Genome-wide characterization of the tomato SlMGR gene family and the biological function of SlMGR10 in bacteria and Arabidopsis.

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 IiSPL gene family and IiSPL9 functional exploration

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.

Genomic characterization, expression and functional analysis of the plant homeodomain (PHD) family in tomato (Solanum lycopersicum L.) under abiotic stresses

Together, these findings provide a foundation for functional characterization and useful information for future research on the role of SlPHD family members in plant abiotic stress tolerance.

Characterization, evolution, and expression profiling of cotton DUF677 protein family and their potential role in drought and salt stress response

The membrane-bound proteins belonging to DUF677 (domain of unknown function 677) are found mainly in green plants. The function of the DUF677 gene (AT14A) has been investigated in Arabidopsis and tomato in relation to drought stress tolerance. Overexpression of AT14A improves drought tolerance in tomato, promotes growth in Arabidopsis during drought stress, and confers tolerance against oxidative damage caused by drought stress in suspension-cultured A. thaliana. However, the role of the DUF677 gene family has not yet been reported in cotton. We identified 148 DUF677 genes from 15 selected plant species using domain-based and homology-supported bioinformatics approaches and classified them into two major groups (I and II) based on phylogenetic analysis. Group I is further divided into two sub-groups (IA and IB). Structural analysis revealed the presence of a few introns in the DUF677 genes. The evolution and expansion of the DUF677 protein family were primarily driven by segmental duplication. Seventy-one miRNAs were predicted to target 29 GhDUF677 genes, including Ghi-MIR397, Ghi-MIR8722, and Ghi-MIRN1429. Several cis-elements, such as MBS, ABRE, TCA elements, and W-Box, which were known to play a role in abiotic stress response, were observed in the promoter region of GhDUF677 genes. RNA-seq data were analyzed for tissue-specific expression, and qRT‒PCR was performed on six selected genes. The outcomes revealed high levels of GhDUF677 gene expression across different tissues under abiotic stress conditions. This study provides a genome-wide bioinformatics and expression-based characterization of the DUF677 gene family in cotton, identifying candidate genes potentially associated with drought and salt stress responses. While the findings are based on evolutionary, regulatory, and transcriptomic evidence, they do not constitute direct functional validation. Instead, this study establishes a theoretical and genomic foundation for future functional studies aimed at elucidating the precise roles of DUF677 genes in cotton stress tolerance.

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.