Search Results (1,571)

Candidatus Hepatincolaceae is a poorly characterized family of obligate Alphaproteobacterial symbionts that are widely detected in ecdysozoans. They were previously assumed to play a nutrient-scavenging role in the gut lumen. In this study, two high-quality metagenome-assembled genomes (MAGs, 1.39 Mb and 1.48 Mb in size) were recovered from the gut of the snapping shrimp Alpheus brevicristatus via metagenomic sequencing. Phylogenetic and whole-genome similarity analyses confirm that these two MAGs represent two novel, undescribed genera within the family Ca. Hepatincolaceae. Metabolic reconstruction reveals that they not only retain the canonical nutrient-scavenging pathways conserved across all Hepatincolaceae members, but also encode previously undocumented functional modules for antioxidant defense, vitamin B₁ and B₂ biosynthesis, and short-chain fatty acid production. They maintain a high oxygen-affinity cytochrome bd terminal oxidase to thrive in the anoxic gut microenvironment. Consistent with their symbiotic lifestyle, their genomes exhibit typical signatures of reductive evolution, such as reduced genome size, low GC content, and gene loss in amino acid and nucleotide de novo biosynthesis pathways. This study presents the first reported high-quality genomes of marine Ca. Hepatincolaceae symbionts, which are predicted to possess multiple metabolic functions extending beyond nutritional mutualism. Full article

Sugarcane (Saccharum spp.) is a globally vital high-biomass sugar crop with a massive demand for potassium (K). Low-K⁺ stress severely restricts its yield and stress resistance. Plasma membrane intrinsic proteins (PIPs) play pivotal roles in transmembrane water transport and ion homeostasis; however, their evolutionary characteristics and molecular mechanisms underlying nutritional stress responses in the complex polyploid sugarcane remain poorly understood. In this study, genome-wide identification in the sugarcane cultivar XTT22 yielded 149 PIP gene family members (comprising 54 PIP1s and 95 PIP2s). Phylogenetic and chromosomal localization analyses demonstrated that the sugarcane PIP family underwent drastic paralogous expansion during evolution, with tandem duplication acting as the core driving force for the dramatic expansion of the PIP2 subfamily. Spatiotemporal expression profiling unveiled significant modular functional division among PIP genes, identifying a core co-expression group driving rapid early seedling elongation and a PIP2-specific expression cluster dedicated to the physiological homeostasis of mature stems. Notably, the core member ScPIP2-70 exhibited significant early-induced responses at both transcriptional and protein levels in roots under low-K⁺ stress. Functional complementation assays in the K⁺-uptake deficient yeast strain R5421 further confirmed that the heterologous expression of ScPIP2-70 effectively rescued the growth defects of yeast under low-K⁺ conditions, demonstrating its potential transmembrane K⁺ transport activity. This study not only comprehensively elucidates the evolutionary dynamics and spatiotemporal expression profiles of the sugarcane PIP gene family but also uncovers the novel pleiotropic function of ScPIP2-70 in mediating low-K⁺ stress tolerance, providing critical theoretical support and candidate gene resources for breeding “potassium-efficient” sugarcane cultivars via modern biotechnology. Full article

