Genome-wide identification and characterization of the kinesin gene family in upland cotton (Gossypium hirsutum L.)

Kinesin (KIN) genes play vital functions in plant development and the stress response. However, no comprehensive analysis of this gene family has been reported for cotton. In the present study, we performed a genome-wide investigation and comprehensive analysis of KIN genes in Gossypium hirsutum. A total of 172 putative GhKIN genes were identified in the cotton genome, classified into eight subfamilies (KIN1-KIN8) according to a phylogenetic tree. The GhKINs showed an uneven distribution on chromosomes. Gene duplication analysis indicated that segmental duplication was the only driving force for the expansion of the GhKIN gene family. Segmental duplication gene pairs all have undergone purification selection in the process of evolution. Different subfamily genes had differences in gene structure and motif composition, but the same subfamily showed some similarity. The promoter regions of GhKIN genes contained abundant stress- and hormone-related cis-elements. Based on the published RNA-seq data, 56 common potential candidate genes among these 172 GhKINs were used to identify the spatiotemporal expression patterns in different tissues and abiotic stress response patterns under different treatments (drought, salt, heat and cold). Real-time fluorescence quantitative PCR (RTqPCR) analysis further revealed the expression patterns of 15 GhKINs under drought and salt stress. GhKIN14 and 27 were downregulated under both stress conditions, while GhKIN18, 65, 101, 106, and 137 were upregulated at certain time points. Weighted gene coexpression network analysis (WGCNA) showed that five GhKIN genes, GhKIN13, GhKIN14, GhKIN27, GhKIN140 and GhKIN152, may be important genes regulating the salt stress response. Our study comprehensively analyzes the GhKIN genes in Gossypium hirsutum, providing a new perspective on the functional roles of GhKINs in cotton development and stress adaptation.