Polyploid Genome Assembly Service
In our initial experiments, we’ve found that low heterozygosity allotetraploids are better treated resolving to the level of subgenome rather than haplotype. Attempting to resolve low heterozygosity polyploids will likely result in low completeness of the haplotype-resolved assemblies. Higher heterozygosity allotetraploids contain sufficient variation to enable resolution at the haplotype level. The workflow is shown in Figure 1.
Figure 1. High-heterozygosity workflow.
An allotetraploid grass with estimated heterozygosity of 0.1% was assembled. High BUSCO completeness and contiguity were demonstrated (Table 1).
| Assembly | Pseudo-haploid | Subgenome1 | Subgenome2 |
|---|---|---|---|
| Assembly Size (Kb) | 1,690 | 1,116 | 662 |
| N50 (Mb) | 105.3 | 264.6 | 98.2 |
| L50 | 5 | 2 | 3 |
| N90 (Mb) | 71.9 | 102.3 | 74.4 |
| L90 | 13 | 7 | 7 |
| BUSCO Complete (C)% | 97.7% | 94.3% | 94.2% |
Table 1. An allotetraploid grass with low heterozygosity assembled.
An allotetraploid grass with estimated heterozygosity of 1% was assembled. High BUSCO completeness and contiguity were demonstrated (Table 2).
| Assembly | Pseudo-haploid | Sub1Hap1 | Sub1Hap2 | Sub2Hap1 | Sub2Hap2 |
|---|---|---|---|---|---|
| Assembly Size (Kb) | 3,978 | 2,694 | 2,651 | 2,675 | 2,055 |
| N50 (Mb) | 72.5 | 167.9 | 167.8 | 164.9 | 156.2 |
| L50 | 17 | 7 | 7 | 8 | 7 |
| N90 (Mb) | 18.4 | 135.4 | 153.1 | 26.4 | 97.1 |
| L90 | 57 | 14 | 14 | 16 | 13 |
| BUSCO Complete (C)% | 97.7% | 98.0% | 98.0% | 97.7% | 98.4% |
Table 2. An allotetraploid grass with high heterozygosity assembled.
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