title: Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences.
abstract: Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld, 4072, Australia.
authors.forename: Peterson W
authors.initials: PW
authors.lastname: Wambugu
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld, 4072, Australia.
authors.forename: Marta
authors.initials: M
authors.lastname: Brozynska
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld, 4072, Australia.
authors.forename: Agnelo
authors.initials: A
authors.lastname: Furtado
authors.affiliation: Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Waters
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld, 4072, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Henry
mesh_terms: D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D023061:Gene Order; D054628:Genome, Chloroplast; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny