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Linked-read sequenc...
Linked-read sequencing enables haplotype-resolved resequencing at population scale
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- Lutgen, Dave (författare)
- Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany.
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- Ritter, Raphael (författare)
- Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany.
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- Olsen, Remi-André (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden.
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- Schielzeth, Holger (författare)
- Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany.
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- Gruselius, Joel (författare)
- Karolinska Inst, Dept Biosci & Nutr, Sci Life Lab, Stockholm, Sweden.
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- Ewels, Philip (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden.
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- Garcia, Jesus T. (författare)
- CSIC UCLM JCCM, Inst Invest Recursos Cineget IREC, Ciudad Real, Spain.
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- Shirihai, Hadoram (författare)
- Nat Hist Museum Bern, Bern, Switzerland.
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- Schweizer, Manuel (författare)
- Nat Hist Museum Bern, Bern, Switzerland.;Univ Bern, Inst Ecol & Evolut, Bern, Switzerland.
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- Suh, Alexander (författare)
- Uppsala universitet,Evolutionsbiologi,Science for Life Laboratory, SciLifeLab,Systematisk biologi,Uppsala Univ, Dept Organismal Biol Systemat Biol, Evolutionary Biol Ctr EBC, Uppsala, Sweden.;Univ East Anglia, Sch Biol Sci, Norwich, Norfolk, England.
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- Burri, Reto (författare)
- Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany.
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Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany Institutionen för biokemi och biofysik (creator_code:org_t)
- 2020-06-29
- 2020
- Engelska.
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Ingår i: Molecular Ecology Resources. - : WILEY. - 1755-098X .- 1755-0998. ; 20:5, s. 1311-1322
- Relaterad länk:
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https://doi.org/10.1...
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https://onlinelibrar...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Nyckelord
- admixture
- demography
- introgression
- phasing
- population genomics
- selective sweeps
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Lutgen, Dave
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Ritter, Raphael
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Olsen, Remi-Andr ...
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Schielzeth, Holg ...
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Gruselius, Joel
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Ewels, Philip
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visa fler...
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Garcia, Jesus T.
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Shirihai, Hadora ...
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Schweizer, Manue ...
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Suh, Alexander
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Burri, Reto
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visa färre...
- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Evolutionsbiolog ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Genetik
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Bioinformatik oc ...
- Artiklar i publikationen
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Molecular Ecolog ...
- Av lärosätet
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Uppsala universitet
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Stockholms universitet
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Karolinska Institutet