Melatonin is an important stress-protective agent in plant growth. Methyltransferase (ASMT) is an important enzyme in the concluding phase of melatonin production in plants. In this study, we performed the genome-wide identification and functional investigation of the ASMT gene family in hexaploid wheat and 14 other plants. ASMT genes in 15 plants were identified by using HMM scanning against the proteomes derived from a single representative reference genome for each species. They were classified into three subfamilies I-III by constructing four types of phylogenetic trees (Neighbour-joining with p-distance model, Neighbour-joining with JTT model, Maximum likelihood, and Bayesian inference). Based on exon–intron structure and domain diagrams, a conserved structural pattern characterized by successive intron phases 1 and 0 (the “1-0” pattern) was found in ASMT genes during evolution. Collinear events analysis indicated that polyploidization and tandem duplication synergistically promote the expansion of T. aestivum ASMT members. Cis-acting element analysis revealed that numerous stress- and hormone-responsive motifs (such as ABRE and LTR) were present in ASMTs of wheat, suggesting a role for ASMTs in adaptive signal transduction. Transcriptome analysis revealed that specific T. aestivum ASMT genes were strongly responsive to stress; for instance, II_TraesCS2B02G041200 and II_TraesCS2B02G606200 were strongly upregulated under drought and salt stress, respectively. To independently confirm the stress responsiveness of these candidates in a different genetic background, we performed quantitative real-time PCR (qRT-PCR) on selected genes under drought and salt treatments. The result showed that the expression trends of transcriptome and qRT-PCR were almost the same, identifying these ASMT genes as strong stress-responsive candidates under drought and salt treatments. In this study, we performed identification, classification, evolution analysis and expression pattern analysis of ASMTs in wheat and 14 other plants. Our study will provide a framework for the targeted genetic improvement of melatonin-mediated stress resistance. Full article

Annamocarya sinensis is a Plant Species with Extremely Small Populations (PSESP) of great ecological and research value. Water conditions serve as a key environmental factor that profoundly shapes its growth, physiological homeostasis and stress adaptation. WRKY transcription factor families constitute the core molecular regulatory modules orchestrating plant responses to water-related stresses and environmental fluctuations. This study performs a systematic identification and bioinformatics analysis of the WRKY gene family in A. sinensis, combined with RT-qPCR to verify and analyze its expression patterns under water stress. The results identified a total of 92 WRKY genes unevenly distributed across 16 chromosomes, classified into three distinct subfamilies with obvious conservation of conserved motifs; the gene promoters were enriched with drought cis-elements, and fragment duplication drove the expansion of the family; this family had a high collinearity with the homologous genes of Arabidopsis thaliana, and its evolutionary function was conserved. RT-qPCR confirmed that AsWRKY3, AsWRKY11, AsWRKY17, AsWRKY53 and AsWRKY72 showed differential expression under water stress and were involved in regulating the processes of drought and waterlogging tolerance. Under drought stress, all five genes exhibited an upregulation trend, albeit with slightly varying response intensities; under waterlogging stress, AsWRKY3 and AsWRKY17 demonstrated strong enhanced responses, AsWRKY11 and AsWRKY53 showed early-response patterns, whereas AsWRKY72 exhibited a downregulation trend. In summary, fragment duplication and family differentiation enhanced the functional diversity of the WRKY family, providing a genetic basis for the adaptation of A. sinensis to changes in water availability. The research findings not only provide crucial theoretical clues for exploring the potential environmental adaptation and molecular evolution mechanisms of extremely small population plants, but also offer essential genetic resources and scientific foundations for species conservation, restoring wild populations, and conducting stress-resistant molecular breeding. Full article

Background/Objectives: Soybean (Glycine max) productivity is increasingly constrained by soil salinity. WIP transcription factors, a subfamily of C2H2-type zinc finger proteins, regulate cell division, differentiation, and tissue patterning in several plant species, but this gene family had not previously been systematically characterized in soybean or any other major legume crop. This study aimed to identify and characterize the GmWIP gene family genome-wide and evaluate its potential involvement in the soybean salt-stress response. Methods: Genome-wide identification of GmWIP genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4.ann1 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, and promoter cis-acting elements. Tissue-specific expression was examined using transcriptome data, and GmWIP responses to salt stress were profiled by RT-qPCR in roots, stems, and leaves of a salt-tolerant cultivar (HN531) and a salt-sensitive cultivar (HN563), alongside physiological measurements of oxidative stress and osmotic adjustment. Results: Thirty GmWIP genes were identified, with molecular weights from 26.90 to 57.52 kDa, distributed unevenly across 15 soybean chromosomes, with chromosomes 11, 12, and 13 forming a major hotspot (53.3% of the family). Duplication analysis detected 54 reconciled segmental duplicate gene pairs, all exhibiting Ka/Ks values < 1 (ranging from 0.0351 to 0.4471; mean 0.214), consistent with purifying selection acting on this gene set. GmWIP promoters were enriched for ABRE, MBS, and MeJA cis-acting elements. RT-qPCR showed genotype- and tissue-dependent differential expression under salt stress (e.g., up to 14.9-fold induction of GmWIP22 in HN531 stems), paralleled by superior proline accumulation (+45%), soluble sugars, and CAT activity (+38%) alongside reduced MDA accumulation in the tolerant cultivar. Conclusions: The GmWIP gene family has expanded substantially in soybean relative to previously characterized species and shows genotype-dependent transcriptional responses to salt stress, suggesting that specific GmWIP members are candidate regulators of salt tolerance and warrant further functional investigation. Full article

