 266003, China
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24
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Ye X, Song T, Liu C, Feng H, Liu Z. Identification of fruit related microRNAs in cucumber (Cucumis sativus L.) using high-throughput sequencing technology. Hereditas 2015; 151:220-8. [PMID: 25588308 DOI: 10.1111/hrd2.00057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/09/2014] [Indexed: 12/01/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 21 nt noncoding RNAs that influence the phenotypes of different species through the post-transcriptional regulation of gene expression. Although many miRNAs have been identified in a few model plants, less is known about miRNAs specific to cucumber (Cucumis sativus L.). In this study, two libraries of cucumber RNA, one based on fruit samples and another based on mixed samples from leaves, stems, and roots, were prepared for deep-sequencing. A total of 110 sequences were matched to known miRNAs in 47 families, while 56 sequences in 46 families are newly identified in cucumber. Of these, 77 known and 44 new miRNAs were differentially expressed, with a fold-change of at least 2 and p-value < 0.05. In addition, we predicted the potential targets of known and new miRNAs. The identification and characterization of known and new miRNAs will enable us to better understand the role of these miRNAs in the formation of cucumber fruit.
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Affiliation(s)
- Xueling Ye
- College of Horticulture, Shenyang Agriculture University, Shenyang, China
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25
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Zhang F, Dong W, Huang L, Song A, Wang H, Fang W, Chen F, Teng N. Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing. PLoS One 2015; 10:e0124371. [PMID: 25909659 PMCID: PMC4409343 DOI: 10.1371/journal.pone.0124371] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/27/2015] [Indexed: 12/22/2022] Open
Abstract
Background MicroRNAs (miRNAs) are important regulators in plant development. They post-transcriptionally regulate gene expression during various biological and metabolic processes by binding to the 3’-untranslated region of target mRNAs to facilitate mRNA degradation or inhibit translation. Chrysanthemum (Chrysanthemum morifolium) is one of the most important ornamental flowers with increasing demand each year. However, embryo abortion is the main reason for chrysanthemum cross breeding failure. To date, there have been no experiments examining the expression of miRNAs associated with chrysanthemum embryo development. Therefore, we sequenced three small RNA libraries to identify miRNAs and their functions. Our results will provide molecular insights into chrysanthemum embryo abortion. Results Three small RNA libraries were built from normal chrysanthemum ovules at 12 days after pollination (DAP), and normal and abnormal chrysanthemum ovules at 18 DAP. We validated 228 miRNAs with significant changes in expression frequency during embryonic development. Comparative profiling revealed that 69 miRNAs exhibited significant differential expression between normal and abnormal embryos at 18 DAP. In addition, a total of 1037 miRNA target genes were predicted, and their annotations were defined by transcriptome data. Target genes associated with metabolic pathways were most highly represented according to the annotation. Moreover, 52 predicted target genes were identified to be associated with embryonic development, including 31 transcription factors and 21 additional genes. Gene ontology (GO) annotation also revealed that high-ranking miRNA target genes related to cellular processes and metabolic processes were involved in transcription regulation and the embryo developmental process. Conclusions The present study generated three miRNA libraries and gained information on miRNAs and their targets in the chrysanthemum embryo. These results enrich the growing database of new miRNAs and lay the foundation for the further understanding of miRNA biological function in the regulation of chrysanthemum embryo abortion.
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Affiliation(s)
- Fengjiao Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China
| | - Wen Dong
- China Rural Technology Development Center, Beijing, China
| | - Lulu Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China
- * E-mail:
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26
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Xie F, Zhang B. microRNA evolution and expression analysis in polyploidized cotton genome. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:421-34. [PMID: 25561162 DOI: 10.1111/pbi.12295] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 05/28/2023]
Abstract
Cotton (Gossypium hirsutum L.), the most important fibre plant in the world, is a tetraploid species, originating from the reunion of two ancestral cotton species ~1-2 million years ago. It has been reported that a great number of genes were quickly erased or preferentially remained after whole-genome duplication, ultimately leading to morphogenesis evolution. However, microRNAs (miRNAs), a new class of gene regulators, have not been well studied in polyploidization. Here, we systematically investigated miRNA evolution amongst cultivated upland cotton G. hirsutum (AADD) and its two ancestors, G. arboreum (AA) and G. raimondii (DD). Our results show that certain highly conserved miRNAs were likely to be lost, whereas certain were remained after genome polyploidization. Cotton-specific miRNAs might undergo remarkably expansion, resulting in overall miRNA increase in upland cotton. Based on the sequenced genomes of G. arboreum and G. raimondii, we are capable for the first time to categorize the origin of miRNAs and coding genes in upland cotton. Different genome-derived miRNAs and miRNA*s displayed asymmetric expression pattern, implicating their diverse functions in upland cotton. No miRNA targeting preference was observed between different genome-derived miRNAs. The origin of miRNAs and coding genes has no impact on becoming miRNAs and their targets, despite some miRNAs and their targets are extremely conserved in the three cotton species. GO- and KEGG-based analysis of conserved miRNAs show that conserved miRNAs and their targets participate in a series of important biological processes and metabolism pathways. Additionally, A-derived miRNAs might be more responsible for ovule and fibre development.
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Affiliation(s)
- Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC, USA
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27
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Valach M, Burger G, Gray MW, Lang BF. Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules. Nucleic Acids Res 2014; 42:13764-77. [PMID: 25429974 PMCID: PMC4267664 DOI: 10.1093/nar/gku1266] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/14/2014] [Accepted: 11/17/2014] [Indexed: 11/13/2022] Open
Abstract
5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator.
