Table 2.
Comparisons of homologous chromosomes of H. tuberosus.
| Length (Mb) | Gene number | Single-copy genes | Genes used for phylogenya | Phylogenetic tree topologyb | Intra-A1/A2/B identityc |
Inter-A1/A2/B identityd | |
|---|---|---|---|---|---|---|---|
| Chr01 | 173–212 | 3212–3716 | 607 | 227 | ([H1,H2],[H3,H4],[H5,H6]) | 97.16% | 97.04% |
| Chr02 | 130–200 | 2374–3198 | 542 | 542 | ([H1,H2], [H3,H4], [H5,H6]) | 97.24% | 96.99% |
| Chr03 | 206–230 | 3663–4109 | 864 | 864 | ([H1,H2], [H3,H4], [H5,H6]) | 97.19% | 96.98% |
| Chr04 | 166–255 | 2615–4539 | 383 | 383 | ([H1,H2], [H3,H4], [H5,H6]) | 98.67% | 97.16% |
| Chr05 | 144–193 | 2628–3140 | 548 | 240 | ([H1,H2], [H3,H4], [H5,H6]) | 97.69% | 97.32% |
| Chr06 | 159–209 | 3230–3917 | 691 | 691 | ([H1,H2], [H3,H4], [H5,H6]) | 98.00% | 97.14% |
| Chr07 | 155–173 | 2309–2795 | 509 | 509 | ([H1,H2], [H3,H4], [H5,H6]) | 98.02% | 97.81% |
| Chr08 | 193–229 | 3290–3858 | 735 | 735 | ([H1,H2], [H3,H4], [H5,H6]) | 97.81% | 97.42% |
| Chr09 | 193–226 | 3531–4336 | 748 | 748 | ([H1,H2], [H3,H4], [H5,H6]) | 97.90% | 97.41% |
| Chr10 | 198–228 | 3443–3997 | 760 | 760 | ([H1,H2], [H3,H4], [H5,H6]) | 97.46% | 97.24% |
| Chr11 | 188–223 | 3286–3942 | 678 | 678 | ([H1,H2], [H3,H4], [H5,H6]) | 97.43% | 97.22% |
| Chr12 | 148–201 | 2599–3657 | 495 | 495 | ([H1,H2], [H3,H4], [H5,H6]) | 98.88% | 97.67% |
| Chr13 | 190–227 | 3156–3989 | 421 | 421 | ([H1,H2], [H3,H4], [H5,H6]) | 97.52% | 97.09% |
| Chr14 | 184–205 | 3702–4104 | 867 | 867 | ([H1,H2], [H3,H4], [H5,H6]) | 97.84% | 97.31% |
| Chr15 | 99–166 | 1998–3079 | 438 | 165 | ([H1,H2], [H3,H4], [H5,H6]) | 97.55% | 97.13% |
| Chr16 | 205–246 | 3419–4461 | 716 | 716 | ([H1,H2], [H3,H4], [H5,H6]) | 97.60% | 97.26% |
| Chr17 | 199–235 | 3454–4215 | 620 | 620 | ([H1,H2], [H3,H4], [H5,H6]) | 97.56% | 97.42% |
a
Number of single-copy genes used to infer the phylogenetic tree of six homologous chromosomes in each group. For chr01, chr05, and chr15, only single-copy genes with alignment identity of 92%–100% were used.
b
A phylogenetic tree was constructed from the CMSA of single-copy genes (gap regions were trimmed out).
c
Average alignment identity of single-copy genes between two homologous chromosomes of the same subgenome: A1 (H1 and H2), A2 (H3 and H4), or B (H5 and H6).
d
Average alignment identity of single-copy genes between two homologous chromosomes of different subgenomes: A1 and A2, A1 and B, or A2 and B.