Molecular Mechanisms of Genome Variation and Evolution of Cotton and Related Species Revealed by Systems Genomics Analysis

Recent advent of high-throughput sequencing technologies has led to a large number of genomes sequenced. However, it remains unclear how the genome of an organism, as an organismic entity, varies and evolves. Cotton and its related species are not only the world’s leading textile fiber and bioenergy oil crops and germplasm, but also a model system for studies of plant genome variation and evolution, and polyploidization. Here, we comprehensively investigated the genomes of cotton and a large number of its related species (Gossypium species) using a systems genomics approach to address the molecular mechanisms of the genome variation and evolution of plants, especially those of polyploid plants. We first reconstructed the phylogenetic tree of the Gossypium species and deciphered the genome origin of the polyploid cottons using a genome-wide approach. Then, we studied the family size or copy number genetic variation and evolution of the fundamental function elements (FFE) constituting the cotton genomes, including genes (GEN), DNA transposable elements (DTE), retro-transposable elements (RTE), simple sequence repeats (SSR) and low complexity repeats (LCR). Third, we examined the relationships and interactions of the FFE in terms of FFE family size variation and evolution. Finally, we investigated the roles of the variation of the FFE family size and FFE families’ interaction in host plant genetic variation and evolution, with an emphasis on those of poplyploid cottons. Therefore, this study provides novel molecular mechanisms of the genome variation and evolution not only for Gossypium species, but also for polyploid cottons.