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MESH Headings
- Coccidia/genetics
- Databases, Nucleic Acid
- Genes, Mitochondrial
- Genes, rRNA
- Genome, Mitochondrial
- Genome, Plastid
- Nucleic Acid Conformation
- Phaeophyceae/genetics
- RNA/chemistry
- RNA/genetics
- RNA, Mitochondrial
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/classification
- RNA, Ribosomal, 5S/genetics
- Sequence Analysis, RNA
- Stramenopiles/genetics
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4B2, Canada
| | - B Franz Lang
- Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada
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28
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Tian Y, Tian Y, Luo X, Zhou T, Huang Z, Liu Y, Qiu Y, Hou B, Sun D, Deng H, Qian S, Yao K. Identification and characterization of microRNAs related to salt stress in broccoli, using high-throughput sequencing and bioinformatics analysis. BMC PLANT BIOLOGY 2014; 14:226. [PMID: 25181943 PMCID: PMC4167151 DOI: 10.1186/s12870-014-0226-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 08/12/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a new class of endogenous regulators of a broad range of physiological processes, which act by regulating gene expression post-transcriptionally. The brassica vegetable, broccoli (Brassica oleracea var. italica), is very popular with a wide range of consumers, but environmental stresses such as salinity are a problem worldwide in restricting its growth and yield. Little is known about the role of miRNAs in the response of broccoli to salt stress. In this study, broccoli subjected to salt stress and broccoli grown under control conditions were analyzed by high-throughput sequencing. Differential miRNA expression was confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR). The prediction of miRNA targets was undertaken using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) database and Gene Ontology (GO)-enrichment analyses. RESULTS Two libraries of small (or short) RNAs (sRNAs) were constructed and sequenced by high-throughput Solexa sequencing. A total of 24,511,963 and 21,034,728 clean reads, representing 9,861,236 (40.23%) and 8,574,665 (40.76%) unique reads, were obtained for control and salt-stressed broccoli, respectively. Furthermore, 42 putative known and 39 putative candidate miRNAs that were differentially expressed between control and salt-stressed broccoli were revealed by their read counts and confirmed by the use of stem-loop real-time RT-PCR. Amongst these, the putative conserved miRNAs, miR393 and miR855, and two putative candidate miRNAs, miR3 and miR34, were the most strongly down-regulated when broccoli was salt-stressed, whereas the putative conserved miRNA, miR396a, and the putative candidate miRNA, miR37, were the most up-regulated. Finally, analysis of the predicted gene targets of miRNAs using the GO and KO databases indicated that a range of metabolic and other cellular functions known to be associated with salt stress were up-regulated in broccoli treated with salt. CONCLUSION A comprehensive study of broccoli miRNA in relation to salt stress has been performed. We report significant data on the miRNA profile of broccoli that will underpin further studies on stress responses in broccoli and related species. The differential regulation of miRNAs between control and salt-stressed broccoli indicates that miRNAs play an integral role in the regulation of responses to salt stress.
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Affiliation(s)
- Yunhong Tian
- />Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong Province People’s Republic of China
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Yunming Tian
- />State Key Laboratory of Oncology of Southern China, Guangzhou, Guangdong Province People’s Republic of China
- />Department of Radiation Oncology, Cancer Center of Sun Yat-Sen University, Guangzhou, Guangdong Province People’s Republic of China
| | - Xiaojun Luo
- />Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong Province People’s Republic of China
| | - Tao Zhou
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Zuoping Huang
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Ying Liu
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Yihan Qiu
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Bing Hou
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Dan Sun
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Hongyu Deng
- />Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong Province People’s Republic of China
| | - Shen Qian
- />Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province People’s Republic of China
| | - Kaitai Yao
- />Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong Province People’s Republic of China
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Rogato A, Richard H, Sarazin A, Voss B, Cheminant Navarro S, Champeimont R, Navarro L, Carbone A, Hess WR, Falciatore A. The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. BMC Genomics 2014; 15:698. [PMID: 25142710 PMCID: PMC4247016 DOI: 10.1186/1471-2164-15-698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 07/30/2014] [Indexed: 11/10/2022] Open
Abstract
Background Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms. Results Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions. Conclusions P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-698) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Hugues Richard
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Laboratory of Computational and Quantitative Biology, F-75006 Paris, France.
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Li J, Cai Y, Ye L, Wang S, Che J, You Z, Yu J, Zhong B. MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori. BMC Genomics 2014; 15:410. [PMID: 24885170 PMCID: PMC4045974 DOI: 10.1186/1471-2164-15-410] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. RESULTS Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, of the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs. Functional categorization classifies the targets into complex pathways that include both cellular and metabolic processes, especially protein synthesis and processing. CONCLUSION The enrichment of target genes in the ribosome-related pathway indicates that miRNAs may directly regulate translation. Our findings pave a way for further functional elucidation of these miRNAs and their targets in silk production.
