Nuclear Factor Y (NF-Y) represents a group of transcription factors commonly present in higher eukaryotes, typically consisting of three subunits: NF-YA, NF-YB, and NF-YC. They play crucial roles in the embryonic development, photosynthesis, flowering, abiotic stress responses, and other essential processes in plants. To better understand the genome-wide NF-Y domain-containing proteins, the protein physicochemical properties, chromosomal localization, synteny, phylogenetic relationships, genomic structure, promoter cis-elements, and protein interaction network of NtNF-Ys in tobacco (Nicotiana tabacum L.) were systematically analyzed. In this study, we identified 58 NtNF-Ys in tobacco, respectively, and divided into three subfamilies corresponding to their phylogenetic relationships. Their tissue specificity and expression pattern analyses for leaf development, drought and saline-alkali stress, and ABA response were carried out using RNA-seq or qRT-PCR. These findings illuminate the role of NtNF-Ys in regulating plant leaf development, drought and saline-alkali stress tolerance, and ABA response. This study offers new insights to enhance our understanding of the roles of NtNF-Ys and identify potential genes involved in leaf development, as well as drought and saline-alkali stress tolerance of plants.

The impact of microplastic pollution has emerged as a significant global ecological concern. Various organisms have exhibited alterations in behavior or metabolic activities following exposure to microplastics (MPs). Mosquitoes, as crucial disease vectors, are particularly susceptible MPs exposure in the environment. Recent studies have demonstrated that MPs ingested by mosquitoes can be detected in vivo, potentially being transmitted during their different life cycles. However, it remains unclear whether MPs in vivo could affect mosquito infection with arboviruses. In this study, we identified that the physical adsorption effect of MPs is also effective against arboviruses, enabling the adsorption of Zika virus particles onto their surfaces. We established an exposure model by feeding adult Aedes albopictus (Skuse, 1895) (Diptera: Culicidae) with 1 μm MPs at concentrations of 5 and 50 μg/mL in 8 % sucrose solution. The transmission rate of ZIKV and population transmission rate in the laboratorial Ae. albopictus exposure model began to decrease from day 7, showing statistically significant differences compared to the control group on days 10 and 14 (**, p < 0.01), significantly affecting their vector efficiency. This phenomenon is not solely dependent on the physical adsorption of MPs to arboviruses. Transcriptome analysis indicated that exposure to MPs influenced the expression levels of genes associated with mosquito virus infection, altering the function of relevant pathways, which consequently reduces their capability to transmit arbovirus. These findings suggest that exposure to MPs significantly affects the vector efficiency of mosquitoes, providing novel perspectives for the ecological risk assessment of MPs.

The white button mushroom (Agaricus bisporus), widely cultivated worldwide as an edible mushroom, is susceptible to browning, which significantly impacts its nutritional and commercial value. Extensive research has enhanced our understanding of the mechanisms underlying this browning process. Although the role of DNA methylation in regulating gene expression has been studied in many fungi, information specifically concerning DNA methylation during the browning in A. bisporus is still limited. In this study, we initially evaluated the impact of temperatures (4 ℃ and room temperature) on discoloration in A. bisporus, and samples with similar discoloration under different temperatures were collected for transcriptome and DNA methylation sequencing. The results revealed that DNA methylation was positively correlated with browning, suggesting its involvement during the browning in A. bisporus. Further analysis showed the heightened methylation levels were primarily attributed to increased methylation at CHG and CHH sites. By joint analysis of transcriptome and DNA methylome, 342 genes with significant expression changes were identified to be affected by DNA methylation, and finally 13 genes were considered as important browning genes under different signaling pathways, such as ABA/ET pathway. Notably, four DNA methyltransferases were identified and validated to play important role during browning in A. bisporus. Altogether, this study provides theoretical insights into the functions of DNMTs in A. bisporus, and offers new perspectives on the role of DNA methylation in edible mushrooms.

Huanglongbing (HLB), a global citrus threat, is transmitted by Diaphorina citri Kuwayama, a widespread insect pest. The disease's rapid spread and incurability necessitate efficient, sustainable control strategies. This study investigates heat shock protein 70 (HSP70) genes in D. citri, known to play a pivotal role in insect survival and stress response. The genome-wide identification, gene structure analysis, and conserved protein domain analysis of 22 HSP70 genes in D. citri were performed. Furthermore, the expression of these genes during HLB infection or developmental processes was gauged. Phylogenetic analysis revealed the functional categorization of the identified genes, while gene structure and conserved motifs offered insights into gene function. The expression analysis unveiled dynamic profiles in response to infection and across development stages, potentially aiding future targeted pest control strategies. These findings offer promising leads for the design of novel inhibitors or RNAi strategies targeting D. citri and HLB.

Fungal secondary metabolites are considered as important resources for drug discovery. Despite various methods being employed to facilitate the discovery of new fungal secondary metabolites, the trend of identifying novel secondary metabolites from fungi is inevitably slowing down. Under laboratory conditions, the majority of biosynthetic gene clusters, which store information for secondary metabolites, remain inactive. Therefore, establishing the link between biosynthetic gene clusters and secondary metabolites would contribute to understanding the genetic logic underlying secondary metabolite biosynthesis and alleviating the current challenges in discovering novel natural products. Bioinformatics methods have garnered significant attention due to their powerful capabilities in data mining and analysis, playing a crucial role in various aspects. Thus, we have summarized successful cases since 2016 in which bioinformatics methods were utilized to establish the link between fungal biosynthetic gene clusters and secondary metabolites, focusing on their biosynthetic gene clusters and associated secondary metabolites, with the goal of aiding the field of natural product discovery.

Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.

