Linked-read sequencing enables haplotype-resolved resequencing at population scale

Abstract

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences -including the quantification and dating of admixture, introgression and demographic events, and the inference of selective sweeps -are still limited by the lack of high-quality haplotype information. In this respect, the newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25x, 20x, 15x, 10x, 7x, and 5x) with high-coverage data (46-68x) of seven bird genomes suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15x coverage, phased haplotypes span about 90% of the genome assembly, with 50 and 90 percent of the phased sequence located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90), respectively. Phasing accuracy reaches beyond 99% starting from 15x coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1Mb (N50/N90) at 25x coverage), but only marginally improved phasing accuracy. Finally, phasing contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing data at population scale.

Genome Report:De novogenome assembly and annotation for the Taita white-eye (Zosterops silvanus)

“…Linked-read sequencing has a huge potential for generating decent draft bird genome assemblies (Toomey et al 2018, Boman et al 2019, Kinsella et al 2019, Lutgen et al 2020. 10X Genomics Chromium is the most commonly used linked-read library preparation at present, but other linked-read methods , Redin et al 2019 are equally promising but have yet to be tested on birds.…”

SpecHap: a diploid phasing algorithm based on spectral graph theory

“…In addition to the wet-lab based phasing (Redin et al ., 2019), computational approaches including population-based phasing, Mendel’s Law based phasing and SIH are also widely adopted (Majidian and Sedlazeck, 2020). (i) Although performed at a lower coverage, the population based phasing requires a haplotype population structure model and can only phase common variations (Lutgen et al ., 2020). Genomes of multiple non-human individuals in one population under natural condition are often difficult to obtain.…”

The population genomics of invasive species

“…Though linked-read sequencing approaches show great promise in population genomics (e.g ., Lutgen et al, 2020), many platforms are currently prohibitively expensive. One notable exception is haplotagging, a recent low-cost linked-read sequencing method (Meier et al, 2020).…”