Genome-Wide Analysis Elucidates the Role of Genes in Stress Responses of Cotton.

The gene family has been well studied for its role in the regulation of plant flowering time. However, their role remains poorly understood in cotton. To better understand the possible roles of in cotton, we performed a comprehensive genome-wide analysis of genes in cotton. Phylogenetic tree analysis showed that genes naturally clustered into three groups. Segmental duplication and whole genome duplication (WGD), which occurred before polyploidy, were important contributors to its expansion within the At ("t" indicates tetraploid) and Dt subgenomes, particularly in Group III. Long-terminal repeat retroelements were identified as the main transposable elements accompanying 18 genes. The genotype of displayed low diversity; it was a candidate involved in domestication. Selection pressure analyses indicated that relaxed purifying selection might have provided the main impetus during the evolution of genes in upland cotton. In addition, the high expression in the torus and calycle indicated that genes might affect flowering. The genes from Group II, and those from Group III involved in segmental duplication or WGD, might play important roles in response to drought and salt stress. Overall, this comprehensive genome-wide study of the gene family would facilitate further detailed studies in cotton.