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Affiliation(s)
- Jisheng Li
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
- />Institute of Sericulture, Chengde Medical University, Chengde, 067000 P.R. China
| | - Yimei Cai
- />Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
| | - Lupeng Ye
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Shaohua Wang
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Jiaqian Che
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Zhengying You
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Jun Yu
- />Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
| | - Boxiong Zhong
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
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Sha Z, Gong G, Wang S, Lu Y, Wang L, Wang Q, Chen S. Identification and characterization of Cynoglossus semilaevis microRNA response to Vibrio anguillarum infection through high-throughput sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 44:59-69. [PMID: 24296438 DOI: 10.1016/j.dci.2013.11.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNA) play key regulatory roles in diverse biological processes. Cynoglossus semilaevis is an important commercial mariculture fish species in China. To identify miRNAs and investigate immune-related miRNAs of C. semilaevis, we performed high-throughput sequencing on three small RNA libraries prepared from C. semilaevis immune tissues (liver, head kidney, spleen, and intestine). One library was prepared under normal conditions (control, CG); two were prepared during Vibrio anguillarum infection, where vibriosis symptoms were obvious and non-obvious (HOSG and NOSG, respectively). We obtained 11,216,875, 12,313,404, and 11,398,695 clean reads per library, respectively. Bioinformatic analysis identified 452 miRNAs, including 24 putative novel miRNAs. We analyzed differentially expressed miRNAs between two libraries using pairwise comparison. For NOSG-CG, there was significant differential expression of 175 (38.72%) miRNAs. There was significant differential expression of 215 (47.57%) miRNAs between HOSG and CG. Compared with CG, The HOSG-NOSG comparison revealed significantly different expression of 122 (26.99%) miRNAs respectively. Real-time quantitative PCR (RT-qPCR) experiments were performed for 10 miRNAs of the three samples, and agreement was found between the sequencing and RT-qPCR data. For miRNAs that were significantly differentially expressed, functional annotation of target genes by Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that a set of miRNAs that were expressed highly abundantly and significantly differentially were might involved in immune system development and immune response. To our understanding, this is the first report of comprehensive identification of C. semilaevis miRNAs being differentially regulated in immune tissues (liver, head kidney, spleen, and intestine) in normal conditions relating to V. anguillarum infection. Many miRNAs were differentially regulated upon pathogen exposure. This work provides an opportunity for further understanding of the molecular mechanisms of miRNA regulation in C. semilaevis host-pathogen interactions.
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Affiliation(s)
- Zhenxia Sha
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.
| | - Guangye Gong
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China
| | - Shaolin Wang
- Department of Psychiatry & Neurobiology Science, University of Virginia, VA 22911, USA
| | - Yang Lu
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China
| | - Lei Wang
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China
| | - Qilong Wang
- Tengzhou Fisheries Service Center, Tengzhou 277500, PR China
| | - Songlin Chen
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.
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Characterization of conserved microRNAs from five different cucurbit species using computational and experimental analysis. Biochimie 2014; 102:137-44. [PMID: 24657600 DOI: 10.1016/j.biochi.2014.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
MicroRNAs (miRNAs) are ∼21 nt non-coding small RNAs which regulate gene expression at the post-transcriptional level in plants and animals. Until recently, only limited numbers of miRNAs were identified in Cucurbitaceae, a large flowering plant family. In this study, 220 potential miRNA candidates were identified from five species of Cucurbitaceae family using a comparative genome-based computational analysis. A comprehensive bioinformatic analysis of EST (expressed sequence tag) and GSS (genomic survey sequence) data of five cucurbit species showed that at least 41, 108, 21, 17 and 33 miRNAs existed in Cucumis sativus, Cucumis melo, Citrullus lanatus, Siraitia grosvenorii and Cucurbita pepo, respectively. Quantitative real-time PCR (qRT-PCR) analysis revealed the differentially expression levels of miRNAs in the four tissues of cucumber and melon. These identified miRNAs in the five species potentially targeted 578 protein-coding genes and one target of the C. melo miRNA cme-miR160a-5p was verified by 5' RLM-RACE. GO and KEGG analysis suggested that many melon miRNAs might involve in nucleotide metabolism, oxidative phosphorylation, cell redox homeostasis and signal transduction.
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Chen F, Li J, Zhang H, Xu J, Tao Z, Shen J, Shen J, Lu L, Li C. Identification of differentially expressed known and novel miRNAs in broodiness of goose. Mol Biol Rep 2014; 41:2767-77. [DOI: 10.1007/s11033-014-3131-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 01/11/2014] [Indexed: 01/02/2023]
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Gu Y, Liu Y, Zhang J, Liu H, Hu Y, Du H, Li Y, Chen J, Wei B, Huang Y. Identification and characterization of microRNAs in the developing maize endosperm. Genomics 2013; 102:472-8. [PMID: 24021532 DOI: 10.1016/j.ygeno.2013.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 08/04/2013] [Accepted: 08/22/2013] [Indexed: 11/16/2022]
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that are approximately 20-22 nucleotides long. miRNAs have been shown to be important regulators that control a large variety of biological functions in eukaryotic cells. To investigate the roles of miRNAs in maize endosperm development, two small RNA libraries of maize endosperm at two developmental stages were sequenced. A total of 17,773,394 and 18,586,523 small RNA raw reads were obtained, respectively. Further analysis identified and characterized 95 known miRNAs belonging to 20 miRNA families. In addition, 18 novel miRNAs were identified and grouped into 11 families. Potential targets for 5 of the novel miRNA families were successfully predicted. We had also identified 12 corresponding miRNAs* of these novel miRNAs. In summary, we investigated expression patterns of miRNA in maize endosperm at key developmental stages and identified miRNAs that are likely to playing an important role in endosperm development.
