Molecular Mechanisms of Polyploid Plant Formation and Evolution Revealed by Systems Genomics Analysis

Polyploidization is a predominant process in the course of flowering plant speciation and evolution. It is estimated that approximately 70% of flowering plants are polyploids, including a number of crop species important in agriculture, environments, forestry and bioenergy. However, little is known about how a polyploid plant species is formed and evolves in the post-polyploidization at the genome level. Wheat and its related species are an excellent model system for study of the molecular mechanisms underlying the formation and evolution of polyploid species. Here, we report the molecular mechanisms of polyploid plant formation and evolution revealed by systems genomics analysis of a large number of naturally-occurring and artificially synthesized polyploid wheats. We first scrutinized the family sizes or copy numbers and their genetic variation and evolution of different fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retro-transposable elements (RTE), simple sequence repeats (SSR) and low complexity repeats (LCR). Then, we examined the relationships and interactions of the FFE in terms of FFE family sizes and sequences. Finally, we investigated the roles of the variation of the FFE family size and FFE family interaction in the genetic variation and evolution of host plants. Therefore, this study provides novel molecular mechanisms of the formation and evolution of polyploid plants.