Fig. 2

Syntelog-based ancestral haplotypes suggest widespread genomic introgression in rice evolution. a Ancestral haplotype landscape of SGs on chromosome 4. An SNP-based phylogeny of rice groups is illustrated on the left. For each SG, seven blocks with different colors represent different haplotypes of predicted protein sequences. Candidate introgression regions are numbered by genomic length and marked by gray blocks. The centromere position information of chromosome 4 is obtained from the Rice Genome Annotation Project and indicated by a red triangle. Functionally important genes are annotated within each block, and domestication genes are highlighted in red. b Haplotype divergence between XI and GJ for all SGs on chromosome 4. c Significance test on the non-random distribution of clustered SGs in introgression blocks by sampling 100,000 replicates. The horizontal red dashed line represents a P value of 0.01. d Phylogeny analysis of four large introgression blocks (length greater than 300 Kbp) indicates a single origin of domestication alleles from the Or-3 wild group. Four wild groups are highlighted in different colors. e Introgression blocks from proto-GJ to XI based on the evidence of haplotype similarity, phylogeny and ABBA-BABA tests. f Complex genomic contributions from wild groups to the emergence of aus group revealed by the phylogenetic trees in 64 introgression blocks