Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons.

Allotetraploid cotton () species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, [(AD), ] and [(AD), ], and one early form of domesticated , race [(AD), ]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid clade and resolved the evolutionary relationships of , , and domesticated . We describe genomic structural variation that arose during evolution and describe its correlates-including phenotypic differentiation, genetic isolation, and genetic convergence-that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.