Functional structure analysis and genome-wide identification of CNX gene family in cotton

Abstract Background Under abiotic stress conditions, cotton growth is inhibited and yield losses are severe. Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screening of stress-related candidate genes. Results A total of 60 CNX family members have been identified in Gossypium hirsutum , G. barbadense , G. arboreum , and G. raimondii , and they were divided into two categories: CNX and CRT genes. Through the construction of a phylogenetic tree, they were subdivided into three classes. Further analysis of chromosome localization, conserved promoters, gene structure and selection under pressure showed that the family members were highly conserved in the evolution process. Analysis of cis -acting elements in the promoter regions showed that CNX family genes contain regulatory elements for growth and development, anaerobic, drought, defense and stress response, and plant hormones. Using RNA-seq data to study the expression pattern of GhCNX genes under cold, hot, salt stress and Polyethylene glycol, it was observed that the gene expression levels changed by different degrees under different stress conditions, indicating that GhCNX members were involved in the regulation of multiple biological stresses. Conclusion This study provides an insight into the members of cotton CNX genes. The results of this study suggested that CNX family members play a role in defense against adversity and provide a foundation for the discovery of stress-related genes.