Biodegradation is critical for eliminating plastic contaminants from environments, and understanding its mechanisms under in situ conditions is crucial. The plastic biodegradation process in sediments, a major reservoir of plastic contamination with reduced redox conditions, remains elusive. This study compared the plastisphere communities and metabolic potentials of typical polyethylene (PE) contaminants collected from the Pearl River Estuary to their counterparts in the surrounding sediments. The results revealed a distinct plastisphere community composition, with the consistent enrichment of a group of core plastisphere populations compared to those of the sediments. Functional genes related to both potential aerobic and anaerobic PE biodegradation were encoded by the core plastisphere populations. Microcosm incubations were performed to assess the PE biodegradation potentials under denitrifying conditions. The results demonstrated that the polyethylene (PE) mineralization efficiencies were comparable under aerobic and denitrifying conditions through incubations with 13C-PE. Development of functional groups on PE surfaces and the reduction in molecular weights further supported PE biodegradation under denitrifying conditions. The elevated laccase and lignin peroxidase activities implied their potential contribution to PE depolymerization under denitrifying conditions. Together, the sediment plastisphere microbiome holds the potential for plastic degradation under denitrifying conditions, which should be considered when assessing the fate of plastic contaminants.

Predicting prokaryotic phenotypes-observable traits that govern functionality, adaptability, and interactions-holds significant potential for fields such as biotechnology, environmental sciences, and evolutionary biology. In this study, we leverage machine learning to explore the relationship between prokaryotic genotypes and phenotypes. Utilizing the highly standardized datasets in the BacDive database, we model eight physiological properties based on protein family inventories, evaluate model performance using multiple metrics, and examine the biological implications of our predictions. The high confidence values achieved underscore the importance of data quality and quantity for reliably inferring bacterial phenotypes. Our approach generates 50,396 completely new datapoints for 15,938 strains, now openly available in the BacDive database, thereby enriching existing phenotypic resources and enabling further research. The open-source software we provide can be readily applied to other datasets, such as those from metagenomic studies, and to various applications, including assessing the potential of soil bacteria for bioremediation.

Cell elongation is an important process during cotton fiber development, ultimately determining the length of mature fibers. Myo-inositol oxygenase (MIOX) pathway provides pivotal precursors for the synthesis of non-cellulosic polysaccharides in plant cell walls. However, the role of MIOX gene in cotton fiber development has not been reported. Here, we hypothesized that Gossypium barbadense MIOX gene GbMIOX8 (GbM_D05G1480.1) could regulate fiber length by modulating cell wall composition. To test this hypothesis, we characterized the functional properties of GbMIOX8. GbMIOX8 preferentially expressed during fiber initiation and elongation in cotton and encodes non-secretory protein targeted to the cytoplasm. Overexpression of GbMIOX8 afforded transgenic A. thaliana significantly longer leaf trichomes, as well as longer hypocotyl cells compared to the wild type, with increases of at least 11 % and up to 23 %. We further overexpressed GbMIOX8 in cotton and found that transgenic cotton displayed fiber length that was increased by an average of 1.61 mm in the T1 generation and 1.93 mm in the T2 generation, respectively. Similar to Arabidopsis, transgenic cotton exhibited at least a threefold increase in myo-inositol oxygenase activity and content, boosting glucuronic acid production and reducing inositol. Furthermore, pectin and cellulose contents rose in transgenic cottons, with average rises of 19 % and 38 % respectively, indicating enhanced biosynthesis of these two cell wall components. These results revealed that GbMIOX8 played an important role in the elongation of plant cells by altering cell wall components and could be valuable for cotton fiber quality improvement.

Proteases regulate important biological functions. Here, we present the structural and functional characterization of three previously uncharacterized aspartic proteases in Pseudomonas aeruginosa. We show that these proteases have structural hallmarks of retropepsin peptidases and play redundant roles for cell survival under hypoosmotic stress conditions. Consequently, we named them retropepsin-like osmotic stress tolerance peptidases (Rlo). Our research shows that while Rlo proteases are homologous to RimB, an aspartic peptidase involved in rhizosphere colonization and plant infection, they contain N-terminal signal peptides and perform distinct biological functions. Mutants lacking all three secreted Rlo peptidases show defects in antibiotic resistance, biofilm formation, and cell morphology. These defects are rescued by mutations in the inactive transglutaminase transmembrane protein RloB and the cytoplasmic ATP-grasp protein RloC, two previously uncharacterized genes in the same operon as one of the Rlo proteases. These studies identify Rlo proteases and rlo operon products as critical factors in clinically relevant processes, making them appealing targets for therapeutic strategies against Pseudomonas infections.IMPORTANCEBacterial infections have become harder to treat due to the ability of pathogens to adapt to different environments and the rise of antimicrobial resistance. This has led to longer illnesses, increased medical costs, and higher mortality rates. The opportunistic pathogen Pseudomonas aeruginosa is particularly problematic because of its inherent resistance to many antibiotics and its capacity to form biofilms, structures that allow bacteria to withstand hostile conditions. Our study uncovers a new class of retropepsin-like proteases in P. aeruginosa that are required for biofilm formation and bacterial survival under stress conditions, including antibiotic exposure. By identifying critical factors that determine bacterial fitness and adaptability, our research lays the foundation for developing new therapeutic strategies against bacterial infections.

The characterization of gene sets is a recurring task in computational biology. Identifying specific properties of a hit set compared to a reference set can reveal biological roles and mechanisms, and can lead to the prediction of new hits. However, collecting the features to evaluate can be time consuming, and implementing an informative but compact graphical representation of the multiple comparisons can be challenging, particularly for bench scientists. Here, I present Qarles (quick characterization of large sets of genes), a web server that annotates Saccharomyces cerevisiae gene sets by querying a database of 31 features widely used by the yeast community and that identifies their specific properties, providing publication-ready figures and reliable statistics. Qarles has a deliberately simple user interface with all the functionality in a single web page and a fast response time to facilitate adoption by the scientific community. Qarles provides a rich and compact graphical output, including up to five gene set comparisons across 31 features in a single dotplot, and interactive boxplots to enable the identification of outliers. Qarles can also predict new hit genes by using a random forest trained on the selected features. The web server is freely available at https://qarles.org.

China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.

