title: Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.
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.
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia.
authors.forename: Marta
authors.initials: M
authors.lastname: Brozynska
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.|International Rice Research Institute, T.T. Chang Genetic Resources Center, Los Baños, Laguna, Philippines.
authors.forename: Dario
authors.initials: D
authors.lastname: Copetti
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia.
authors.forename: Agnelo
authors.initials: A
authors.lastname: Furtado
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.|International Rice Research Institute, T.T. Chang Genetic Resources Center, Los Baños, Laguna, Philippines.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia.
authors.forename: Darren
authors.initials: D
authors.lastname: Crayn
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Toowoomba, QLD, Australia.
authors.forename: Glen
authors.initials: G
authors.lastname: Fox
authors.affiliation: Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
authors.forename: Ryuji
authors.initials: R
authors.lastname: Ishikawa
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Henry
mesh_terms: D019143:Evolution, Molecular; D054628:Genome, Chloroplast / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins
keywords: 
  Oryza
  ; assembly; molecular clock; phylogeny; sequencing; wild rice