The Molecular Basis of Plant Polyploidization Revealed by Systems Genome Analysis of Wheat and Related Species

Polyploidization is a predominant process in flowering plant speciation and evolution. It is estimated that approximately 70% of flowering plants, including numerous agriculturally important crops such as wheat, cotton, potato and sugarcane, are polyploids. However, little is known about how a polyploid species forms and evolves at the molecular level. Recent advent of the new molecular basis of biology: the DNA “Jigsaw Puzzle” Structure Model (Wu et al 2006, Genomics 88:394-406) and next-generation high-throughput sequencing technologies has shed light on systems analysis of plant polyploidization at the molecular level. Here we report the molecular basis of plant polyploidization revealed by systems analysis of genome sequences and transcriptomes of 350 wheat lines with 2x (133), 4x (48) and 6x (168) ploidy levels, including 238 naturally-occurring lines and 112 synthetic hexaploid lines. We first scrutinized the variations of contents, family sizes or copy numbers and interactions 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), in the processes of polyploidizaiton and evolution. Then, we examined the contribution of each parental line to the resultant polyploid at the genome level and the variations of expression and regulatory networks of different genes. Finally, we investigated the variation and evolution of the polyploid genomes from newly-born to naturally established polyploid species. This study, therefore, provides a novel molecular basis of plant polyploidization, thus having significantly advanced our understanding of polyploid plant speciation, variation and evolution.