Polyploid Genome Assembly Service

We launched our haplotype-resolved genome assembly service for diploid organisms in late 2021. Building on the great reception to our diploid service we are now pleased to offer a similar service for polyploids. Polyploids are the most challenging genomes to assemble. At Dovetail Genomics®, we use a unique combination of PacBio HiFi long reads and Dovetail® Omni-C® proximity ligation, plus a proprietary and bespoke bioinformatics workflow, to build high-quality polyploid genome assemblies from scratch.

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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If you would like to arrange a consultation to discuss a polyploid de novo assembly project or simply need more information, click the Learn More button below. We’d love to hear from you!