Fig. 3: The syntenic pangenome.
a, Phylogenomic profiling of clusters of syntenic genes across 30 Oryza (sub)genomes (the nine tetraploid and two diploid species presented here and ten additional diploid species listed in Supplementary Table 8) and outgroup species L. perrieri. In the heat map, each row represents a (sub)genome, and each column shows a syntenic cluster (that is, a grouping of syntenic homologous genes across two or more Oryza species and/or between Oryza and L. perrieri). The minimum number of genes in a cluster is two homologous genes in two different species or genera. Clustering of the Oryza (sub)genomes was based on presence and absence patterns of syntenic clusters using Euclidean distance and is shown as a dendrogram on top of the figure. For each syntenic cluster, gene copy-number variation is represented as follows: gene absence, light gray; one gene copy, blue; two gene copies, yellow; three or more gene copies, red. On the left side, vertical bars represent the genome type of the (sub)genomes: AA, dark blue; BB, red; CC, dark green; DD, purple; EE, black; KK, sky blue; LL, orange; HH, light green; JJ, lilac; FF, light gray; GG, light blue; O (outgroup), peach. b, Histogram showing the frequency distribution of syntenic clusters in the 30 (sub)genomes shown in a and shared by increasing numbers of Oryza (sub)genomes (x axis). The legend shows the percentage of core (found in all 30 subgenomes), softcore (found in 27–29 subgenomes), dispensable (found in 2–26 subgenomes) and private syntenic clusters. c, Percentages of genes classified in the different syntenic cluster categories (core (blue), softcore (green) and dispensable (yellow)) in the 30 Oryza (sub)genomes. Percentages of genes classified in private syntenic clusters are not shown.
