Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Plant Biotechnol J. 2017 Jun;15(6):765-774. doi: 10.1111/pbi.12674. Epub 2017 Jan 23.

Abstract

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

Keywords: Oryza; assembly; molecular clock; phylogeny; sequencing; wild rice.

MeSH terms

  • Evolution, Molecular
  • Genome, Chloroplast / genetics
  • Genome, Plant / genetics*
  • High-Throughput Nucleotide Sequencing
  • Oryza / genetics*
  • Phylogeny
  • Plant Proteins / genetics*
  • Sequence Analysis, DNA

Substances

  • Plant Proteins

Associated data

  • GENBANK/GCA_000338895.2