Nanopore-based detection and characterization of yam viruses

被引：0

作者：

Denis Filloux

Emmanuel Fernandez

Etienne Loire

Lisa Claude

Serge Galzi

Thierry Candresse

Stephan Winter

M. L. Jeeva

T. Makeshkumar

Darren P. Martin

Philippe Roumagnac

机构：

[1] CIRAD,Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine

[2] BGPI,undefined

[3] BGPI,undefined

[4] INRA,undefined

[5] CIRAD,undefined

[6] SupAgro,undefined

[7] Univ Montpellier,undefined

[8] CIRAD,undefined

[9] UMR ASTRE,undefined

[10] ASTRE,undefined

[11] Univ Montpellier,undefined

[12] CIRAD,undefined

[13] INRA,undefined

[14] UMR 1332 BFP,undefined

[15] INRA,undefined

[16] University Bordeaux,undefined

[17] CS20032,undefined

[18] DSMZ Plant Virus Department,undefined

[19] ICAR-Central Tuber Crops Research Institute,undefined

[20] University of Cape Town,undefined

来源：

Scientific Reports | / 8卷

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摘要：

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

引用

共 123 条

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