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). <br>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 &lt; 0.05; chi-squared test) the more gene rich copy of the region and the individual genes within it was assigned to the A subgenome and the less gene rich copy of the region and the individual genes within it was assigned to the B subgenome. <br><br>Methods for identifying and assigning syntenic genes across the other grass species included in this analysis followed the procedure outlined in:<br>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<br><br>