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Affiliation(s)
- Yong Gu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural Universities, Ya'an, Sichuan 625014, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural Universities, Ya'an, Sichuan 625014, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengd u, Sichuan 611130, China
| | - Hai Du
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yangping Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jiang Chen
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Bin Wei
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yubi Huang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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Yang L, Jue D, Li W, Zhang R, Chen M, Yang Q. Identification of MiRNA from eggplant (Solanum melongena L.) by small RNA deep sequencing and their response to Verticillium dahliae infection. PLoS One 2013; 8:e72840. [PMID: 24015279 PMCID: PMC3754920 DOI: 10.1371/journal.pone.0072840] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 07/16/2013] [Indexed: 12/19/2022] Open
Abstract
MiRNAs are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including eggplant (Solanum melongena L.). To identify miRNAs in eggplant and their response to Verticillium dahliae infection, a fungal pathogen for which clear understanding of infection mechanisms and effective cure methods are currently lacking, we deep-sequenced two small RNA (sRNA) libraries prepared from mock-infected and infected seedlings of eggplants. Specifically, 30,830,792 reads produced 7,716,328 unique miRNAs representing 99 known miRNA families that have been identified in other plant species. Two novel putative miRNAs were predicted with eggplant ESTs. The potential targets of the identified known and novel miRNAs were also predicted based on sequence homology search. It was observed that the length distribution of obtained sRNAs and the expression of 6 miRNA families were obviously different between the two libraries. These results provide a framework for further analysis of miRNAs and their role in regulating plant response to fungal infection and Verticillium wilt in particular.
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Affiliation(s)
- Liu Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, P.R. China
| | - Dengwei Jue
- College of Life Sciences, Nanjing Agricultural University, Nanjing, P.R. China
| | - Wang Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, P.R. China
| | - Ruijie Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, P.R. China
| | - Min Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, P.R. China
| | - Qing Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, P.R. China
- * E-mail:
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Gross J, Wajid S, Price DC, Zelzion E, Li J, Chan CX, Bhattacharya D. Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa. PLoS One 2013; 8:e67669. [PMID: 23844054 PMCID: PMC3700990 DOI: 10.1371/journal.pone.0067669] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/21/2013] [Indexed: 12/12/2022] Open
Abstract
RNAi (RNA interference) relies on the production of small RNAs (sRNAs) from double-stranded RNA and comprises a major pathway in eukaryotes to restrict the propagation of selfish genetic elements. Amplification of the initial RNAi signal by generation of multiple secondary sRNAs from a targeted mRNA is catalyzed by RNA-dependent RNA polymerases (RdRPs). This phenomenon is known as transitivity and is particularly important in plants to limit the spread of viruses. Here we describe, using a genome-wide approach, the distribution of sRNAs in the glaucophyte alga Cyanophora paradoxa. C. paradoxa is a member of the supergroup Plantae (also known as Archaeplastida) that includes red algae, green algae, and plants. The ancient (>1 billion years ago) split of glaucophytes within Plantae suggests that C. paradoxa may be a useful model to learn about the early evolution of RNAi in the supergroup that ultimately gave rise to plants. Using next-generation sequencing and bioinformatic analyses we find that sRNAs in C. paradoxa are preferentially associated with mRNAs, including a large number of transcripts that encode proteins arising from different functional categories. This pattern of exonic sRNAs appears to be a general trend that affects a large fraction of mRNAs in the cell. In several cases we observe that sRNAs have a bias for a specific strand of the mRNA, including many instances of antisense predominance. The genome of C. paradoxa encodes four sequences that are homologous to RdRPs in Arabidopsis thaliana. We discuss the possibility that exonic sRNAs in the glaucophyte may be secondarily derived from mRNAs by the action of RdRPs. If this hypothesis is confirmed, then transitivity may have had an ancient origin in Plantae.
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Affiliation(s)
- Jeferson Gross
- Department of Ecology, Evolution, and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Sana Wajid
- Department of Ecology, Evolution, and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Dana C. Price
- Department of Ecology, Evolution, and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Ehud Zelzion
- Department of Ecology, Evolution, and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Junyi Li
- Department of Ecology, Evolution, and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Cheong Xin Chan
- The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, Brisbane, Australia
| | - Debashish Bhattacharya
- Department of Ecology, Evolution, and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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Hwang DG, Park JH, Lim JY, Kim D, Choi Y, Kim S, Reeves G, Yeom SI, Lee JS, Park M, Kim S, Choi IY, Choi D, Shin C. The hot pepper (Capsicum annuum) microRNA transcriptome reveals novel and conserved targets: a foundation for understanding MicroRNA functional roles in hot pepper. PLoS One 2013; 8:e64238. [PMID: 23737975 PMCID: PMC3667847 DOI: 10.1371/journal.pone.0064238] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 04/10/2013] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. Here, we employed high-throughput sequencing technology to identify miRNAs in pepper extensively from 10 different libraries, including leaf, stem, root, flower, and six developmental stage fruits. Based on a bioinformatics pipeline, we successfully identified 29 and 35 families of conserved and novel miRNAs, respectively. Northern blot analysis was used to validate further the expression of representative miRNAs and to analyze their tissue-specific or developmental stage-specific expression patterns. Moreover, we computationally predicted miRNA targets, many of which were experimentally confirmed using 5′ rapid amplification of cDNA ends analysis. One of the validated novel targets of miR-396 was a domain rearranged methyltransferase, the major de novo methylation enzyme, involved in RNA-directed DNA methylation in plants. This work provides the first reliable draft of the pepper miRNA transcriptome. It offers an expanded picture of pepper miRNAs in relation to other plants, providing a basis for understanding the functional roles of miRNAs in pepper.