Tremella sanguinea is a morphologically distinctive gelatinous mycoparasite of Stereum within Tremellales whose generic placement has remained unresolved for lack of high-quality genomic resources. We combined Oxford Nanopore long-read sequencing, short-read whole-genome sequencing and Hi-C chromatin conformation capture to assemble the first telomere-to-telomere (T2T) genome of this species: 21.44 Mb in nine gap-free chromosomes, with telomeric repeats recovered at all 18 chromosome ends. Phylogenomic analysis of nine Tremellales genomes, including the type species of Phaeotremella, placed T. sanguinea within Phaeotremella as sister to P. skinneri (divergence 24.50 Ma; 95% HPD 22.14–26.89) rather than within Tremella sensu stricto, corroborating at genome scale a placement previously indicated by multi-locus data, providing the first divergence-time estimates for the lineage, and reconciling its position with its dark, foliose basidiocarp morphology. Gene family evolution was contraction-biased, most strongly at the Phaeotremella crown node (92 expansions vs. 855 contractions). The carbohydrate-active enzyme repertoire of T. sanguinea (185 genes) fell within the range reported for Tremellales, whereas families that expanded on its branch were significantly enriched for transport functions, including dipeptide and allantoate transport. These results indicate that T. sanguinea acquires host-derived nutrients through uptake of small molecules rather than through an expanded hydrolytic repertoire, and provide genomic evidence for revising its generic placement within the segregate genera of Tremella sensu lato. Full article

Rising temperatures pose daunting challenges for sustainable yield and nutritional quality of rice (Oryza sativa L.), thus putting food security at risk. Limited information exists regarding cis-acting regulatory elements and candidate genes controlling the heat shock transcription factor (HSF) gene family in rice. Therefore, the present study identified HSF genes in the japonica (Nipponbare) and indica (9311) rice cultivars through in silico repositories. Three candidate genes (HSFC2B, HSFB1, and HSFC2A) were selected for qRT-PCR analysis to validate their expression patterns under heat stress (HS). The present findings reported a total of 25 OsHSF genes through in silico genome-wide identification. Comparative analysis illustrated that the OsHSF genes had structural similarities but different expression and transcriptional regulation between the two cultivars. HSF genes were unevenly distributed across the 12 rice chromosomes, suggesting that tandem duplication and gene repetition may have contributed to the evolution of novel genes. Phylogenetic analysis revealed that all OsHSF gene family members have shared common ancestry, but several genes lack introns, potentially facilitating swift stress responses as indicated by gene structure analysis. Expression analysis revealed that candidate genes were active, with HSFC2A exhibiting the highest level of expression in the japonica cultivar compared to indica under heat-stressed conditions. HSFC2B gene showed a higher statistical difference in its response between cultivars, time points, and cultivar vs. time points interactions compared to HSFC2A and HSFB1. These findings offer valuable insights into the function of OsHSF genes that will contribute to the development of climate-resilient rice cultivars. Full article

