Fig. 3
From: A syntelog-based pan-genome provides insights into rice domestication and de-domestication
Structural variations in rice de-domestication. a Dot plots comparing all 74 assemblies against the de-domestication genomic island (from 6.0 to 6.5 Mbp) on chromosome 7 of Nipponbare. The predominant translocations in wild and weedy accessions are highlighted by red boxes. The pink seed icons behind the accession IDs represent red or brown pericarp. b Phylogeny revealed by SNPs in the Rc region indicates introgression from Or-1 and Or-3 to XI and GJ, respectively. Labels with green, red, yellow, and blue represent accessions from Or-4, Or-3, Or-2, and Or-1, respectively. Blue dots represent weedy accessions. The numbers on each branch indicate bootstrap values of less than 90%, based on 1000 replicates. c Structural variations in OsC1 between the weedy and cultivated GJ accessions. Black rectangles represent exons. d Structural variations in Bh4 between weedy and cultivated accessions and their seed appearances