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Affiliation(s)
- Dong-Gyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
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Lin Y, Lai Z. Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.). PLoS One 2013; 8:e60337. [PMID: 23593197 PMCID: PMC3623967 DOI: 10.1371/journal.pone.0060337] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/25/2013] [Indexed: 01/27/2023] Open
Abstract
Somatic embryogenesis (SE), which resembles zygotic embryogenesis, is an essential component of the process of plant cell differentiation and embryo development. Although microRNAs (miRNAs) are important regulators of many plant develop- mental processes, their roles in SE have not been thoroughly investigated. In this study, we used deep-sequencing, computational, and qPCR methods to identify, profile, and describe conserved and novel miRNAs involved in longan (Dimocarpus longan) SE. A total of 643 conserved and 29 novel miRNAs (including star strands) from more than 169 miRNA families were identified in longan embryogenic tissue using Solexa sequencing. By combining computational and degradome sequencing approaches, we were able to predict 2063 targets of 272 miRNAs and verify 862 targets of 181 miRNAs. Target annotation revealed that the putative targets were involved in a broad variety of biological processes, including plant metabolism, signal transduction, and stimulus response. Analysis of stage- and tissue-specific expressions of 20 conserved and 4 novel miRNAs indicated their possible roles in longan SE. These miRNAs were dlo-miR156 family members and dlo-miR166c* associated with early embryonic culture developmental stages; dlo-miR26, dlo-miR160a, and families dlo-miR159, dlo-miR390, and dlo-miR398b related to heart-shaped and torpedo- shaped embryo formation; dlo-miR4a, dlo-miR24, dlo-miR167a, dlo-miR168a*, dlo-miR397a, dlo-miR398b.1, dlo-miR398b.2, dlo-miR808 and dlo-miR5077 involved in cotyledonary embryonic development; and dlo-miR17 and dlo-miR2089*-1 that have regulatory roles during longan SE. In addition, dlo-miR167a, dlo-miR808, and dlo-miR5077 may be required for mature embryo formation. This study is the first reported investigation of longan SE involving large-scale cloning, characterization, and expression profiling of miRNAs and their targets. The reported results contribute to our knowledge of somatic embryo miRNAs and provide insights into miRNA biogenesis and expression in plant somatic embryo development.
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Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry, Fuzhou, Fujian, China
- * E-mail:
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Xie C, Li B, Xu Y, Ji D, Chen C. Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers. BMC Genomics 2013; 14:107. [PMID: 23414227 PMCID: PMC3626662 DOI: 10.1186/1471-2164-14-107] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 02/02/2013] [Indexed: 01/12/2023] Open
Abstract
Background Pyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the molecular mechanisms of specific traits. Thus, high-throughput sequencing is needed to generate a number of transcriptome sequences to be used for gene discovery and molecular marker development. Results In this study, high-throughput sequencing was used to analyze the global transcriptome of P. haitanensis. Approximately 103 million 90 bp paired-end reads were generated using an Illumina HiSeq 2000. De novo assembly with paired-end information yielded 24,575 unigenes with an average length of 645 bp. Based on sequence similarity searches with known proteins, a total of 16,377 (66.64%) genes were identified. Of these annotated unigenes, 5,471 and 9,168 unigenes were assigned to gene ontology and clusters of orthologous groups, respectively. Searching against the KEGG database indicated that 12,167 (49.51%) unigenes mapped to 124 KEGG pathways. Among the carbon fixation pathways, almost all the essential genes related to the C3- and C4-pathways for P. haitanensis were discovered. Significantly different expression levels of three key genes (Rubisco, PEPC and PEPCK) in different lifecycle stages of P. haitanensis indicated that the carbon fixation pathway in the conchocelis and thallus were different, and the C4-like pathway might play important roles in the conchocelis stage. In addition, 2,727 cSSRs loci were identified in the unigenes. Among them, trinucleotide SSRs were the dominant repeat motif (87.17%, 2,377) and GCC/CCG motifs were the most common repeats (60.07%, 1,638). High quality primers to 824 loci were designed and 100 primer pairs were randomly evaluated in six strains of P. haitanensis. Eighty-seven primer pairs successfully yielded amplicons. Conclusion This study generated a large number of putative P. haitanensis transcript sequences, which can be used for novel gene discovery and gene expression profiling analyses under different physiological conditions. A number of the cSSR markers identified can be used for molecular markers and will facilitate marker assisted selection in P. haitanensis breeding. These sequences and markers will provide valuable resources for further P. haitanensis studies.
