Interrelated Evolution of Two Grass Chromosomes Through Illegitimate Recombination, Resulting in Homoeologous Chromosomal Stratification

Whole genome duplication ~70 million years ago (mya) provided raw material for grass diversification. Comparison of rice, sorghum, maize, and Brachypodium genomes revealed that one paleo-duplicated chromosome pair has experienced very different evolution than the others. The two chromosomes have experienced illegitimate recombination for tens of millions of years, which has been temporally restricted in a stepwise manner, producing chromosome structural stratification. These strata formed independently in different grass lineages, with their similarities (low Ks of paleo-duplicated genes) preserved in parallel for millions of years since divergence of these lineages. Both intriguing and perplexing is a distal chromosomal region with the greatest DNA similarity between surviving duplicated genes but the highest concentration of lineage-specific gene pairs found anywhere in these genomes and a significantly elevated gene evolutionary rate, providing a potential foundation for Bateson-Dobzhansky-Muller speciation. Intragenomic similarity near this chromosomal terminus may be important in hom(e)ologous chromosome pairing. Chromosome structural stratification, together with enrichment of autoimmune response-related (NBS-LRR) genes and accelerated DNA rearrangement and gene loss, confer striking resemblance of this grass chromosome pair to the sex chromosomes of other taxa.