A proposal to rationalize within-species plant virus nomenclature: benefits and implications of inaction

Jones, R. A. C.; Kehoe, Monica A.

doi:10.1007/s00705-016-2848-1

Cited by 28 publications

(11 citation statements)

References 31 publications

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“…However, an analysis based on pairwise comparisons of DNA-A nucleotide sequences of ToLCNDV isolates reported so far and following ICTV demarcation criteria for begomoviruses [3] suggested the presence of a novel strain spreading in the western Mediterranean Basin. Furthermore, several additional strains might be present in the population, that await further study before names are given [37]. The presence of three differentiated strains within the ToLCNDV complex already has been suggested by Jyothsna et al on the basis of nucleotide sequence identity [38] after the analysis of a more limited number of sequences.…”

Section: Discussionmentioning

confidence: 99%

A Novel Strain of Tomato Leaf Curl New Delhi Virus Has Spread to the Mediterranean Basin

Fortes

Sánchez-Campos

Fiallo‐Olivé

et al. 2016

Viruses

112

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Tomato leaf curl New Delhi virus (ToLCNDV) is a whitefly-transmitted bipartite begomovirus (genus Begomovirus, family Geminiviridae) that causes damage to multiple cultivated plant species mainly belonging to the Solanaceae and Cucurbitaceae families. ToLCNDV was limited to Asian countries until 2012, when it was first reported in Spain, causing severe epidemics in cucurbit crops. Here, we show that a genetically-uniform ToLCNDV population is present in Spain, compatible with a recent introduction. Analyses of ToLCNDV isolates reported from other parts of the world indicated that this virus has a highly heterogeneous population genetically with no evident geographical, plant host or year-based phylogenetic groups observed. Isolates emerging in Spain belong to a strain that seems to have evolved by recombination. Isolates of this strain seem adapted to infecting cucurbits, but poorly infect tomatoes.

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Section: Discussionmentioning

confidence: 99%

A Novel Strain of Tomato Leaf Curl New Delhi Virus Has Spread to the Mediterranean Basin

Fortes

Sánchez-Campos

Fiallo‐Olivé

et al. 2016

Viruses

112

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“…Thus the two nomenclatural systems, host genetics versus virus genetics, mostly coincide, but not always. For example, PVY D belongs to phylogroup C, non-recombinant PVY z isolates to phylogroup O (Jones and Kehoe 2016; Kehoe and Jones 2016), and recombinant PVY z isolates to R2 (Kerlan et al. 2011; Karasev and Gray 2013).…”

Section: Introductionmentioning

confidence: 99%

Potato virus Y; the Andean connection

et al. 2019

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Potato virus Y (PVY) causes disease in potatoes and other solanaceous crops. The appearance of its necrogenic strains in the 1980s made it the most economically important virus of potatoes. We report the isolation and genomic sequences of 32 Peruvian isolates of PVY which, together with 428 published PVY genomic sequences, gave an alignment of 460 sequences. Of these 190 (41%) were non-recombinant, and 162 of these provided a dated phylogeny, that corresponds well with the likely history of PVY, and show that PVY originated in South America which is where potatoes were first domesticated. The most basal divergences of the PVY population produced the N and C: O phylogroups; the origin of the N phylogroup is clearly Andean, but that of the O and C phylogroups is unknown, although they may have been first to establish in European crops. The current PVY population originated around 156 CE. PVY was probably first taken from South America to Europe in the 16th century in tubers. Most of the present PVY diversity emerged in the second half of the 19th century, after the Phytophthora infestans epidemics of the mid-19th century destroyed the European crop and stimulated potato breeding. Imported breeding lines were shared, and there was no quarantine. The early O population was joined later by N phylogroup isolates and their recombinants generated the R1 and R2 populations of damaging necrogenic strains. Our dating study has confirmed that human activity has dominated the phylodynamics of PVY for the last two millennia.

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“…However, as more genomes have been sequenced and more potato hypersensitivity genes found (Singh et al 2008; Moury 2010; Karasev et al 2011; Karasev and Gray 2013; Jones 2014; Rowley, Gray, and Karasev 2015; Kehoe and Jones 2016), continued use of the same names for biological and phylogenetic groups has proved to be increasingly confusing due to the lack of complete coincidence between them. A new strain nomenclature system for sub-dividing the phylogenetic groups using Latinised numerals has therefore been proposed (Jones 2014; Jones and Kehoe 2016; Kehoe and Jones 2016). Their groupings correlate with the five broad ‘phylogroups’ we discuss in this article; the traditional C, O, and N groups plus two groups of recombinants, R1 and R2.…”

Section: Introductionmentioning

confidence: 99%

The phylogenetics of the global population of potato virus Y and its necrogenic recombinants

et al. 2017

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Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall into five groupings, which mostly, but not exclusively, correspond with groupings already devised using biological and taxonomic data. Only 42 percent of the sequences are not recombinant, and all these fall into one or other of three phylogroups; the previously named C (common), O (ordinary), and N (necrotic) groups. There are also two other distinct groups of isolates all of which are recombinant; the R-1 isolates have N (5′ terminal minor) and O (major) parents, and the R-2 isolates have R-1 (major) and N (3′ terminal minor) parents. Many isolates also have additional minor intra- and inter-group recombinant genomic regions. The complex interrelationships between the genomes were resolved by progressively identifying and removing recombinants using partitioned sequences of synonymous codons. Least squared dating and BEAST analyses of two datasets of gene sequences from non-recombinant heterochronously-sampled isolates (seventy-three non-recombinant major ORFs and 166 partial ORFs) found the 95% confidence intervals of the TMRCA estimates overlap around 1,000 CE (Common Era; AD). We attempted to identify the most accurate datings by comparing the estimated phylogenetic dates with historical events in the worldwide adoption of potato and other PVY hosts as crops, but found that more evidence from gene sequences of non-potato isolates, especially from South America, was required.

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A proposal to rationalize within-species plant virus nomenclature: benefits and implications of inaction

Cited by 28 publications

References 31 publications

A Novel Strain of Tomato Leaf Curl New Delhi Virus Has Spread to the Mediterranean Basin

A Novel Strain of Tomato Leaf Curl New Delhi Virus Has Spread to the Mediterranean Basin

Potato virus Y; the Andean connection

The phylogenetics of the global population of potato virus Y and its necrogenic recombinants

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