Fig. 7: Retention and losses of ancestral genes from rho.

a Illustration of an interspecific collinear block among grasses used for inferring ancestral genes. Numbers in squares represent different genes; the same number among species indicates the same orthogroup. Pink and green squares indicate the retention in pairs and in single-copy, respectively. Orange squares indicate the inferred ancestral genes before rho. The orthogroup with thick lines indicates duplicates phylogenetically mapped at Poaceae (see details in Supplementary Fig. 49). b Number of ancestral genes from rho in pair and in single-copy among grasses. The cladogram depicts subfamilial relationships of grasses simplified from the tree in Supplementary Fig. 48. Pink numbers, the number of ancestral gene pairs retained as two copies; blue numbers, the number of ancestral gene pairs retained as single copy; and green numbers, the number of single-copy ancestral gene retained. c Bar plots showing the number of the rho-derived orthogroups with four different retention/loss patterns. Type-I represents the single-copy orthogroups with further lineage-specific duplications in at least one subfamily. Type-II represents the single-copy orthogroups with no more than one gene being retained in each species. Type-III represents the orthogroups with two copies being retained in each subfamily. Type-IV represents the orthogroups with two copies being retained in at least one subfamily and losses of detected copies in at least one subfamily. Sample gene trees of the types I through IV can be found in Supplementary Figs. 50–53. Numbers on the right of the bars represent the number of orthogroups. See Supplementary Data 5 for the retention number in each subfamily of these orthogroups. d Illustration of four schematic retention/loss patterns of the orthogroups in type-IV. Number on the branch represents the number of orthogroups (See Supplementary Data 5). Type-IV-1 represents a different number of retained subfamilies between the rho-derived paralogues. Type-IV-2 represents reciprocal losses of subfamilies between the rho-derived duplicates. Type-IV-3 represents losses of one detected copy in one subfamily. Type-IV-4 represents losses of the rho-derived paralogs in one or more subfamilies. Source data are provided in a Source Data file.