Genome-Wide Identification and Expression Analysis Unveil the Involvement of the Cold Shock Protein (CSP) Gene Family in Cotton Hypothermia Stress.

Cold shock proteins (CSPs) are DNA/RNA binding proteins with crucial regulatory roles in plant growth, development, and stress responses. In this study, we employed bioinformatics tools to identify and analyze the physicochemical properties, conserved domains, gene structure, phylogenetic relationships, cis-acting elements, subcellular localization, and expression patterns of the cotton gene family. A total of 62 CSP proteins were identified across four cotton varieties (, , , ) and five plant varieties (, , , , and ). Phylogenetic analysis categorized cotton CSP proteins into three evolutionary branches, revealing similar gene structures and motif distributions within each branch. Analysis of gene structural domains highlighted the conserved CSD and CCHC domains across all cotton families. Subcellular localization predictions indicated predominant nuclear localization for . Examination of cis-elements in gene promoters revealed a variety of elements responsive to growth, development, light response, hormones, and abiotic stresses, suggesting the potential regulation of the cotton family by different hormones and their involvement in diverse stress responses. RT-qPCR results suggested that , , , and may play roles in cotton's response to low-temperature stress. In conclusion, our findings underscore the significant role of the gene family in cotton's response to low-temperature stress, providing a foundational basis for further investigations into the functional aspects and molecular mechanisms of cotton's response to low temperatures.