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.