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Affiliation(s)
- Chaotian Xie
- Fisheries College, Jimei University, Xiamen, Fujian Province 361021, People's Republic of China
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Hao DC, Yang L, Xiao PG, Liu M. Identification of Taxus microRNAs and their targets with high-throughput sequencing and degradome analysis. PHYSIOLOGIA PLANTARUM 2012; 146:388-403. [PMID: 22708792 DOI: 10.1111/j.1399-3054.2012.01668.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant microRNAs (miRNAs) have an impact in the regulation of several biological processes such as development, growth and metabolism by negatively controlling gene expression at the post-transcriptional level. However, the role of these small molecules in the medicinal gymnosperm species Taxus remained elusive. To elucidate the role of miRNAs in Taxus we used a deep sequencing approach to analyze the small RNA and degradome sequence tags of Taxus mairei leaves. For miRNAs, the sequencing library generated 14.9 million short sequences, resulting in 13.1 million clean reads. The library contains predominantly small RNAs with 21 nucleotide length, followed by 19-nt and 20-nt small RNAs. Around 29% of total small RNAs are matched to the T. mairei transcriptome. By sequence alignment, we identified 871 mature miRNAs, 15 miRNA* and 869 miRNA precursors representing known plant miRNA families. There are 547 unique small RNA matching the miRNA precursors. We predict 37 candidate novel miRNAs from the unannotated small RNAs that could be mapped to the reference transcriptome. The expression of the selected candidates was for the first time quantified by real-time reverse transcription polymerase chain reaction. The novel miRNA m0034 turns out to be from the intron sequence of the paclitaxel biosynthetic gene taxadiene synthase. The 21 potential targets of nine novel miRNAs are also predicted. Additionally, 56 targets for known miRNA families and 15 targets for novel candidate miRNA families were identified by high-throughput degradome-sequencing approach. It is found that two paclitaxel biosynthetic genes, taxane 13α hydroxylase and taxane 2α-O-benzoyltransferase, are the cleavage targets of miR164 and miR171, respectively. This study represents the first transcriptome-based analysis of miRNAs and degradome in gymnosperms.
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Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment, Dalian Jiaotong University, Dalian, 116028, China.
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Bozorov TA, Baldwin IT, Kim SG. Identification and profiling of miRNAs during herbivory reveals jasmonate-dependent and -independent patterns of accumulation in Nicotiana attenuata. BMC PLANT BIOLOGY 2012; 12:209. [PMID: 23134682 PMCID: PMC3502350 DOI: 10.1186/1471-2229-12-209] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/04/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant microRNAs (miRNAs) play key roles in the transcriptional responses to environmental stresses. However, the role of miRNAs in responses to insect herbivory has not been thoroughly explored. To identify herbivory-responsive miRNAs, we identified conserved miRNAs in the ecological model plant Nicotiana attenuata whose interactions with herbivores have been well-characterized in both laboratory and field studies. RESULTS We identified 59 miRNAs from 36 families, and two endogenous trans-acting small interfering RNAs (tasiRNA) targeted by miRNAs. We characterized the response of the precursor and mature miRNAs to simulated attack from the specialist herbivore Manduca sexta by quantitative PCR analysis and used ir-aoc RNAi transformants, deficient in jasmonate biosynthesis, to identify jasmonate-dependent and -independent miRNA regulation. Expression analysis revealed that groups of miRNAs and tasiRNAs were specifically regulated by either mechanical wounding or wounding plus oral secretions from M. sexta larvae, and these small RNAs were accumulated in jasmonate-dependent or -independent manners. Moreover, cDNA microarray analysis indicated that the expression patterns of the corresponding target genes were correlated with the accumulation of miRNAs and tasiRNAs. CONCLUSIONS We show that a group of miRNAs and tasiRNAs orchestrates the expression of target genes involved in N. attenuata's responses to herbivore attack.
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Affiliation(s)
- Tohir A Bozorov
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, Jena, D-07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, Jena, D-07745, Germany
| | - Sang-Gyu Kim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, Jena, D-07745, Germany
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Mandhan V, Kaur J, Singh K. smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni. BMC PLANT BIOLOGY 2012; 12:197. [PMID: 23116282 PMCID: PMC3502355 DOI: 10.1186/1471-2229-12-197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 10/29/2012] [Indexed: 05/30/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. RESULTS To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. CONCLUSIONS This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to understand their roles in key stevia traits.
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Affiliation(s)
- Vibha Mandhan
- Department of Biotechnology, Panjab University, Sector 14, Chandigarh, 160014, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Sector 14, Chandigarh, 160014, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Sector 14, Chandigarh, 160014, India
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Comparative Analysis of MicroRNAs between Sporophyte and Gametophyte of Porphyra yezoensis. Comp Funct Genomics 2012; 2012:912843. [PMID: 23055822 PMCID: PMC3463926 DOI: 10.1155/2012/912843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/06/2012] [Accepted: 08/22/2012] [Indexed: 01/07/2023] Open
Abstract
Porphyra yezoensis Ueda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry. The two generations of Porphyra yezoensis, the sporophyte and the gametophyte, have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. To identify miRNAs and their probable roles in P. yezoensis development, we constructed and sequenced libraries of small RNA from P. yezoensis sporophytes and gametophytes. The sequencing data were analyzed, and 14 miRNAs were identified, with only one common to these two samples. Our results show that P. yezoensis has a complex small RNA processing system containing novel miRNAs that have no identifiable homolog in other organisms. These miRNAs might have important regulatory roles in development of the different generations of P. yezoensis.
