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.

Polyploid assembly is dependent on the level of heterozygosity in the genome. Genomes with lower heterozygosity (for example, <1%) perform best with our low-heterozygosity (LH) workflow, resolving to the sub-genome (but not haplotype) level (Figure 1).

Figure 1. Low-heterozygosity (LH) workflow.

Genomes with higher heterozygosity can be resolved to the haplotype-level using our high-heterozygosity (HH) workflow (Figure 2).

Figure 2. High-heterozygosity (HH) workflow.

An allotetraploid grass with estimated heterozygosity of 0.1% was assembled using the LH workflow. 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 using the LH workflow.

An allotetraploid grass with estimated heterozygosity of 1% was assembled using the HH workflow. 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 using the HH workflow.

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