Fig. 2

Phasing and arrangement of the heterozygotic genome assembly. a Examples of haplotype-phased gene models. Gene models predicted from the initial “haplotype-fused” assembly are phased according to read mapping and SNP analysis using the Illumina short-read sequences of putative parental species. Genes were phased into one parental haplotype if a gene was aligned only by reads from one parental species (unique mapping) or had at least twofold as many supports for SNPs by reads of one parental species (phased by SNP). Genes with similar supports of read mapping for both parental species are defined as common type. Colored dots denote SNPs identified in the aligned reads. b Chromosomal arrangement of the gene-phased genome assembly of wild P. yedoensis (Pyn) onto the P. persica (Pp) genome. c Distribution of haplotype-phased genes in the tentative chromosomes of wild P. yedoensis. Colored dots or lines represent maternal-phased genes (red), paternal-phased genes (blue), or common genes (gray)