Universität zu Köln

Bachmann, Jorg A., Tedder, Andrew ORCID: 0000-0002-7378-4673, Laenen, Benjamin, Steige, Kim A. and Slotte, Tanja ORCID: 0000-0001-6020-5102 (2018). Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella. G3-Genes Genomes Genet., 8 (4). S. 1327 - 1334. BETHESDA: GENETICS SOCIETY AMERICA. ISSN 2160-1836

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Abstract

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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Bachmann, Jorg A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Tedder, Andrew UNSPECIFIED orcid.org/0000-0002-7378-4673 UNSPECIFIED Laenen, Benjamin UNSPECIFIED UNSPECIFIED UNSPECIFIED Steige, Kim A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Slotte, Tanja UNSPECIFIED orcid.org/0000-0001-6020-5102 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-189951
DOI:	10.1534/g3.117.300467
Journal or Publication Title:	G3-Genes Genomes Genet.
Volume:	8
Number:	4
Page Range:	S. 1327 - 1334
Date:	2018
Publisher:	GENETICS SOCIETY AMERICA
Place of Publication:	BETHESDA
ISSN:	2160-1836
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language SELF-INCOMPATIBILITY LOCUS; ARABIDOPSIS-LYRATA; S-LOCUS; EVOLUTION; GENE; DNA; TECHNOLOGIES; BRASSICACEAE; ALIGNMENT; THALIANA Multiple languages Genetics & Heredity Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/18995