Seventy Million Years of Concerted Evolution of a Homoeologous Chromosome Pair, in Parallel in Major Poaceae Lineages

Whole genome duplication ~70 million years ago provided raw material for Poaceae diversification. Comparison of rice, sorghum, maize, and Brachypodium genomes revealed that one paleo-duplicated chromosome pair has experienced very different evolution than all others, with illegitimate recombination producing chromosome structural stratification 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. 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.