Despite considerable scrutiny of mammalian arterivirus genomes, their genomic architecture remains incomplete, with several unannotated non-structural proteins (NSPs) and the enigmatic absence of methyltransferase (MTase) domains. Additionally, the host range of arteriviruses has expanded to include seven newly sequenced genomes from non-mammalian hosts, which remain largely unannotated and await detailed comparisons alongside mammalian isolates. Utilizing comparative genomics approaches and comprehensive sequence-structure analysis, we provide enhanced genomic architecture and annotations for arterivirus genomes. We identified the previously unannotated C-terminal domain of NSP3 as a winged helix-turn-helix domain and classified NSP7 as a new small β-barrel domain, both likely involved in interactions with viral RNA. NSP12 is identified as a derived variant of the N7-MTase-like Rossmann fold domain that retains core structural alignment with N7-MTases in Nidovirales but likely lacks enzymatic functionality due to the erosion of catalytic residues, indicating a unique role specific to mammalian arteriviruses. In contrast, non-mammalian arteriviruses sporadically retain a 2'-O-MTase and an exonuclease (ExoN) domain, which are typically absent in mammalian arteriviruses, highlighting contrasting evolutionary trends and variations in their molecular toolkit. Similar lineage-specific patterns are observed in the diversification of papain-like proteases and structural proteins. Overall, the study extends our knowledge of arterivirus genomic diversity and evolution.

Long noncoding RNAs (lncRNAs) can regulate gene expression by "sponging" microRNAs (miRNAs), reducing their inhibitory effects on mRNAs. However, this mechanism has been minimally investigated in preimplantation embryo development. In this study, we revisited existing RNA sequencing and small RNA sequencing data to investigate the role of lncRNAs in in vitro-produced bovine preimplantation embryos. Our findings revealed that although lncRNAs exhibit expression patterns similar to mRNAs, maternal lncRNAs degrade earlier than mRNAs during embryonic genome activation (EGA). Weighted gene co-expression network analysis identified 27 modules of mRNA and lncRNA, with enrichment analysis showing a significant negative correlation between the polycomb repressive complex pathway and blastocyst formation (R2 = -0.98). Additionally, bioinformatics analysis was used to predict and construct lncRNA-miRNA-mRNA networks, highlighting that lncRNAs bind more to miRNAs compared with mRNAs. Moreover, lncRNA-induced lncRNA-miRNA-mRNA axes participated in mRNA degradation and biogenesis around the EGA stage. These interactions became stronger after EGA, especially after the 16-cell stage. Overall, our study provides new insights into lncRNA-mediated regulatory networks during bovine preimplantation development.

Identifying structural relationships between proteins is crucial for understanding their functions and evolutionary histories. We present ISS_ProtSci, a Python package designed for structural similarity searches within the AlphaFold Database v2 (AFDB2). ISS_ProtSci incorporates DaliLite to identify geometrically similar structures and uses a transitive closure algorithm to iteratively explore neighboring shells of proteins. The precomputed all-against-all comparisons generated by Foldseek, chosen for its speed, are validated by DaliLite for precision. Search results are annotated with metadata from UniProtKB and Pfam protein family classifications, using hmmsearch to identify protein domains. Outputs, including Dali pairwise alignment data, are provided in TSV format for easy filtering and analysis. Our method offers a significant improvement in recall over existing tools like Foldseek, especially in detecting more distantly related proteins. This is particularly valuable in structurally diverse protein families where traditional sequence-based or fast structural methods struggle. ISS_ProtSci delivers practical runtimes and flexibility, allowing users to input a PDB file, define the minimum size of the common core, and evaluate results using Pfam clans. In evaluating our method across 12 test cases based on Pfam clans, we achieved over 99% recall of relevant proteins, even in challenging cases where Foldseek's recall dropped below 50%. ISS_ProtSci not only identifies closely related proteins but also uncovers previously unrecognized structural relationships, contributing to more accurate protein family classifications. The software can be downloaded from http://ekhidna2.biocenter.helsinki.fi/ISS_ProtSci/.

In Arabidopsis thaliana, micro-RNA regulation is primarily controlled by DCL1, an RNase III enzyme, and its associated proteins. DCL1, together with DRB2, governs a specific group of miRNAs that induce the inhibition of target mRNA translation. DRB2 is a multi-domain protein containing two N-terminal dsRNA binding domains (dsRBD) separated by a linker, followed by an unstructured C-terminal tail. The two dsRBDs in DRB2 are involved in recognizing the miRNA precursor and aiding DCL1 in generating 21-nucleotide-long miRNA. Our study presents a nearly complete backbone chemical shift assignment of both dsRBDs and the side-chain assignment of the first dsRBD in DRB2. The data presented here lays the groundwork for future investigations into the structural, dynamic, and functional aspects of DRB2.

Fruits undergo a similar ripening process, yet they exhibit a range of differences in color, taste, and shape, both across different species and within the same species. How does this diversity arise? We uncovered a conserved fruit ripening process in lychee fruit in which a NAC transcription factor, LcNAC1, acts as a master regulator. LcNAC1 regulates the expression of two terpene synthase genes, LcTPSa1 and LcTPSa2, which belong to a gene cluster consisting of four TPS genes. LcTPSa1-LcTPSa3 are responsible for catalyzing the production of farnesol, which in turn dictates the aromatic diversity in fruit of different lychee varieties. Through comparative, transcriptomic, and genomic analyses across various lychee varieties, we found these four TPS genes exhibit distinct expression levels due to natural genetic variation. These include copy number variations, presence/absence variations, insertions and deletions, and single nucleotide polymorphisms, many of which affect the binding affinity of LcNAC1. A single nucleotide mutation in LcTPSa1 caused a premature translational termination, resulting in a truncated version of the TPS protein, which surprisingly remains functional. All these genomic changes in the LcNAC1-regulated TPS genes are likely to contribute to the great aromatic diversity observed in lychee fruit. This diversification of fruit aroma in lychee varieties offers a compelling example of how species- or variety-specific traits evolve - the phenotypic diversity is primarily derived from natural genetic variation accumulated in downstream structural genes within an evolutionarily conserved regulatory circuit.

The Rib domain, a conserved structural element found in Gram-positive bacterial cell surface proteins, plays a role in bacterial virulence and is a potential target for vaccine development. Despite the availability of high-resolution crystallographic structures, the precise functional role of the Rib domain remains elusive. Here, we report the chemical shift assignments of the Rib domain from a cell surface protein of Limosilactobacillus reuteri, providing a foundational step toward understanding its potential involvement in host-bacteria interactions.

