Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella
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
References
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing.
Citations
Datasets Mentioned
Methods Mentioned
Software Mentioned
Related Concepts
Related Feeds
Artificial Chromosomes
Artificial chromosomes are genetically engineered chromosomes derived from the DNA of a species. Discover the latest research on artificial chromosomes here.