Comprehensive Identification and Expression Analysis of CRY Gene Family in Gossypium

Background: The cryptochromes (CRY) comprise a specific blue light receptor for plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance. Results: : In the present work, a systematical analysis of CRY gene family from five allotetraploid cotton species, G. hirsutum , G. barbadense , G. tomentosum , G. mustelinum and G. darwinii together with seven diploid species. There were 18, 17, 17, 17, and 17 CRYs identified in G. hirsutum , G. barbadense , G. tomentosum , G. mustelinum and G. darwinii , respectively, whereas five to nine CRY genes were identified in the diploid species. Phylogenetic analysis of the protein-coding sequences revealed that CRY genes from the allotetraploids G. hirsutum and G. barbadense , three diploid cotton species ( G. raimondii , G. herbaceum , and G. arboreum ), and Arabidopsis thaliana could be classified into seven clades. Synteny analysis suggested that the homoeolog of G. hirsutum Gh_A02G0384 has undergone an evolutionary loss event in the other four allotetraploid cotton species. Cis -element analysis predicated the possible functions of CRY genes in G. hirsutum . Public RNA-seq data were investigated to analyze the expression patterns of G. hirsutum CRY genes in various tissues as well as gene expressions under abiotic stress treatments. Conclusion: These results indicated the possible functions of G. hirsutum CRY genes in differential tissues as well as in response to abiotic stress during the cotton plants life cycle.