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Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
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Number of Authors: 52018 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 4, p. 1327-1333Article in journal (Refereed) Published
Abstract [en]

Rapid 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 5.7x10(-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.

Place, publisher, year, edition, pages
2018. Vol. 8, no 4, p. 1327-1333
Keywords [en]
single-molecule real-time sequencing, bacterial artificial chromosomes, sequencing errors, assembly, self-incompatibility locus, Capsella, Brassicaceae
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-156060DOI: 10.1534/g3.117.300467ISI: 000428693600022PubMedID: 29476024OAI: oai:DiVA.org:su-156060DiVA, id: diva2:1209778
Available from: 2018-05-24 Created: 2018-05-24 Last updated: 2018-05-24Bibliographically approved

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Bachmann, Jörg A.Tedder, AndrewLaenen, BenjaminSteige, Kim A.Slotte, Tanja
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