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

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Giolai, Michael, Paajanen, Pirita, Verweij, Walter, Witek, Kamil, Jones, Jonathan D. G. and Clark, Matthew D. (2017) Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire. BMC Genomics, 18. ISSN 1471-2164

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Abstract

Background: 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. Results: 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. Conclusion: The described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project.

Item Type: Article
Faculty \ School: Faculty of Science > School of Environmental Sciences
Faculty of Science > School of Mathematics
Faculty of Science > The Sainsbury Laboratory
Faculty of Science > School of Biological Sciences
UEA Research Groups: Faculty of Science > Research Groups > Plant Sciences
Related URLs:
Depositing User: Pure Connector
Date Deposited: 02 Aug 2017 05:06
Last Modified: 22 Oct 2022 02:57
URI: https://ueaeprints.uea.ac.uk/id/eprint/64320
DOI: 10.1186/s12864-017-3936-7

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