Crop protection is undergoing significant evolution, transitioning towards sustainable approaches that minimize impacts on the environment and human health. Exogenous application of double-stranded RNA (dsRNA) that silences pest or pathogen genes via RNA interference (RNAi) has promise as a safe and effective next-generation crop protection platform without the need for genetic modification. However, exogenous dsRNA application at scale presents challenges. Specifically, a single dsRNA sequence needs to balance targeting the standing variation in a target pest or pathogen group against the potential for adverse impacts in a vast array of non-target and beneficial organisms at the application site and broader environment. To address these competing demands, we present dsRNAmax (https://github.com/sfletc/dsRNAmax), a software package that employs k-mer-based assembly of chimeric dsRNA sequences to target multiple related RNA sequences, to broaden the target spectrum. The package ensures that designed dsRNAs have no defined contiguous sequence homology with any off-target sequences, which can range from single transcriptomes through to metagenome sequence data and beyond. The efficacy of this package is demonstrated by a dsRNAmax-designed dsRNA that inhibits multiple root-knot nematode species but not a non-target nematode species, despite its susceptibility to environmental RNAi and high homology of the target gene.

Phakopsora pachyrhizi, an obligate biotrophic rust fungus, is the causal agent of Asian Soybean Rust (ASR) disease. Here, we utilized whole-genome data to explore the evolutionary patterns and population structure across 45 P. pachyrhizi isolates collected from 1972 to 2017 from diverse geographic regions worldwide. We also characterized in-silico mating-type (MAT) genes of P. pachyrhizi, in the predicted proteome of three isolates, to investigate the sexual compatibility system. Our molecular phylogenetic analysis in P. pachyrhizi inferred two distinct evolutionary lineages structured on a temporal scale, with lineage Pp1 grouping isolates obtained from 1972 to 1994, while more recently collected isolates formed a second lineage, Pp2. We found higher levels of genetic diversity in lineage Pp1, whereas lineage Pp2 exhibited a strong clonal genetic structure, with a significant lower diversity. The widespread propagation of P. pachyrhizi clonal spores across soybean-growing regions likely explains the absence of a large-scale spatial genetic structure within each lineage. Two independent isolates (TW72-1 and AU79-1) showed moderate levels of genetic admixture, suggesting potential somatic hybridization between the two P. pachyrhizi lineages. We observed no clear congruence between virulence levels of P. pachyrhizi isolates and their phylogenetic patterns. Our findings support a probable tetrapolar mating system in P. pachyrhizi. Taken together, our study offers new insights into the evolutionary history of P. pachyrhizi and demonstrates that multiple MAT genes are highly expressed during the later stages of soybean infection, suggesting their potential role in the formation of urediniospores within the life cycle of P. pachyrhizi.

Protein function prediction is a fundamental cornerstone in bioinformatics, providing critical insights into biological processes and disease mechanisms. Despite significant advances, challenges persist due to data sparsity and functional ambiguity. We introduce GOHPro (GO Similarity-based Heterogeneous Network Propagation), a novel method that constructs a heterogeneous network by integrating protein functional similarity (derived from domain profiles and modular complexes) with GO semantic relationships. This method applies a network propagation algorithm to prioritize annotations based on multi-omics context. When evaluated on yeast and human datasets, GOHPro outperformed six state-of-the-art methods. Specifically, it achieved Fmax improvements ranging from 6.8 to 47.5% over methods like exp2GO across the Biological Process (BP), Molecular Function (MF), and Cellular Component (CC) ontologies in both yeast and human species. Rigorous case studies on proteins with shared domains, such as AAA + ATPases, demonstrated GOHPro's ability to resolve functional ambiguity by leveraging contextual interactions and modular complexes. Further validation on the CAFA3 benchmark confirmed its generalizability, with Fmax gains exceeding 62% compared to baseline approaches in human species. Our analysis revealed that homology and network connectivity critically influence prediction robustness, with the modular similarity network compensating for evolutionary gaps in dark proteins. The framework's extensibility to de novo structural predictions highlights its potential to bridge the annotation gap in uncharacterized proteomes.

Pyrroloquinoline quinone (PQQ) is a soluble redox cofactor used by diverse bacteria. Many Gram-negative bacteria that encode PQQ-dependent enzymes do not produce it and instead obtain it from the environment. To achieve this, Escherichia coli uses the TonB-dependent transporter PqqU as a high-affinity PQQ importer. Here, we show that PqqU binds PQQ with high affinity and determine the high-resolution structure of the PqqU-PQQ complex, revealing that PqqU undergoes conformational changes in PQQ binding to capture the cofactor in an internal cavity. We show that these conformational changes preclude the binding of a bacteriophage, which targets PqqU as a cell surface receptor. Guided by the PqqU-PQQ structure, we identify amino acids essential for PQQ import and leverage this information to map the presence of PqqU across Gram-negative bacteria. This reveals that PqqU is encoded by Gram-negative bacteria from at least 22 phyla occupying diverse habitats, indicating that PQQ is an important cofactor for bacteria that adopt diverse lifestyles and metabolic strategies.

The plasmodium interspersed repeats (pir) multigene family is found across malaria parasite genomes, first discovered in the human-infecting species Plasmodium vivax, where they were initially named the virs. Their function remains unknown, although studies have suggested a role in virulence of the asexual blood stages. Sub-families of the P. vivax pir/virs have been identified, and are found in isolates from across the world, however their transcription at different localities and in different stages of the life cycle have not been quantified. Multiple transcriptomic studies of the parasite have been conducted, but many map the pir reads to existing reference genomes (as part of standard bioinformatic practice), which may miss members of the multigene family due to its inherent variability. This obscures our understanding of how the pir sub-families in P. vivax may be contributing to human/vector infection.

To overcome the issue of hidden pir diversity from utilising a reference genome, we employed de novo transcriptome assembly to construct the pir 'reference' of different parasite isolates from published and novel RNAseq datasets. For this purpose, a pipeline was written in Nextflow, and first tested on data from the rodent-infecting P. c. chabaudi parasite to ascertain its efficacy on a sample with a full, genome-based set of pir gene sequences. The pipeline assembled hundreds of pirs from the studies included. By performing BLAST sequence identity comparisons with reference genome pirs (including P. vivax and related species) we found a clustered network of transcripts which corresponded well with prior sub-family annotations, albeit requiring some updated nomenclature. Mapping the RNAseq datasets to the de novo transcriptome references revealed that the transcription of these updated pir gene sub-families is generally consistent across the different geographical regions. From this transcriptional quantification, a time course of mosquito bloodmeals (after feeding on an infected patient) highlighted the first evidence of ookinete stage pir transcription in a human-infective malaria parasite.

