Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire

The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified. Sequence yields per MinION run are lower than Illumina, making targeted resequencing an efficient approach. While MinION generates long reads similar to PacBio it doesn’t generate the highly accurate multipass consensus reads, which presents downstream bioinformatics challenges. Here we demonstrate how MinION data can be used for RenSeq achieving similar results to the PacBio and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline. The described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project.

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Author Giolai, Michael
Last Updated November 20, 2019, 16:49 (UTC)
Created August 1, 2019, 10:30 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1186/s12864-017-3936-7
DOI 10.1186/s12864-017-3936-7
Date Last Updated 2018-12-30T03:15:19.010473
Evidence open (via page says license)
Funder code(s) Biotechnology and Biological Sciences Research Council (BB/L009757/1, BB/J004669/1, BB/J010375/1)
Journal Is Open Access true
Open Access Status gold
PDF URL https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-017-3936-7
Publisher URL https://doi.org/10.1186/s12864-017-3936-7