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dc.contributor.authorBachmann, J.A.
dc.contributor.authorTedder, Andrew
dc.contributor.authorLaenen, B.
dc.contributor.authorSteige, K.A.
dc.contributor.authorSlotte, T.
dc.date.accessioned2019-09-13T09:42:40Z
dc.date.accessioned2019-10-01T15:16:31Z
dc.date.available2019-09-13T09:42:40Z
dc.date.available2019-10-01T15:16:31Z
dc.date.issued2018-04
dc.identifier.citationBachmann JA, Tedder A, Laenen B et al (2018) Targeted long-read sequencing of a locus under long-term balancing selection in Capsella. G3: Genes, Genomes, Genetics. 8(4): 1327-1333.en_US
dc.identifier.urihttp://hdl.handle.net/10454/17277
dc.descriptionYesen_US
dc.description.abstractRapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7×10−5. A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach.en_US
dc.description.sponsorshipThis study was supported by a grant from the Swedish Research Council to T.S.en_US
dc.language.isoenen_US
dc.relation.isreferencedbyhttps://doi.org/10.1534/g3.117.300467en_US
dc.rights© 2018 Bachmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/ by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.subjectSingle-molecule real-time sequencingen_US
dc.subjectBacterial artificial chromosomesen_US
dc.subjectSequencing errorsen_US
dc.subjectAssemblyen_US
dc.subjectSelf-incompatibility locusen_US
dc.subjectCapsellaen_US
dc.subjectBrassicaceaeen_US
dc.titleTargeted long-read sequencing of a locus under long-term balancing selection in Capsellaen_US
dc.status.refereedYesen_US
dc.date.Accepted2018-02-20
dc.date.application2018-02-20
dc.typeArticleen_US
dc.type.versionPublished versionen_US
dc.date.updated2019-09-13T08:42:41Z
refterms.dateFOA2019-10-01T15:17:10Z


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