De novo transcriptome assembly is a valuable tool for understanding highly variable multigene families from Plasmodium spp., and with pipeline software these can be applied more easily and at scale. Despite a global distribution, P. vivax has a conserved pir sub-family structure-both in terms of genome copy number and transcription. We suggest that this indicates important roles of the distinct sub-families, or a genetic mechanism maintaining their preservation. Furthermore, a burst of pir transcription in the mosquito stages of development is the first glint of ookinete pir expression for a human-infective malaria parasite, suggesting a role for the gene family at a new stage of the lifecycle.

Lobsters, aquatic organisms of significant economic value, hold an important position in the global aquaculture and fisheries industries. However, due to overfishing and ecological change, the populations of certain lobster species have declined dramatically, prompting conservation efforts in various countries. However, limited genomics research has restricted our capacity to conserve and exploit lobster germplasm resources. Here, we present a chromosome-level reference genome for Panulirus homarus homarus constructed using PacBio long-read sequencing and Hi-C data. The genome assembly size was 2.61 Gb, with a contig N50 of 5.43 Mb, and a scaffold N50 of 36.69 Mb. The assembled sequences were anchored to 73 chromosomes, covering 96.05% of the total genome. A total of 25,580 protein-coding genes were predicted, and 99.98% of the genes were functionally annotated using various protein databases. The high-quality genome assembly provides a valuable resource for studying the biology and evolutionary history of P. h. homarus, and could facilitate sustainable resource management, aquaculture, and conservation of the species.

Theileriosis exerts a substantial impact on ruminants, resulting in significant economic losses within the animal husbandry sector. The current vaccine, a live attenuated parasite, has several limitations that hinder effective disease control. This study utilized immunoinformatics to prioritize potential vaccine candidates and pointed to the design of a novel mRNA vaccine against Theileria annulata using in silico methods. Nine antigenic proteins were selected using various software, and their epitopes were identified through immunoinformatics tools. These epitopes were assessed for their biological traits and homology. Their presentation by major histocompatibility complex (MHC) cells and other immune cells was analyzed using molecular docking techniques. A multi-epitope protein was then modeled and optimized, followed by structural and stability analyses of the mRNA vaccine construct. Finally, the immune response to the new vaccine was simulated. The identified epitopes were localized within the antigen-binding sites of their respective MHC alleles. The newly formulated vaccine demonstrated stability, exhibited no toxicity, and showed non-allergenic characteristics. It effectively elicited responses from both the humoral and cellular immune systems. The findings suggest that the desired engineered mRNA vaccine paves the way for the development of the deterrence of theileriosis. This potential merits additional exploration through rigorous laboratory experiments and subsequent clinical trials.IMPORTANCEThis study presents a cutting-edge approach in vaccine design against bovine theileriosis, a devastating disease affecting cattle globally. By leveraging immunoinformatics methodologies, a novel mRNA vaccine candidate was tailored using computational analyzes of Theileria annulata proteins. Antigenic protein identification, epitope evaluation, and structural optimization of the multi-epitope mRNA vaccine are pivotal advancements in vaccine development. Using computational modeling tools to predict immune responses enhances the efficiency and accuracy of vaccine design, potentially revolutionizing preventive strategies against bovine theileriosis. This research not only demonstrates the potential of immunoinformatics in vaccine innovation but also sheds light on a promising avenue for combating a significant livestock health concern, offering hope for more effective and targeted veterinary interventions.

Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.

Quinoa is a resilient crop with significant genetic diversity, enabling it to thrive in various climates. This study focuses on the Universal Stress Protein (USP) gene family in quinoa. It helps plants maintain homeostasis in response to drought, high salinity, extreme temperatures, and scavenging reactive oxygen species. The research conducted a genome-wide analysis of C. quinoa USP genes (CqUSPs). The gene structure, distribution of motifs, phylogenetic history, and duplication of CqUSPs were analysed. Analysis of cis-elements, protein-protein interactions, and micro-RNAs that target CqUSPs revealed important insights into the regulatory mechanisms, functional associations and post-transcriptional control of these genes. We have identified 41 sequences inside the allotetraploid genome. Domain architecture helped us understand the multifunctional nature of CqUSPs. Analysis of transcriptome data has demonstrated that the CqUSP gene family plays a role in the defence response to drought and heat stress conditions in quinoa. Protein-protein interaction studies showed their roles in amino acid metabolism, chaperone activity, ubiquitination, and DNA repair mechanisms. This comprehensive study reveals the identification and characterisation of CqUSP genes, offering valuable insights for further exploration of abiotic stress tolerance in quinoa. Additional research, such as expression profiling, might assist in confirming the stress-specific transcriptional regulation of these genes. To the best of our knowledge this the first detailed study conducted on the identification and interaction network of USP gene family in quinoa.

The marbled orb-weaver spider, Araneus marmoreus (Araneae: Araneidae), is distinguished by its unique inflated, pumpkin-like abdomen. Numerous genome studies have been conducted on Araneidae species, providing insights into their unique biological traits. However, studies on A. marmoreus remain limited, despite its ecological significance and intriguing morphology. The lack of a high-quality reference genome has further hindered in-depth exploration of its evolutionary biology and ecological dynamics. Here, we present a chromosome-level genome assembly for A. marmoreus, generated using a combination of Illumina, PacBio, and Hi-C sequencing technologies. The assembled genome is 2.39 Gb in size, comprising 13 chromosomes, with a scaffold N50 of 181.8 Mb and a contig N50 of 721.3 kb. The assembly achieved a BUSCO completeness score of 97.1% (n = 2,934), including 91.0% complete and single-copy BUSCOs and 6.1% complete and duplicated BUSCOs. Repetitive sequences accounted for 59.25% of the genome, and 23,381 protein-coding genes were annotated. This high-quality genome provides a valuable resource for advancing research into the evolutionary genomics and ecological dynamics of A. marmoreus.

