Comparative Analysis of Genomic Structural Variants in the Cotton Genus

Approximately 1-2 million years ago, the A-genome and the D-genome of cotton hybridized to form a novel allopolyploid, the putative progenitor of today’s cotton fiber producing species. Genomic divergence in the Gossypium genus has given rise to many species-specific chromosomal structural rearrangements. To date, most differences between cotton species have been sequenced-based. We use variations in chromosome structure, including inversions, translocations, insertions and deletions to quantify the genetic distances between cotton genomes. Few comparisons could be made between the A- and D- genome because of the massive transposable element expansion during their divergence from a common ancestor. Variations in the At and Dt-genomes of G. hirsutum and G. barbadense were compared to their respective diploid relatives. We placed the structural variations on the accepted phylogeny of the cotton genus. This provided insights into the evolutionary history of cotton and an example to investigations of other plant genera. Further examination of these results will improve our understanding of polyploidization, hybridization, and genome evolution.