Data from: The rice paradox: multiple origins but single domestication in Asian rice

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

### 用于G-Phocs分析的基因组坐标
本研究用于G-Phocs分析的粳稻（Oryza sativa japonica）参考基因组坐标以BED格式存储，对应文件为`NEUTRAL_LOCI.FINAL.BED`。

### 四折叠简并位点文件（PHYLIP格式）
本研究涉及的所有物种的串联四折叠简并位点序列，以PHYLIP格式存储，用于通过RAxML构建物种系统发育树。物种名称缩写对应关系如下：NIV代表尼瓦拉野生稻（O. nivara）；PUN代表斑点野生稻（O. punctata）；RUF代表普通野生稻（O. rufipogon）；SAA_DJ123代表水稻aus亚种品种DJ123（Oryza sativa aus cv. DJ123）；SAA_KASALATH代表水稻aus亚种品种Kasalath（Oryza sativa aus cv. Kasalath）；SAI代表水稻籼亚种品种93-11（Oryza sativa indica cv. 93-11）；SAI_IR64代表水稻籼亚种品种IR64（Oryza sativa indica cv. IR64）；SAJ代表粳稻（Oryza sativa japonica）。对应文件为`FourD_site.phylip`。

### 粳稻基因及其同源序列比对文件（FASTA格式）
本数据集包含粳稻基因模型及其来自以下物种的同源序列比对结果，以FASTA格式存储：水稻籼亚种、水稻aus亚种、普通野生稻、尼瓦拉野生稻、巴蒂野生稻及斑点野生稻。每个粳稻基因对应一个独立目录，目录内包含3个文件：`*.4D.fa`为四折叠简并位点序列；`*.CDS-3.fa`为编码DNA序列的第3位密码子位点序列；`*.CDS.fa`为完整编码DNA序列。物种名称缩写对应关系如下：BAR代表巴蒂野生稻（O. barthii）；NIV代表尼瓦拉野生稻（O. nivara）；PUN代表斑点野生稻（O. punctata）；RUF代表普通野生稻（O. rufipogon）；SAA_DJ123代表水稻aus亚种品种DJ123；SAA_KASALATH代表水稻aus亚种品种Kasalath；SAI代表水稻籼亚种品种93-11；SAI_IR64代表水稻籼亚种品种IR64；SAJ代表粳稻。对应压缩包为`Gene_FASTA.tar.gz`。

### 多基因组比对文件（MAF格式）
本数据集包含栽培稻与野生稻基因组的多序列比对结果，以MAF格式存储。以粳稻基因组作为参考序列，比对物种涵盖普通野生稻、水稻籼亚种93-11、水稻籼亚种IR64、水稻aus亚种DJ123、水稻aus亚种Kasalath、尼瓦拉野生稻、光稃野生稻（O. glaberrima）、巴蒂野生稻、glumaepatula野生稻（O. glumaepatula）、长雄蕊野生稻（O. longistaminata）、南方野生稻（O. meridionalis）、斑点野生稻及短花药野生稻（O. brachyantha）。所有比对均通过LASTZ与MULTIZ软件完成，对应压缩包为`MULTIZ_MAF.tar.gz`。

### 具有显著phastCons得分的粳稻基因组坐标
本数据集包含phastCons得分大于0.8的粳稻基因组坐标，以BED格式存储。将间距小于10bp的显著区域进行合并，并纳入侧翼100bp的序列区域，对应文件为`phastcons.gt0.8.bed`。

### RepeatModeler鉴定的重复序列
本数据集包含通过RepeatModeler从以下物种基因组中鉴定得到的重复DNA序列：粳稻、水稻籼亚种93-11、普通野生稻、尼瓦拉野生稻、光稃野生稻、巴蒂野生稻、glumaepatula野生稻、长雄蕊野生稻、南方野生稻、斑点野生稻及短花药野生稻，对应压缩包为`repeatclassified.tar.gz`。