Apicomplexan parasites are single-celled obligate intracellular eukaryotic organisms that cause significant animal and human disease and pose a substantial health and socioeconomic burden worldwide. Eimeria acervulina is one such parasite of chickens, representative of several Eimeria species causing coccidiosis disease. A complete assembly of the E. acervulina genome may help identify markers of drug-resistance and design recombinant vaccines. We sequenced E. acervulina APU1 strain using Oxford Nanopore Sequencing and Illumina technology in combination with a Hi-C (Omni-C) proximity linkage library and achieved a chromosomal scale assembly using the MaSuRCA assembler. The final assembly was 52 Mb. with 15 chromosomes and 99% BUSCO completeness. A total of 7,621 genes were predicted using a pipeline of BRAKER3, GeneMark-ETP and AUGUSTUS, of which 4,647 (60.97%) have a predicted Pfam function and 1,962 (25.74%) have Gene Ontology (GO) terms matching molecular, biological, and functional classes. Stage-specific transcriptome analysis revealed 9,761 transcripts. This genome assembly and transcriptome analysis provides the foundation for identifying biologically important candidates for anticoccidial drug and vaccine development.

Zoea II syndrome poses a significant threat to the larval stage of Pacific white shrimp (Litopenaeus vannamei), significantly reducing larval yield in shrimp hatcheries. Understanding the molecular mechanisms of zoea II syndrome and developing effective intervention strategies are crucial for its prevention and control. In this study, we conducted comparative transcriptomic analyses of healthy larvae and those with zoea II syndrome. Our results revealed that the syndrome disrupts key biological pathways involved in stress responses, immunity, metabolism, and development. Notably, the endoplasmic reticulum (ER) stress pathway played a key role, with the protein kinase R-like ER kinase (PERK) gene markedly upregulated, making it a promising target for intervention. We designed multi-target siRNAs and delivered a combination of siRNAs (siPERK-1 + 2 + 3) to Litopenaeus vannamei embryos via transfection, achieving approximately 60 % silencing of PERK. This intervention significantly increased larval survival rates to over 50 %, compared to 22 % in untreated controls under standard conditions. Furthermore, PERK silencing reduced the overexpression of genes related to immune, antioxidant, metabolic, and stress responses, while promoting the expression of genes related to growth and development. These results highlight the pivotal role of the ER stress response in zoea II syndrome and demonstrate that PERK silencing offers a promising therapeutic intervention strategy to improve larval survival in shrimp aquaculture.

Limonene is a chiral, high-demand monoterpene that has wide applications in therapeutics, cosmetics, biofuels, agri-food, biomaterials, and solvent industries. However, its biosynthesis by microbial cell factories is often limited by the poor activity of limonene synthase (LS). Optimization of the rate-limiting enzyme is thus crucial for boosting limonene production. Here, we report the identification of ten LS homologues from sequence data mining and their testing in cells accumulating geranyl pyrophosphate (GPP) or neryl pyrophosphate (NPP) for limonene production. The selectivity of these enzymes toward GPP or NPP was investigated, leading to the identification of a limonene synthase from Agastache rugosa that displays a clear substrate preference for NPP over GPP in vivo. This enzyme was selected as a template for engineering. Using in silico analyses and mutagenesis, several mutants were engineered that revealed differences in substrate specificity. Among them, a combination of mutations (S8K/I265V/E276P/P277R/A281K/N282T/I285Q/I286L) improved limonene production by 4.8- and 1.9-fold with the GPP and NPP pathways, respectively. The mutant predominantly produced (+)-limonene from GPP and a mixture of limonene from NPP, with ∼85-90% of (+)-limonene. This decreased the selectivity for NPP by 2.4-fold. This supports the improved biological production of limonene enantiomers from renewable carbon sources.

Rhynchosporium commune is a fungal pathogen responsible for causing scald disease in barley, leading to significant yield losses and reduced grain quality in susceptible cultivars. Effector proteins secreted by R. commune play crucial roles in manipulating host defenses and facilitating infection. Hence, this study aimed to identify and characterize effector candidates (ECs) in R. commune using a comprehensive bioinformatics approach combined with experimental validation. Initially, a dataset of 12,211 genes from the R. commune strain UK7 genome was analyzed to identify potential ECs, resulting in the selection of 48 candidate proteins. These candidates were further validated using RNA-Seq analysis, which confirmed significant expression of 27 ECs during infection. Our analysis re-identified key effectors, including CZT06923 and CZT13833, with 100% identity to NIP3 and NIP2, respectively, in R. commune. Novel ECs, such as CZT07600, CZT13755, and CZT13375, were identified with lower identity to NIP2, suggesting potential variants. Additionally, structural analysis revealed that CZT07873 EC indicates significant structural similarity to known fungal effector. qRT-PCR validation confirmed the differential expression of CZS93219 and CZT13755, with peak expression at 9 and 12 dpi, respectively. This comprehensive approach enhances our understanding of R. commune's pathogenic mechanisms and provides insights into potential targets for developing disease management strategies in barley cultivation.

Nuclear receptors (NRs) constitute a superfamily of transcription factors that regulate diverse biological processes. In insects, NRs not only govern essential physiological functions including metabolism, development, and reproduction, but also play pivotal roles in regulating caste differentiation and division of labor within social insect colonies. Pseudoregma bambucicola is a species of social aphid in which adults exhibit a specialized reproductive division of labor. This unique system produces first-instar nymphs and soldiers, which share an identical genetic background yet exhibit distinct morphological and behavioral traits. Although NRs exhibit pleiotropic regulatory capacities, their roles in the unique developmental patterns of P. bambucicola remain unclear.

This study identified 21 NR genes based on the genomic data of P. bambucicola and analyzed the duplication and loss events of these genes through phylogenetic analysis. Additionally, differential expression of NR genes was analyzed using transcriptomic data. The TLL exhibited significant differential expression in adults with distinct reproductive behaviors, suggesting its involvement in the regulation of reproductive division of labor. E75 and HNF4 were found to be important for the post-embryonic development of soldiers. Furthermore, quantitative real-time PCR confirmed caste-specific expression patterns of HR4 and HR39, indicating their potential involvement in morphological differentiation and developmental regulation among castes.

This study conducted bioinformatic identification of NR genes in the social aphid P. bambucicola, and investigated their potential roles in morphological differentiation and behavioral division through analysis of differential gene expression. The findings provide preliminary evidence for the functional significance of NR genes in social aphids, while offering novel insights for subsequent research exploration.

