Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics

TLDR

A ~70‑million‑year‑old polyploidization event predates cereal divergence and, through subsequent diploidization, has shaped Poaceae genomes, with comparative gene order analyses revealing structural rearrangements and suggesting further ancient duplications remain to be discovered. The study aims to map duplication event timings onto taxonomic relationships to better interpret comparative gene orders for crop improvement and biodiversity research. The authors identified homoeologous chromosomes from the ancient duplication that explain many incongruent loci between rice and sorghum, attributing these discrepancies to differential gene loss during diploidization. The prevalence of predicted homoeologs among duplicated sorghum loci confirms that the ancient polyploidization event was shared by sorghum and rice.

Abstract

Integration of structural genomic data from a largely assembled rice genome sequence, with phylogenetic analysis of sequence samples for many other taxa, suggests that a polyploidization event occurred ≈70 million years ago, before the divergence of the major cereals from one another but after the divergence of the Poales from the Liliales and Zingiberales. Ancient polyploidization and subsequent “diploidization” (loss) of many duplicated gene copies has thus shaped the genomes of all Poaceae cereal, forage, and biomass crops. The Poaceae appear to have evolved as separate lineages for ≈50 million years, or two-thirds of the time since the duplication event. Chromosomes that are predicted to be homoeologs resulting from this ancient duplication event account for a disproportionate share of incongruent loci found by comparison of the rice sequence to a detailed sorghum sequence-tagged site-based genetic map. Differential gene loss during diploidization may have contributed many of these incongruities. Such predicted homoeologs also account for a disproportionate share of duplicated sorghum loci, further supporting the hypothesis that the polyploidization event was common to sorghum and rice. Comparative gene orders along paleo-homoeologous chromosomal segments provide a means to make phylogenetic inferences about chromosome structural rearrangements that differentiate among the grasses. Superimposition of the timing of major duplication events on taxonomic relationships leads to improved understanding of comparative gene orders, enhancing the value of data from botanical models for crop improvement and for further exploration of genomic biodiversity. Additional ancient duplication events probably remain to be discovered in other angiosperm lineages.