Fig. 1
From: A syntelog-based pan-genome provides insights into rice domestication and de-domestication
A syntelog-based pangenome of rice. a Consensus quality values and number of homozygous SNPs based on self-mapping for genomes in four pan-genome projects. b Phylogeny of rice genomes used in this study and their pairwise synteny kinship. c The relationship among rice genomes measured by genetic distance (IBD, identity-by-descent) based on SNPs and synteny based on gene orders. d Number of syntelog groups (SGs) represented in all 74 rice genomes versus the number of genomes. The subspecies pan-genome compositions for GJ and XI were extracted from the whole rice pan-genome. The numbers of core (present in the genomes of all accessions), soft-core (present in the genomes of > 90% accessions), dispensable (present in the genomes of less than 90% of all but at least two accessions), private (only present in a single genome), and absent SGs (identified by using all populations but absent in sub-population) were counted