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

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 inference of selective sweeps – are still limited
by the lack of high-quality haplotype information. 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 mapped to a
reference 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 phased sequences located in
phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). 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. Phase block
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 at population scale.