Whereas alignment has been fundamental to sequence-based assessments of protein homology, it is ineffective for intrinsically disordered regions (IDRs) due to their lowered sequence conservation and unique sequence properties. Here, we present a web server implementation of SHARK (bio-shark.org), an alignment-free algorithm for homology classification that compares the overall amino acid composition and short regions (k-mers) shared between sequences (SHARK-scores). The output of such k-mer-based comparisons is used by SHARK-dive, a machine learning classifier to detect homology between unalignable, disordered sequences. SHARK-web provides sequence-versus-database assessment of protein sequence homology akin to conventional tools such as BLAST and HMMER. Additionally, we provide precomputed sets of IDR sequences from 16 model organism proteomes facilitating searches against species-specific IDR-omes. SHARK-dive offers superior overall homology detection performance to BLAST and HMMER, driven by a large increase in sensitivity to low sequence identity homologs, and can be used to facilitate the study of sequence-function relationships in disordered, difficult-to-align regions.

Lipoxygenases (LOXs) are key enzymes in plant lipid metabolism and stress responses, yet their genomic organization and functional dynamics in Luffa aegyptiaca-a species of culinary, medicinal, and ornamental importance-remain unexplored. Here, we present the first genome-wide identification and characterization of the LOX gene family in L. aegyptiaca, revealing 29 LOX genes, including 14 members of 13S-lipoxygenases (13-LOX) and 15 members of 9S-lipoxygenases (9-LOX), respectively. Notably, tandem duplication events shaped the expansion of LOX genes, with 24 genes clustered in two loci, suggesting functional diversification to enhance environmental adaptability. Phylogenetic analysis demonstrated evolutionary conservation of LOX genes across Cucurbitaceae species, while collinearity analysis highlighted conserved genomic organization. Promoter cis-element profiling identified stress- and hormone-responsive motifs, implicating LOX genes in developmental and stress regulatory networks. Tissue-specific expression patterns revealed 18 LOX genes predominantly expressed in tendril, fruit, root, and male flower, linking them to organ-specific physiological roles. Crucially, under heat stress, 9 out of 11 expressed LOX genes were significantly downregulated, indicating their potential role in thermal stress adaptation through metabolic reconfiguration. This study provides foundational insights into the LOX family's contribution to L. aegyptiaca's resilience and offers genetic targets for breeding strategies to improve stress tolerance in cucurbit crops.

Caspases are cysteine-dependent aspartate-directed proteases which have critical functions in programmed cell death and inflammation. Their catalytic activity depends on a catalytic dyad of cysteine and histidine within a characteristic protein fold, the so-called caspase domain. Here, we investigated the evolution of caspase-16 (CASP16), an enigmatic member of the caspase family, for which only a partial human gene had been reported previously. The presence of CASP16 orthologs in placental mammals, marsupials and monotremes suggests that caspase-16 originated prior to the divergence of the main phylogenetic clades of mammals. Caspase-16 proteins of various species contain a carboxy-terminal caspase domain and an amino-terminal prodomain predicted to fold into a caspase domain-like structure, which is a unique feature among caspases known so far. Comparative sequence analysis indicates that the prodomain of caspase-16 has evolved by the duplication of exons encoding the caspase domain, whereby the catalytic site was lost in the amino-terminal domain and conserved in the carboxy-terminal domain of caspase-16. The murine and human orthologs of CASP16 contain frameshift mutations and therefore represent pseudogenes (CASP16P). CASP16 of the chimpanzee displays more than 98% nucleotide sequence identity with the human CASP16P gene but, like CASP16 genes of other primates, has an intact protein coding sequence. We conclude that caspase-16 structurally differs from other mammalian caspases, and the pseudogenization of CASP16 distinguishes humans from their phylogenetically closest relatives.

Elsholtzia splendens, a perennial herb native to East Asia, is valued for its ornamental and medicinal uses, particularly in treating inflammatory and febrile conditions. Recent studies have highlighted its antibacterial, anti-inflammatory, antidepressant, antithrombotic, and lipid-lowering properties of its compounds. Additionally, E. splendens shows potential for phytoremediation owing to its ability to hyperaccumulate copper (Cu), lead (Pb), zinc (Zn), and cadmium (Cd). However, its role in remediation conflicts with its medicinal use because of the risk of heavy metal accumulation. Genome sequencing will be key to boosting beneficial compound production and reducing heavy metal risks. In this study, we generated a high-resolution, haplotype-resolved, chromosome-scale genome sequence of E. splendens using PacBio Revio long-read, Illumina short-read, and Hi-C sequencing technologies. The haplotype genome assemblies, spanned 275.4 and 265.0 Mbp with a scaffold N50 of 33.9 and 33.8 Mbp for haplotype 1 and 2, respectively. This assembly provides valuable insights into medicinal compound biosynthesis and supports genetic conservation efforts, facilitating future genetic and biotechnological applications of E. splendens for medicinal and ecological uses.

