Nanopore-based detection and characterization of yam viruses

• DOI: 10.1038/s41598-018-36042-7
• Publication Date: 2018-12-10T19:05:52Z
• Authors: Denis Filloux; Emmanuel Fernandez; Etienne Loire; Lisa Claude; Serge Galzi; Thierry Candresse; Stephan Winter; M. L. Jeeva; T. Makeshkumar; Darren P. Martin; Philippe Roumagnac
• Keywords: Minion; Sanger sequencing; Viral quasispecies; Illumina dye sequencing; Sequence (biology)

Abstract We here assessed the capability of MinION sequencing approach to detect and characterize viruses infecting a water yam plant. This platform consistently revealed presence several plant virus species, including Dioscorea bacilliform , Yam mild mosaic chlorotic necrosis . A potentially novel ampelovirus was also detected by complimentary Illumina approach. The full-length genome sequence determined using Sanger sequencing, which enabled determination coverage accuracy technology. Whereas total mean error rate virus-related reads 11.25%, we show that consensus obtained either de novo assembly or after mapping on genomic >99.8% identical with Sanger-derived reference sequence. From perspective potential disease diagnostic applications these degrees demonstrate can be used both reliably accurately nearly positive-sense single-strand polyadenylated RNA genomes.