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

BMC Genomics

Methodology Article

Michael Giolai¹  Walter Verweij¹  Pirita Paajanen²  Matthew D. Clark³  Kamil Witek⁴  Jonathan D. G. Jones⁴ 

[1] Earlham Institute (EI), Norwich Research Park, NR4 7UZ, Norwich, UK;Earlham Institute (EI), Norwich Research Park, NR4 7UZ, Norwich, UK;John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK;Earlham Institute (EI), Norwich Research Park, NR4 7UZ, Norwich, UK;School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK;The Sainsbury Laboratory, Norwich Research Park, NR4 7UH, Norwich, UK;

关键词: Targeted capture;    Gene enrichment;    Oxford Nanopore technologies;    MinION;    PacBio;    RenSeq;    R-gene;    NLR;    Resistance gene;    Resistance protein;    NLR gene fusions;   

DOI  :  10.1186/s12864-017-3936-7

 received in 2017-02-01, accepted in 2017-07-10,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsSequence 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.ConclusionThe described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project.

【 授权许可】

CC BY   
© The Author(s). 2017