Genome-Wide Identification of the TaBSK Gene Family and Its Salt-Responsive Expression Patterns in Wheat

Genome-wide identification of the RLCK gene family in sugarcane and functional analysis of ScRLCK53 in salt tolerance.

First comprehensive characterization of the RLCK gene family in sugarcane is presented, elucidating its evolutionary features, expression dynamics and functional roles, and providing compelling evidence that ScRLCK53 modulates salt tolerance through activation of the JA signaling pathway.

Genomic Identification and Comprehensive Characterization of the CAMTA Transcription Factor Family in Brassica rapa L.

Calmodulin‐binding transcription activators (CAMTAs) are a key family of transcription factors that regulate gene expression involved in plant development and mediate plant responses to a wide range of biotic and abiotic stresses. Although CAMTA genes have been surveyed in several crop species, their comprehensive characterization in Brassica rapa remains limited. In this study, we performed a genome‐wide analysis and identified 12 BrCAMTA genes, dispersed across 10 chromosomes of the B. rapa genome. Phylogenetic analysis of 84 CAMTA proteins from seven plant species grouped them into four major clades, with BrCAMTAs exhibiting conserved exon–intron structures and motif compositions within their respective phylogenetic groups. Domain analysis revealed that the major CG‐1 domain is conserved across all the genes. Protein–protein interaction analysis indicated that the predicted interacting proteins contain diverse domains and exhibit a variety of functions. Promoter analysis revealed a wide array of cis‐regulatory elements linked to hormone signaling, stress responses, and developmental regulation. RNA‐seq–based expression profiling revealed tissue‐specific expression patterns, with BrCAMTA genes showing high expression in roots, stems, and callus tissues. Notably, BrCAMTA6, BrCAMTA8, and BrCAMTA11 exhibited significantly higher expression across all examined tissues. Collectively, these findings highlight the structural conservation and functional diversity of CAMTA genes in B. rapa and provide a valuable framework for future validation studies that are aimed at understanding their roles in growth, development, and environmental adaptation.

Genome-Wide Identification and Stress Response Analysis of the GATA Gene Family in Eggplant (Solanum melongena L.)

This study elucidates the evolutionary conservation and functional diversity of the eggplant GATA family, providing valuable candidate genes for future functional research and stress-tolerant molecular breeding in eggplant.

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 and evolution of the RCP gene family in soybean uncovers stress-responsive candidates

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.