Syntrophic cocultures (hitherto assumed to be commensalistic) of Clostridium acetobutylicum and Clostridium ljungdahlii, whereby CO2 and H2 produced by the former feed the latter, result in interspecies cell fusion involving large-scale exchange of protein, RNA, and DNA between the two organisms. Although mammalian cell fusion is mechanistically dissected, the mechanism for such microbial-cell fusions is unknown. To start exploring this mechanism, we used RNA sequencing to identify genes differentially expressed in this coculture using two types of comparisons. One type compared coculture to the two monocultures, capturing the combined impact of interactions through soluble signals in the medium and through direct cell-to-cell interactions. The second type compared membrane-separated versus -unseparated cocultures, isolating the impact of interspecies physical contact. While we could not firmly identify specific genes that might drive cell fusion, consistent with our hypothesized model for this interspecies microbial cell fusion, we observed differential regulation of genes involved in C. ljungdahlii's autotrophic Wood-Ljungdahl pathway metabolism and genes of the motility machinery. Unexpectedly, we also identified differential regulation of biosynthetic genes of several amino acids, and notably of arginine and histidine. We verified that they are produced by C. acetobutylicum and are metabolized by C. ljungdahlii to its growth advantage. These and other findings, and notably upregulation of C. acetobutylicum ribosomal-protein genes, paint a more complex syntrophic picture and suggest a mutualistic relationship, whereby beyond CO2 and H2, C. acetobutylicum feeds C. ljungdahlii with growth-boosting amino acids, while benefiting from the H2 utilization by C. ljungdahlii.IMPORTANCEThe construction and study of synthetic microbial cocultures is a growing research area due to the untapped potential of defined multi-species industrial bioprocesses and the utility of defined cocultures for generating insight into complex, undefined, natural microbial consortia. Our previous work showed that coculturing C. acetobutylicum and C. ljungdahlii leads to a unique metabolic phenotype (production of isopropanol) and heterologous cell fusion events. Here, we used RNAseq to explore genes involved in and impacted by these fusions. First, we compared gene expression in coculture to each monoculture. Second, we utilized a transwell system to compare gene expression in mixed cocultures to cocultures with both species physically separated by a permeable membrane, isolating the impact of interspecies "touching" on the transcriptome. This study deepens our mechanistic understanding of the C. acetobutylicum-C. ljungdahlii coculture phenotype, laying the groundwork for reverse genetic studies of heterologous cell fusion in Clostridium cocultures.

Members of the heat shock protein 90 family (HSP90s) are evolutionarily conserved and play crucial roles in protein transport, immune regulation and antigen presentation. In this study, five hsp90s were identified from the genome of large yellow croaker (Larimichthys crocea) and analyzed using bioinformatics. All five identified hsp90s encode proteins with HATPase_c and HSP90 domains, and are mainly localized in the cytoplasm, mitochondria and endoplasmic reticulum. Chromosomal mapping revealed their distribution across three distinct chromosomes. Quantitative real-time PCR (qPCR) analysis showed differential expression patterns of the five hsp90s in 11 tissues. Additionally, their expression dynamics in the liver, spleen, head kidney, gill and blood were analyzed at 3 h, 12 h, 24 h and 48 h post thermal stress, Vibrio parahaemolyticus infection or under a combination of these two stressors. Results showed that the L. crocea hsp90s exhibited distinct expression patterns in response to the above three stimuli in different immune tissues. Notably, hsp90s in the spleen were most responsive. This study systematically clarified for the first time the gene structure characteristics, tissue expression patterns, and environmental stress response mechanisms of the HSP90 family in L. crocea. It confirmed that hsp90s show significant functional differentiation and synergy in response to biotic (pathogen infection) and abiotic (thermal stress) stresses, and provides important clues for a deeper understanding of the genetic basis of environmental adaptation in L. crocea.

Ethylene response factors (ERFs), belonging to the AP2/ERF superfamily, play vital roles in plant growth, development, and stress responses. The evolutionary and expression features of the members of the ERF gene family have not yet been extensively analyzed through comprehensive comparative genomics across various diploid, tetraploid, and hexaploid wheat genomes. In this study, we identified a total of 2,967 ERF genes across one diploid, two tetraploid, and five hexaploid wheat genomes using the characteristics of conserved domains of ERF proteins. Phylogenetic analysis revealed that ERF genes clustered into two main groups. Analyses of expansion of the ERF gene family indicated that the members of IIIc and IX (sub)groups were observed to show the expansion in tetraploid and hexaploid wheat compared to diploid wheat. Tandem duplication was identified as a key mechanism for ERF gene family expansion, with varying proportions across different wheat genomes. Ancient evolutionary evidence was traced using Amborella trichopoda as a reference, revealing the retention of gene copies in both tetraploid and hexaploid wheat. Then, we analyzed the expression of ERF genes under salt stress in Triticum aestivum, identifying 86 consistently up-regulated and 14 down-regulated ERF genes, and reported the stress tolerant and disease resistant ERF genes in hexaploid wheat. These findings provide valuable insights into the evolutionary dynamics and functional features of ERF genes in wheat, paving the way for genetic breeding and molecular improvement of wheat species.

The PADRE (Pathogen and abiotic stress response, cadmium tolerance, disordered region-containing) family of genes, which contains the structural DUF4228 domain of unknown function (DUF), has been reported to be associated with plant responses to abiotic stresses. However, the specific functions of this family in the salt stress response remain unknown. AtPADRE13 is induced by salt stress and ABA (abscisic acid). After the overexpression of AtPADRE13 in Arabidopsis, seeds were found to be insensitive to ABA treatment. After salt treatment, the overexpression lines presented a significantly lower survival rate, increased MDA (Malondialdehyde) content, and reduced antioxidant enzyme activities compared with the wild-type, and were more sensitive to salt stress. Transcriptome data analysis further revealed that AtPADRE13 overexpression resulted in different degrees of down-regulation for a series of positive regulators related to ABA catabolism, transport, and their mediated plant responses to salt stress. In addition, the expression of genes related to ROS (reactive oxygen species) scavenging was down-regulated. In conclusion, AtPADRE13 plays a negative regulatory role in the response to salt stress in Arabidopsis.

The Basic Leucine Zipper (bZIP) transcription factors play a vital role in plant responses to abiotic stress. Despite being studied in various plant species, the function of the bZIP gene family in Soapberry (Sapindus mukorossi Gaertn.), a significant tree species for forestry biomass energy, remains unclear. In this study, we conducted a genome-wide analysis of the bZIP gene family in Soapberry, based on the observation that bZIP transcription factors were enriched in the transcriptome data of Soapberry-grafted stem segments, as revealed by both GO and KEGG analyses. For the first time, we identified 31 SmbZIPs and provided detailed information regarding their physicochemical characteristics, gene structures, protein motifs, phylogenetic relationships, cis-regulatory elements (CREs), and predicted transcriptional regulatory networks. According to our prediction of the SmbZIP-mediated regulatory network and CREs in the promoter region, SmbZIPs may be associated with plant growth and development as well as responses to mechanical wounding stress. By integrating RT-qPCR and RNA-seq analyses, we determined that the expression patterns of SmbZIPs were specific to the graft-healing stages and locations. In conclusion, our study elucidates the potential role of the bZIP gene family in responding to plant wounding stress and facilitating graft healing, thereby providing valuable insights for future functional genomics studies of Soapberry.