Bryophytes possess a gene family repertoire substantially larger than vascular plants, yet the functional evolution of their transcription factors remains poorly understood. We conducted a nested analysis across 144 bryophyte genomes, cataloging 58 transcription factor families and deeply characterizing the C2H2 zinc-finger protein family. We identified 8246 C2H2 zinc-finger genes classified into four structural types based on zinc-finger architecture. Domain-level scanning of 11,565 zinc fingers revised Z-type frequency from ~20% to 4.2%. The plant-specific Q-type was most prevalent in mosses and least prevalent in liverworts, with the major Q-type radiation occurring in seed plants. C2H2 zinc-finger gene expansion in mosses was driven by whole-genome duplication, and gene count correlated with genome size. Through re-analysis of publicly available RNA-seq datasets, cross-species expression profiling showed that mosses mobilized 23–28% of their C2H2 zinc-finger repertoires under dehydration, whereas the liverwort Marchantia polymorpha showed no significant response to osmotic stress and only a weak, transient response to salt. Notably, the aluminum-tolerance regulator STOP1 was downregulated under dehydration. Together, these results suggest a marked divergence in stress-responsive C2H2-ZFP deployment between mosses and liverworts, although the underlying mechanisms remain to be validated functionally. Full article

Fibrillins (FBNs) are conserved plastid-associated proteins implicated in plant development and abiotic stress responses; however, their roles in maize remain unclear. In this study, through a genome-wide bioinformatic analysis, we identified 14 ZmFBN genes in the maize genome and characterized their phylogeny, chromosomal distribution, gene structure, conserved motifs, and promoter cis-elements. ZmFBN members were grouped into several subfamilies that all retain a conserved PAP_fibrillin domain, whereas the variation in exon–intron organization, motif composition, and regulatory elements suggests functional diversification. Expression profiling revealed pronounced tissue-preferential patterns, with many genes highly expressed in leaves and reproductive tissues, and distinct responses to drought, salt, heat, and cold stresses. qRT-PCR assays showed that ZmFBN8 and ZmFBN9 are strongly induced by both salt and PEG-simulated drought, ZmFBN2 and ZmFBN5 are predominantly drought-responsive, and ZmFBN11 is mainly activated by salt. Genome-wide association analysis further detected significant loci near ZmFBN1 and ZmFBN4, whose allelic variants are associated with the survival rate under drought and with key agronomic traits, including the tassel branch number, flowering time, ear diameter, and kernel length. These results demonstrate that ZmFBN genes make diversified contributions to maize growth, development, and stress adaptation and highlight several members as promising targets for functional studies and the molecular breeding of stress-tolerant maize. Moreover, selection pressure analysis indicated ZmFBN7 experienced relaxed purifying selection, and ZmFBN12 underwent positive selection, which drives the functional diversification of the ZmFBN family during maize evolution. Full article

Brassinosteroid signaling kinases (BSKs) act as core signal transducers downstream of Brassinosteroid (BR) perception and integrate plant growth regulation with broad-spectrum biotic and abiotic stress tolerance. Despite well-established functional characterizations of BSK gene families in Arabidopsis thaliana and rice, comprehensive genome-wide profiling and salt response analysis of BSK homologs remain lacking in wheat. In this study, we systematically identified 18 TaBSK family members. Phylogenetic analysis separated wheat TaBSKs into three distinct evolutionary subgroups. The 18 TaBSK loci were unevenly distributed across 14 chromosomes derived from the A, B, and D subgenomes. Motif scanning uncovered 10 universal conserved amino acid motifs, including two signature functional domains: the tetratricopeptide repeat (TPR) and protein kinase catalytic domain (PKc). Intra-genomic collinearity analysis confirmed that segmental duplication constituted the primary evolutionary driver underlying TaBSK family expansion. Extensive cis-regulatory element profiling identified abundant hormone- and stress-responsive cis-motifs. Transcriptome profiling RNA-seq datasets revealed five TaBSK genes exhibiting significant differential transcription under salt stress. Specifically, TaBSK16, TaBSK17, and TaBSK18 were markedly upregulated following salt exposure. Collectively, this study delivers an evolutionary and transcriptional atlas of the wheat TaBSK family and provides candidate genes for functional validation and molecular breeding toward salt-tolerant wheat varieties. Collectively, this study explores the evolution and transcriptional patterns of the wheat TaBSK gene family and provides candidate genes for subsequent functional validation and molecular breeding of salt-tolerant wheat varieties. Full article

