title: Plant virology and next generation sequencing: experiences with a Potyvirus.
abstract: Next generation sequencing is quickly emerging as the go-to tool for plant virologists when sequencing whole virus genomes, and undertaking plant metagenomic studies for new virus discoveries. This study aims to compare the genomic and biological properties of Bean yellow mosaic virus (BYMV) (genus Potyvirus), isolates from Lupinus angustifolius plants with black pod syndrome (BPS), systemic necrosis or non-necrotic symptoms, and from two other plant species. When one Clover yellow vein virus (ClYVV) (genus Potyvirus) and 22 BYMV isolates were sequenced on the Illumina HiSeq2000, one new ClYVV and 23 new BYMV sequences were obtained. When the 23 new BYMV genomes were compared with 17 other BYMV genomes available on Genbank, phylogenetic analysis provided strong support for existence of nine phylogenetic groupings. Biological studies involving seven isolates of BYMV and one of ClYVV gave no symptoms or reactions that could be used to distinguish BYMV isolates from L. angustifolius plants with black pod syndrome from other isolates. Here, we propose that the current system of nomenclature based on biological properties be replaced by numbered groups (I-IX). This is because use of whole genomes revealed that the previous phylogenetic grouping system based on partial sequences of virus genomes and original isolation hosts was unsustainable. This study also demonstrated that, where next generation sequencing is used to obtain complete plant virus genomes, consideration needs to be given to issues regarding sample preparation, adequate levels of coverage across a genome and methods of assembly. It also provided important lessons that will be helpful to other plant virologists using next generation sequencing in the future.
authors.affiliation: School of Plant Biology and Institute of Agriculture, Faculty of Science, University of Western Australia, Crawley, WA, Australia; Crop Protection and Lupin Breeding Branches, Department of Agriculture and Food Western Australia, Perth, WA, Australia.
authors.forename: Monica A
authors.initials: MA
authors.lastname: Kehoe
authors.affiliation: School of Plant Biology and Institute of Agriculture, Faculty of Science, University of Western Australia, Crawley, WA, Australia; Crop Protection and Lupin Breeding Branches, Department of Agriculture and Food Western Australia, Perth, WA, Australia.
authors.forename: Brenda A
authors.initials: BA
authors.lastname: Coutts
authors.affiliation: School of Plant Biology and Institute of Agriculture, Faculty of Science, University of Western Australia, Crawley, WA, Australia; Crop Protection and Lupin Breeding Branches, Department of Agriculture and Food Western Australia, Perth, WA, Australia.
authors.forename: Bevan J
authors.initials: BJ
authors.lastname: Buirchell
authors.affiliation: School of Plant Biology and Institute of Agriculture, Faculty of Science, University of Western Australia, Crawley, WA, Australia; Crop Protection and Lupin Breeding Branches, Department of Agriculture and Food Western Australia, Perth, WA, Australia.
authors.forename: Roger A C
authors.initials: RA
authors.lastname: Jones
mesh_terms: D059014:High-Throughput Nucleotide Sequencing; D031297:Lupinus / Q000821:virology*; D010935:Plant Diseases / Q000821:virology*; D017800:Potyvirus / Q000235:genetics* / Q000302:isolation & purification
references.citation: Plant Dis. 2014 Jun;98(6):739-745
references.pmid: 30708634
references.citation: Mol Plant Pathol. 2009 Jul;10(4):537-45
references.pmid: 19523106
references.citation: Arch Virol. 2005 Mar;150(3):459-79
references.pmid: 15592889
references.citation: Virus Res. 2014 Jun 24;186:20-31
references.pmid: 24361981
references.citation: Arch Virol. 2012 Feb;157(2):271-84
references.pmid: 22075920
references.citation: Arch Virol. 2014 Jun;159(6):1521-5
references.pmid: 24385160
references.citation: J Gen Virol. 1977 Mar;34(3):475-83
references.pmid: 323416
references.citation: Virus Res. 2014 Jun 24;186:3-19
references.pmid: 24275610
references.citation: Intervirology. 1991;32(4):234-45
references.pmid: 1864719
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Plant Dis. 2008 Dec;92(12):1596-1603
references.pmid: 30764292
references.citation: Annu Rev Genet. 2012;46:359-69
references.pmid: 22934641
references.citation: Cell. 2013 Sep 26;155(1):27-38
references.pmid: 24074859
references.citation: Arch Virol. 2011 Mar;156(3):397-403
references.pmid: 21140178
references.citation: Virus Res. 2014 May 12;184:87-92
references.pmid: 24594521
references.citation: Annu Rev Anal Chem (Palo Alto Calif). 2013;6:287-303
references.pmid: 23560931
references.citation: PLoS Pathog. 2013;9(8):e1003337
references.pmid: 23950706
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353