Subgenome composition of allopolyploids and hybrids
Because allopolyploid genotypes were identified in both coarse-texturedP. vaginatum and in P. distichum , we examined levels of heterozygous SNP sharing between these groups to assess whether the additional subgenomes in polyploid P. vaginatum might be shared with P. distichum . Patterns of heterozygous locus sharing indicate that this is not the case. Whereas 28,881 heterozygous loci were unique to coarse-textured individuals and 33,585 heterozygous loci were unique to P. distichum , only 3713 loci were shared between species (Fig. S5). These patterns are consistent with PCA results (Fig. 3, Fig. S3) in indicating that P. distichum is no more closely related to coarse-textured P. vaginatum genotypes (regardless of ploidy) than to fine-textured genotypes. Thus, the triploid coarse-textured P. vaginatum genotypes appear to carry a distinct subgenome from P. distichum from an unknown source.
Heterozygous locus calls further indicated that in addition to ploidy variation, there were also subgenome composition differences within the coarse-textured P. vaginatum group. By counting the number of reference versus alternate reads at heterozygous loci, we could estimate the number of haploid subgenomes within a genotype that are fromP. vaginatum or some other source (see Methods). Accession DG076, a representative diploid coarse-textured genotype (coarse_03; Table S1), followed the expected pattern of a 1:1 ratio of reference to alternate reads (50% reference; Fig. 4A; Fig. S6A). Among the three triploid genotypes, one of them (coarse_01, represented by accession DG117) showed a 1:2 ratio (33.3% reference reads; Fig. 4B; Fig. S6B), while the other two (coarse_02 and coarse_04, represented by accessions DG 107 and DG120, respectively) showed 2:1 ratios (66.6% reference reads; Fig. 4 C-D; Fig. S6 C-D). This difference among triploid genotypes indicates that they do not have the same subgenome composition. More specifically, one genotype appears to carry one copy of the fine-textured P. vaginatum reference genome and two subgenome copies from an unknown source, whereas the other two genotypes appear to have the reverse pattern. Our use of the same set of heterozygous loci in all four of the tested coarse-textured genotypes allows us to infer that the same two subgenomes are present in all of them, but that the number of copies of each subgenome differs.