Genome coordinates used for G-Phocs analysisOryza sativa japonica reference genome coordinates used for the G-Phocs analysis. Coordinates are listed in BED format.NEUTRAL_LOCI.FINAL.BED4D site in phylip formatConcatenated four-fold degenerate sites for all species used in the study. Data is in phylip format and was used for estimating species phylogeny using Raxml for tree building. Names of species were shortened and corresponds to: NIV, O. nivara; PUN, O. punctata; RUF, O. rufipogon; SAA_DJ123, Oryza sativa aus cv. DJ123; SAA_KASALATH, Oryza sativa aus cv. Kasalath; SAI, Oryza sativa indica cv. 93-11; SAI_IR64, Oryza sativa indica cv. IR64; SAJ, Oryza sativa japonicaFourD_site.phylipO. sativa japonica gene and its orthologous sequences alignedOryza sativa japonica gene model and its orthologous sequences from O. sativa indica, O. sativa aus, O. rufipogon, O. nivara, O. barthii, and O. punctata in FASTA format. Each O. sativa japonica gene has a directory and within the directory there are 3 files: *.4D.fa, four-fold degenerate sites; *.CDS-3.fa, 3rd position sites of coding DNA sequence; *.CDS.fa, entire coding DNA sequence. Names of species were shortened and corresponds to: BAR, O. barthii; NIV, O. nivara; PUN, O. punctata; RUF, O. rufipogon; SAA_DJ123, Oryza sativa aus cv. DJ123; SAA_KASALATH, Oryza sativa aus cv. Kasalath; SAI, Oryza sativa indica cv. 93-11; SAI_IR64, Oryza sativa indica cv. IR64; SAJ, Oryza sativa japonicaGene_FASTA.tar.gzMulti-genome alignment in MAF formatGenome alignments for domesticated and wild rice genomes in MAF format. Oryza sativa japonica genome was used as reference and genomes of O. rufipogon, O. sativa indica cv. 93-11, O. sativa indica cv. IR64, O. sativa aus cv. DJ123, O. sativa aus cv. Kasalath, O. nivara, O. glaberrima, O. barthii, O. glumaepatula, O. longistaminata, O. meridionalis, O. punctata, and O. brachyantha were aligned using LASTZ and MULTIZ.MULTIZ_MAF.tar.gzOryza sativa japonica genome coordinates with significant phastcons scoreOryza sativa japonica genome coordinates that had phastcons score greater then 0.8 in BED format. Significant regions that were 10bps apart were merged into one and flanking 100bps were also considered.phastcons.gt0.8.bedRepeatmodeler identified repeat sequencesRepetitive DNA sequences identified by Repeatmodeler from the genomes of O. sativa japonica, O. sativa indica cv. 9311, O. rufipogon, O. nivara, O. glaberrima, O. barthii, O. glumaepatula, O. longistaminata, O. meridionalis, O. punctata, and O. brachyantharepeatclassified.tar.gz

The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ~13.1 – 24.1 kya, which is an order of magnitude older then the earliest archaeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ~18 kya and archaeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (~17%) and aus (~15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.