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Wang K, Li M, Gao F, Li S, Zhu Y, Yang P. Identification of conserved and novel microRNAs from Liriodendron chinense floral tissues. PLoS One 2012; 7:e44696. [PMID: 23028583 PMCID: PMC3445533 DOI: 10.1371/journal.pone.0044696] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 08/09/2012] [Indexed: 12/02/2022] Open
Abstract
Background Liriodendron chinense (L. chinense) is an endangered basal angiosperm plant in China because of its low reproductive efficiency. Recently, miRNAs have obtained great attention because they can play important roles. Through high throughput sequencing technique, large amount of miRNAs were identified from different plant species. But there were few studies about the miRNAs in the basal angiosperms especially in the sexual reproduction process. Results Deep sequencing technology was applied to discover miRNAs in L. chinense flowers at different stages. After bioinformatic analysis, 496 putative conserved miRNAs representing 97 families and 2 novel miRNAs were found. Among them, one is previously regarded as gymnosperm specific. Their expressions were further validated by Real-time PCR for 13 selected miRNAs. Putative targeting genes were predicted and categorized with gene ontology (GO) analysis. About ten percents of the targets are involved in the reproduction process. Further expressional analysis showed that many of these miRNAs were highly related to the reproductive growth. Conclusions This is the first comprehensive identification of conserved and novel miRNAs in L. chinense. The data presented here might not only help to fill the gap of miRNA registered about basal angiosperm plants but also contribute to understanding the evolution of miRNAs. The differential expression of some of the miRNAs and the prediction of their target genes are also helpful in understanding the regulation of L. chinense sexual reproduction.
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Affiliation(s)
- Kun Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
- College of Life Science, Wuhan University, Wuhan, China
| | - Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China
| | - Feng Gao
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
- College of Life Science, Wuhan University, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
- College of Life Science, Wuhan University, Wuhan, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
- College of Life Science, Wuhan University, Wuhan, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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Stiller JW, Perry J, Rymarquis LA, Accerbi M, Green PJ, Prochnik S, Lindquist E, Chan CX, Yarish C, Lin S, Zhuang Y, Blouin NA, Brawley SH. MAJOR DEVELOPMENTAL REGULATORS AND THEIR EXPRESSION IN TWO CLOSELY RELATED SPECIES OF PORPHYRA (RHODOPHYTA)(1). JOURNAL OF PHYCOLOGY 2012; 48:883-96. [PMID: 27008999 DOI: 10.1111/j.1529-8817.2012.01138.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Little is known about the genetic and biochemical mechanisms that underlie red algal development, for example, why the group failed to evolve complex parenchyma and tissue differentiation. Here we examined expressed sequence tag (EST) data from two closely related species, Porphyra umbilicalis (L.) J. Agardh and P. purpurea (Roth) C. Agardh, for conserved developmental regulators known from model eukaryotes, and their expression levels in several developmental stages. Genes for most major developmental families were present, including MADS-box and homeodomain (HD) proteins, SNF2 chromatin-remodelers, and proteins involved in sRNA biogenesis. Some of these genes displayed altered expression correlating with different life history stages or cell types. Notably, two ESTs encoding HD proteins showed eightfold higher expression in the P. purpurea sporophyte (conchocelis) than in the gametophyte (blade), whereas two MADS domain-containing paralogs showed significantly different patterns of expression in the conchocelis and blade respectively. These developmental gene families do not appear to have undergone the kinds of dramatic expansions in copy number found in multicellular land plants and animals, which are important for regulating developmental processes in those groups. Analyses of small RNAs did not validate the presence of miRNAs, but homologs of Argonaute were present. In general, it appears that red algae began with a similar molecular toolkit for directing development as did other multicellular eukaryotes, but probably evolved altered roles for many key proteins, as well as novel mechanisms yet to be discovered.
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Affiliation(s)
- John W Stiller
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Justin Perry
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Linda A Rymarquis
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Monica Accerbi
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Pamela J Green
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Simon Prochnik
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Erika Lindquist
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Cheong Xin Chan
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Charles Yarish
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Senjie Lin
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Yunyun Zhuang
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Nicolas A Blouin
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
| | - Susan H Brawley
- Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA
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Liu Q, Zhang H. Molecular identification and analysis of arsenite stress-responsive miRNAs in rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:6524-36. [PMID: 22712679 DOI: 10.1021/jf300724t] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Arsenic is highly toxic to living organisms including humans and plants. To investigate the responsive functions of miRNAs under arsenite stress, an indica rice, Minghui 86, has been deeply sequenced, and a total of 67 arsenite-responsive miRNAs were identified in rice seedling roots, of which 5 were further validated experimentally. The potential targets of those differential miRNAs include some transcription factors, protein kinases, and DNA- or metal ion-binding proteins that are associated with cellular and metabolic processes, pigmentation, and stress responses. The regulatory roles of four miRNAs on their targets in response to arsenite were further confirmed by real time RT-PCR. Interestingly, osa-miR6256 was originally characterized as a putative exonic miRNA, supporting the notion that miRNAs may also originate from some exons in plants. The first identification of arsenite-responsive miRNAs at the whole genome-wide level will broaden the current understanding of the molecular mechanisms of arsenite responses in rice.
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Affiliation(s)
- Qingpo Liu
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou 311300, People's Republic of China.
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Wang J, Yang X, Xu H, Chi X, Zhang M, Hou X. Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene 2012; 505:300-8. [PMID: 22688123 DOI: 10.1016/j.gene.2012.06.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 05/18/2012] [Accepted: 06/02/2012] [Indexed: 12/23/2022]
Abstract
The microRNAs are a new class of small non-coding endogenous RNAs with lengths of approximately ~21 nt. MicroRNAs perform their biological function via the degradation of the target mRNAs or by inhibiting protein translation. Until recently, only limited numbers of miRNAs were identified in Brassica oleracea, a vegetable widely cultivated around the world. In present study, 193 potential miRNA candidates were identified from 17 expressed sequence tag (ESTs) and 152 genome survey sequences (GSSs) in B. oleracea. These miRNA candidates were classified into 70 families using a well-defined comparative genome-based computational analysis. Most miRNAs belong to the miRNA169, miR5021, miR156 and miR158 families. Of these, 36 miRNA families are firstly found in Brassica species. Around 1393 B. oleracea genes were predicted as candidate targets of 175 miRNAs. The mutual relationship between miRNAs and the candidate target genes was verified by checking differentially expression levels using quantitative real-time polymerase chain reaction (qRT-PCR) and 5' RLM-RACE analyses. These target genes participate in multiple biological and metabolic processes, including signal transduction, stress response, and plant development. Gene Ontology analysis shows that the 818, 514, and 265 target genes are involved in molecular functions, biological processes, and cellular component respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis suggests that these miRNAs might regulate 186 metabolic pathways, including those of lipid, energy, starch and sucrose, fatty acid and nitrogen.
