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Linked-read sequencing enables haplotype-resolved resequencing at population scale
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
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Number of Authors: 112020 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 20, no 5, p. 1311-1322Article in journal (Refereed) Published
Abstract [en]

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 genusOenantheacross 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% 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/1 Mb [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.

Place, publisher, year, edition, pages
2020. Vol. 20, no 5, p. 1311-1322
Keywords [en]
admixture, demography, introgression, phasing, population genomics, selective sweeps
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-184569DOI: 10.1111/1755-0998.13192ISI: 000552422600001PubMedID: 32419391OAI: oai:DiVA.org:su-184569DiVA, id: diva2:1464821
Available from: 2020-09-08 Created: 2020-09-08 Last updated: 2022-02-25Bibliographically approved

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Lutgen, DaveOlsen, Remi-AndréSchielzeth, HolgerEwels, Philip

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