Genome-Wide Identification, Evolutionary Analysis and Comprehensive In Silico Characterization of the GPAT Gene Family in Sunflower (Helianthus annuus L.)

Genome-wide identi fi cation and expression analysis of TPS gene family contributing to cold tolerance in Actinidia arguta

Genome-wide identification and comprehensive characterization of the Aux/IAA gene family in Cucurbita moschata and its responses analysis to abiotic stresses

Auxin is a central phytohormone involved in regulating plant growth, development, and stress responses, with the Aux/IAA gene family functioning as an essential component of the auxin signaling pathway. To elucidate the genomic features and potential functions of the Aux/IAA gene family in pumpkin ( Cucurbita moschata ), we performed a genome-wide identification and systematic characterization. A total of 72 CmIAA genes were identified, encoding proteins ranging from 158 to 1275 amino acids with predicted isoelectric points of 4.57–9.81. These genes were unevenly distributed across 20 chromosomes, with Chr17 harboring the highest number, while no CmIAA genes were detected on Chr3. Phylogenetic analysis classified the genes into nine subgroups (Groups Ⅰ–Ⅸ), with Groups Ⅰ, Ⅵ, and Ⅸ exhibiting relative expansion. Gene structure and conserved motif analyses revealed subgroup-specific motif compositions, with motif 1 representing the core conserved domain. Intraspecific collinearity analysis identified 54 segmentally duplicated gene pairs but no tandem duplication events, whereas interspecific synteny revealed extensive orthologous relationships between pumpkin and Cucurbita pepo and Cucurbita maxima . Promoter analysis showed that CmIAA genes contain multiple cis-elements associated with hormone responses and abiotic stress responses, including ABRE, MBS, and DRE. Tissue expression analysis demonstrated that many CmIAA genes exhibited tissue-preferential expression patterns. Under abiotic stress conditions, CmIAA 69 showed a salt-specific expression pattern, whereas CmIAA 39 and CmIAA 58 responded to both salt and drought treatments, indicating that these CmIAA genes play distinct roles in pumpkin responses to different abiotic stresses. This study systematically characterized the Aux/IAA gene family in pumpkin, highlighting its evolutionary diversity, structural conservation, and distinct regulatory features. These findings provide valuable genetic resources for further functional studies and inform the potential roles of CmIAA genes in abiotic stress responses.

Genome-wide identification and systematic characterization of MATH family genes and expression analysis of response to abiotic stresses in Brassica napus L

Meprin and TRAF-C homology (MATH) proteins function as adaptor molecules and components of E3 ubiquitin ligase complexes. They link receptor-like kinase signalling to downstream regulatory pathways in plants. MATH proteins coordinate growth, hormone signalling, and responses to abiotic stress by modulating ubiquitin-dependent proteostasis. Despite their importance, however, little is known about the diversity, function, and specific regulatory role of the MATH gene family in Brassica napus . We identified 151 BnMATH family genes distributed across the 19 chromosomes of B. napus using a hidden Markov model-based genome-wide search followed by domain validation. Comparative phylogenetic and structural analyses classified these genes into four conserved clades, revealing that extensive segmental and tandem duplication events had driven the family expansion. Promoter analysis revealed more than 6,000 cis-acting regulatory elements associated with hormone- and stress-responsive gene expression. A total of 44 miRNA families targeting BnMATH genes were identified, among which 10 have been previously validated to be involved in biological processes. Transcriptome profiling combined with qRT-PCR validation revealed pronounced tissue-specific and abiotic-stress-responsive expression patterns. Notably, BnMATH06 , BnMATH92, and BnMATH135 were strongly induced by salt and drought stress, suggesting a potential role in stress adaptation. These findings deepen our understanding of the MATH gene family and provide a robust foundation for future functional genomics research targeting their specific biological roles, particularly in hormone-driven regulation and adaptation to abiotic stress.

Genome-Wide Identification of the Maize TALE Gene Family and Their Expression Analysis Under Low-Phosphorus Response in Maize (Zea mays L.)

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.

Genome-Wide Identification of the GmATG Gene Family and Its Response to Multiple Biotic and Abiotic Stresses in Soybean (Glycine max)

This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members.

Genome-Wide Identification, Evolutionary Analysis, and Expression Profiling of the NSUN Gene Family in Maize Reveal Candidate Genes for Stress Adaptation and Agronomic Improvement

The NSUN family is essential for RNA 5-methylcytosine modification (m5C) in eukar-yotes. However, no NSUN genes have been identified in maize, and the characteristics of ZmNSUN genes remain unexplored. Here, we performed a comprehensive in-vestigation of NSUN genes across seven Poaceae species. Our analysis identified a total of 63 Poaceae NSUN genes, including eight ZmNSUN genes in maize. Phylogenetic and feature analyses classified the Poaceae NSUNs into six subgroups (SGs), suggest-ing that the divergence of these SGs may have occurred prior to the divergence between plants and animals. Expression profiling indicated that ZmNSUN genes are generally repressed by heat stress. Co-expression network analysis suggested potential roles of ZmNSUN genes in maize development, and expression quantitative trait locus (eQTL) analysis results demonstrated that expression levels of multiple ZmNSUN genes are significantly associated with maize agronomic traits. Collectively, these findings provide novel insights into the evolutionary dynamics of the NSUN family and highlight specific ZmNSUN genes as promising candidates for molecular breeding to improve maize yield and stress adaptability.