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Affiliation(s)
- Jinyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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Liu Q. Novel miRNAs in the control of arsenite levels in rice. Funct Integr Genomics 2012; 12:649-58. [DOI: 10.1007/s10142-012-0282-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/01/2012] [Accepted: 04/09/2012] [Indexed: 01/08/2023]
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Wan LC, Zhang H, Lu S, Zhang L, Qiu Z, Zhao Y, Zeng QY, Lin J. Transcriptome-wide identification and characterization of miRNAs from Pinus densata. BMC Genomics 2012; 13:132. [PMID: 22480283 PMCID: PMC3347991 DOI: 10.1186/1471-2164-13-132] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 04/06/2012] [Indexed: 11/18/2022] Open
Abstract
Background MicroRNAs (miRNAs) play key roles in diverse developmental processes, nutrient homeostasis and responses to biotic and abiotic stresses. The biogenesis and regulatory functions of miRNAs have been intensively studied in model angiosperms, such as Arabidopsis thaliana, Oryza sativa and Populus trichocarpa. However, global identification of Pinus densata miRNAs has not been reported in previous research. Results Here, we report the identification of 34 conserved miRNAs belonging to 25 miRNA families from a P. densata mRNA transcriptome database using local BLAST and MIREAP programs. The primary and/or precursor sequences of 29 miRNAs were further confirmed by RT-PCR amplification and subsequent sequencing. The average value of the minimal folding free energy indexes of the 34 miRNA precursors was 0.92. Nineteen (58%) mature miRNAs began with a 5' terminal uridine residue. Analysis of miRNA precursors showed that 19 mature miRNAs were novel members of 14 conserved miRNA families, of which 17 miRNAs were further validated by subcloning and sequencing. Using real-time quantitative RT-PCR, we found that the expression levels of 7 miRNAs were more than 2-fold higher in needles than in stems. In addition, 72 P. densata mRNAs were predicted to be targets of 25 miRNA families. Four target genes, including a nodal modulator 1-like protein gene, two GRAS family transcription factor protein genes and one histone deacetylase gene, were experimentally verified to be the targets of 3 P. densata miRNAs, pde-miR162a, pde-miR171a and pde-miR482a, respectively. Conclusions This study led to the discovery of 34 conserved miRNAs comprising 25 miRNA families from Pinus densata. These results lay a solid foundation for further studying the regulative roles of miRNAs in the development, growth and responses to environmental stresses in P. densata.
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Affiliation(s)
- Li-Chuan Wan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Wang C, Han J, Liu C, Kibet KN, Kayesh E, Shangguan L, Li X, Fang J. Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics 2012. [PMID: 22455456 DOI: 10.1186/1471‐2164‐13‐122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNA (miRNA) is a class of functional non-coding small RNA with 19-25 nucleotides in length while Amur grape (Vitis amurensis Rupr.) is an important wild fruit crop with the strongest cold resistance among the Vitis species, is used as an excellent breeding parent for grapevine, and has elicited growing interest in wine production. To date, there is a relatively large number of grapevine miRNAs (vv-miRNAs) from cultivated grapevine varieties such as Vitis vinifera L. and hybrids of V. vinifera and V. labrusca, but there is no report on miRNAs from Vitis amurensis Rupr, a wild grapevine species. RESULTS A small RNA library from Amur grape was constructed and Solexa technology used to perform deep sequencing of the library followed by subsequent bioinformatics analysis to identify new miRNAs. In total, 126 conserved miRNAs belonging to 27 miRNA families were identified, and 34 known but non-conserved miRNAs were also found. Significantly, 72 new potential Amur grape-specific miRNAs were discovered. The sequences of these new potential va-miRNAs were further validated through miR-RACE, and accumulation of 18 new va-miRNAs in seven tissues of grapevines confirmed by real time RT-PCR (qRT-PCR) analysis. The expression levels of va-miRNAs in flowers and berries were found to be basically consistent in identity to those from deep sequenced sRNAs libraries of combined corresponding tissues. We also describe the conservation and variation of va-miRNAs using miR-SNPs and miR-LDs during plant evolution based on comparison of orthologous sequences, and further reveal that the number and sites of miR-SNP in diverse miRNA families exhibit distinct divergence. Finally, 346 target genes for the new miRNAs were predicted and they include a number of Amur grape stress tolerance genes and many genes regulating anthocyanin synthesis and sugar metabolism. CONCLUSIONS Deep sequencing of short RNAs from Amur grape flowers and berries identified 72 new potential miRNAs and 34 known but non-conserved miRNAs, indicating that specific miRNAs exist in Amur grape. These results show that a number of regulatory miRNAs exist in Amur grape and play an important role in Amur grape growth, development, and response to abiotic or biotic stress.
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Affiliation(s)
- Chen Wang
- College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
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