Homeologs from the pregrass duplication sorted by subgenome

A list of approximately 1,200 homeologous (ohnologous) pairs of genes conserved in rice and sorghum which were created in the most recent whole genome duplication prior to the diversification of the grasses, as well as syntenic orthologs of these genes in maize (RefGen v3 and RefGen v4), sorghum (v3), Setaria italica (v2.1 and v2.2), Setaria viridis (v1), Oropetium (v1) and Brachypodium distachyon (v2.1). Gene pairs are sorted into subgenomes A and B based on genomic blocks. Each pair of retained homeologous regions the number of syntenically conserved orthologous genes between rice and sorghum was determined. If the difference in the number of syntenic orthologous genes between the two duplicate regions was statistically significant (p Methods for identifying and assigning syntenic genes across the other grass species included in this analysis followed the procedure outlined in:Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. (2017) “Differentially regulated orthologs in sorghum and the subgenomes of maize.” The Plant Cell doi: 10.1105/tpc.17.00354 bioRxiv preprint doi: 10.1101/120303本数据集包含约1200对水稻与高粱中保守的同源拷贝基因对（homeologous/ohnologous gene pairs），这些基因产生于禾本科植物分化前的最近一次全基因组复制事件；同时还收录了这些基因在以下物种中的共线性直系同源基因（syntenic orthologs）：玉米（RefGen v3与RefGen v4）、高粱（v3）、谷子（Setaria italica，v2.1及v2.2）、青狗尾草（Setaria viridis，v1）、Oropetium（v1）以及二穗短柄草（Brachypodium distachyon，v2.1）。基因对基于基因组区块被划分为亚基因组A与亚基因组B。针对每一对保留的同源拷贝区域，研究人员统计了水稻与高粱间共线性保守直系同源基因的数量。若两个重复区域间的共线性直系同源基因数量差异具有统计学显著性（p<0.05，Wilcoxon秩和检验），则该区域对将被过滤移除。本分析中用于鉴定并分配其他禾本科物种共线性基因的方法，遵循以下文献所述流程：Zhang Y、Ngu DW、Carvalho D、Liang Z、Qiu Y、Roston RL、Schnable JC.（2017）《高粱与玉米亚基因组的差异调控直系同源基因》，《植物细胞》，DOI: 10.1105/tpc.17.00354；bioRxiv预印本，DOI: 10.1101/120303。