Fig. 6: Homoeologous gene retention in Oryza and subgenome equivalence in O. coarctata.
a, Distribution of gene retention (percentage, y axis) in the subgenomes of the tetraploid species (x axis). Each genome type is colored as in Figs. 3a and 4b. The red dashed line indicates the average percentage of gene retention calculated genome-wide for each species. P values from two-sided Wilcoxon rank-sum tests and numbers of sliding windows (n) are shown. b, Transcript abundance of homoeologous genes in O. coarctata and their homologs in O. sativa. Gene expression as log2 (TPM + 1) was measured in the leaf and in the root considering the replicates together. P values from two-sided Wilcoxon rank-sum tests are shown. In a and b, the 50th percentiles are defined by middle lines; lower and upper hinges correspond to the 25th and 75th percentiles. The upper whisker extends from the hinge to the largest value at most 1.5 times the interquartile range from the hinge. The lower whisker extends from the hinge to the smallest value at most 1.5 times the interquartile range of the hinge. Data beyond the end of the whiskers were considered to be outliers and plotted as individual points. c, Homoeologous gene pair expression bias (B) in the leaf (left) and the root (right) of O. coarctata. Blue and orange bars represent the expression of homoeologs biased toward KK (B < −1) and LL (B > 1) subgenomes, respectively. Homoeolog pairs with −1 ≤ B ≤ 1 (gray bars) are defined as nondominantly expressed. N represents the number of homoeologous gene pairs in the three categories (NKK, homoeologous gene dominantly expressed in KK subgenome; NLL, homoeologous gene dominantly expressed in LL subgenome; Nnonbiased, homoeologous gene not dominantly expressed). BKK, BLL and Bnonbiased represent average expression bias for the homoeologous pairs in the respective categories. nf, nonfractionated (homoeologous gene pairs); f, fractionated genes; Os-ph, O. sativa genes homologous to nonfractionated O. coarctata genes (paired homologous); Os-sch, O. sativa genes homologous to fractionated O. coarctata genes (single-copy homologous).
