Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

G3 : Genes - Genomes - Genetics
Jörg A BachmannTanja Slotte

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...Continue Reading

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Citations

Jun 30, 2019·The New Phytologist·Jörg A BachmannTanja Slotte
Mar 22, 2019·Proceedings of the National Academy of Sciences of the United States of America·Ticao ZhangLa Qiong
Jul 21, 2020·Evolutionary Applications·Eléonore DurandVincent Castric

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Datasets Mentioned

BETA
PRJEB24927

Methods Mentioned

BETA
PCR
454 sequencing

Software Mentioned

AMOS
minimus2
pacbio
Celera Assembler
RepeatMasker
mem
MAFFT
Maker
cutadapt
RaXMl

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