The three-amino-acid-loop-extension (TALE) gene family encodes a group of plant-specific homeodomain transcription factors that play indispensable roles in plant growth, development, and adaptation to environmental stresses. Although TALE genes have been extensively investigated in several plant species, their genome-wide characteristics and potential functions in maize, particularly in response to phosphorus deficiency, remain poorly understood. In the present study, a comprehensive genome-wide identification and characterization of the maize TALE gene family were conducted using bioinformatics approaches, followed by an investigation of their transcriptional responses to low-phosphorus (LP) stress. A total of 40 ZmTALE genes (ZmTALE1–ZmTALE40) were identified and phylogenetically classified into four subfamilies: BEL1-like, KNOX I, KNOX II, and KNOX III. Members within the same subfamily exhibited highly conserved gene structures and motif compositions, reflecting their evolutionary conservation. Chromosomal localization and synteny analyses demonstrated that segmental duplication has been the predominant force driving the expansion of the ZmTALE gene family during maize evolution. Promoter analysis revealed that the upstream regulatory regions of ZmTALE genes were enriched in light-responsive, phytohormone-responsive, and abiotic stress-related cis-acting regulatory elements, implying their potential involvement in multiple developmental and stress-responsive pathways. Expression profiling under LP conditions revealed pronounced genotype-dependent transcriptional responses among different maize inbred lines. Notably, ZmTALE1/5/12/14/18/30/31/33/36 were significantly induced by LP stress, whereas ZmTALE10 and ZmTALE37 were markedly repressed. These differentially expressed genes represent promising candidates for further functional investigation of phosphorus-deficiency tolerance in maize. Furthermore, ZmTALE10, ZmTALE14, and ZmTALE31 are nuclear-localized transcriptional activators. Taken together, these findings provide valuable insights into the evolutionary characteristics and potential biological functions of the maize TALE gene family and offer candidate genes for developing phosphorus-efficient maize cultivars through molecular breeding. Full article

The calcium ion-transporting ATPase (Ca²⁺-ATPase) gene family maintains plant intracellular Ca²⁺ homeostasis and regulates growth, development and stress immunity; however, its functions remain poorly characterized in Malus domestica. Here, we performed a genome-wide identification of apple Ca²⁺-ATPase genes and obtained 45 members, which were classified into MdACA (39) and MdECA (6) subfamilies and unevenly distributed on 14 chromosomes. Phylogenetic analysis of Ca²⁺-ATPase genes from Malus domestica, Arabidopsis thaliana, and Oryza sativa classified these proteins into five subgroups. The ACA and ECA subfamilies were highly conserved across species, whereas Group D was apple-specific. Collinearity and Ka/Ks analyses indicated that segmental duplication and purifying selection dominated the evolution of apple Ca²⁺-ATPase genes. Promoter cis-element prediction uncovered numerous regulatory elements related to phytohormone signaling, growth, development and stress defense. Codon usage bias analysis indicated that AUG (methionine) was the dominant codon. Tissue expression profiles showed differential expression of apple Ca²⁺-ATPase genes in various organs. Quantitative real-time PCR (qRT-PCR) assays demonstrated widespread responses of Ca²⁺-ATPase genes to Alternaria alternata infection, exogenous CaCl₂, salicylic acid (SA) and methyl jasmonate (MeJA), among which MdACA39 was strongly induced under all treatments. Subcellular localization verified that MdACA39 resides on the plasma membrane. Moreover, transient overexpression of MdACA39 significantly enhanced apple resistance to A. alternata, likely due to the activation of SA, MeJA and Ca²⁺ signaling-mediated immune pathways, the induction of disease resistance-related genes, and elevated antioxidant enzyme activity. Collectively, this study systematically characterizes the apple Ca²⁺-ATPase family and identifies MdACA39 as a key regulator of fungal resistance, providing valuable gene resources for dissecting Ca²⁺ signaling-mediated disease resistance in apple. Full article

