Characterization, evolution, and expression profiling of cotton DUF677 protein family and their potential role in drought and salt stress response
TL;DR
A genome-wide bioinformatics and expression-based characterization of the DUF677 gene family in cotton is provided, identifying candidate genes potentially associated with drought and salt stress responses and establishing a theoretical and genomic foundation for future functional studies aimed at elucidating the precise roles of DUF677 genes in cotton stress tolerance.
Abstract
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.