BRI1-EMS-SUPPRESSOR 1 (BES1)/BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factors serve as core regulators of brassinosteroid (BR) signal in seed plants, where they control diverse developmental processes, including cell elongation, vascular development, and environmental responses; however, their evolutionary trajectory and functional diversification in early-diverging land plants remain poorly characterized. In this study, we systematically characterized the BES1/BZR1 gene family across 12 representative bryophyte species covering hornworts, liverworts and mosses, with Arabidopsis thaliana included as a vascular plant outgroup. In total, 19 non-redundant BES1/BZR1 homologs were identified within bryophyte genomes. Phylogenetic reconstruction, synteny analysis and Ka/Ks selection pressure analyses collectively revealed that this gene family is evolutionarily conserved throughout bryophytes, with moss-specific lineage expansion; most paralogous gene pairs have experienced strong purifying selection during evolution. Further analyses of gene structural organization, conserved protein motifs and cis-acting promoter elements uncovered universally conserved core domains alongside lineage-specific structural and regulatory variations. Subcellular localization assays demonstrated that the majority of tested bryophyte BES1/BZR1 proteins primarily accumulate in the nucleus, and autoluminescent reporter assays verified that multiple homologs modulate E-box-driven transcriptional activity. Transcriptional expression profiling indicated that BES1/BZR1 genes from Marchantia polymorpha and Sphagnum fallax are transcriptionally responsive to exogenous BR treatment, while several paralogs in S. fallax additionally exhibit altered expression under drought stress. Collectively, our results demonstrate that the BES1/BZR1 family originated at an early stage of land plant evolution, followed by lineage-specific gene expansion and divergent transcriptional regulation in bryophytes. This work advances our understanding of ancestral BR signaling and stress response modules in the early terrestrial plant lineages. Full article

The Fruit-Weight 2.2-Like (FWL) gene family plays crucial roles in determining organ size and stress responsiveness in plants. However, the FWL family members remain largely unexplored in Gossypium species. In this study, we identified and characterized the FWL family in Gossypium hirsutum to investigate their gene expansion, functional evolution, and potential association with key agronomic traits. A total of 51 GhFWLs were identified, and their gene structures, domain compositions, and phylogenetic relationships were comprehensively analyzed. Expression profiling under heat, cold, salt, and drought stress conditions revealed that most GhFWLs participate in abiotic stress response pathways. Haplotype-based association analysis revealed significant associations for 14 GhFWLs with fiber-related traits, suggesting their potential functions in regulating fiber development. Furthermore, silencing the family member GhMCA1 provided supporting evidence for its role in salt stress tolerance. Our findings provided insightful information about the FWL gene family in G. hirsutum and highlighted candidate genes for improving fiber-related traits and stress tolerance through molecular breeding approaches. Full article

Steroid Receptor Coactivators (SRCs) are members of the p160 nuclear receptor coactivator family and play essential roles in regulating transcription, development, metabolism, reproduction, and disease. However, their evolutionary origin and diversification remain poorly understood. Here, we employed a comprehensive comparative genomics approach to investigate the evolution of SRC-1, SRC-2, and SRC-3 across the domains of life. Evaluation of domain-based screening approaches showed that the NCBI Batch Web CD-Search Tool clearly distinguished domains among the three SRC family members. Genome-wide analyses identified 298 canonical SRC proteins in vertebrates, revealing distinct taxonomic distributions among the three paralogs. Comparative analyses of LXXLL motifs suggested both conserved and paralog-specific patterns associated with functional diversification. Analysis of more than 20,000 proteins, including over 4000 SRC-associated domain-containing proteins, revealed a widespread distribution of SRC-associated domains across diverse taxa. These findings support the hypothesis that pre-existing protein modules distributed across diverse taxa may have contributed to the assembly of canonical vertebrate SRC proteins through progressive domain acquisition and recombination. Phylogenetic analyses showed that SRC-1, SRC-2, and SRC-3 form distinct monophyletic clades, consistent with diversification through ancient gene duplication. Overall, these findings provide a comparative genomic framework for investigating the origin, structural evolution, and functional diversification of vertebrate SRC proteins while generating testable hypotheses regarding their evolutionary history. Full article