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

Abstract

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.

The Potyviruses: An Evolutionary Synthesis Is Emerging

“…Thus, the RdRp or the helicase proteins are probably most appropriate for inferring the phylogeny of the potyvirids. A maximum likelihood (ML) phylogeny of 166 potyvirids, calculated using the same methods as [29][30][31], from the protein sequences encoded by the RdRp regions of all genomes with GenBank Reference Sequence Accession Codes (July 2019), together with any others that had unique names. The most closely related non-potyvirid, bufivirus UC1, is included as an outlier.…”

Phylodynamics of sunflower chlorotic mottle virus, a re-emerging pathosystem

“…Table 3). Since recombination confounds phylogenetic analysis (Gibbs et al, 2017), the recombinant sequence (MG885794) was discarded from the dataset.…”

“…In previous studies, Giolitti et al (2010) showed that SCMoV might be a pioneer species descending from PVY, which acquired infectivity to other plant families. Interestingly, the origins and/or first records of some potyviruses, including members of the PVY group, were in South America (Gibbs and Ohshima, 2010; Gibbs et al, 2017). PVY is a major pathogen of potatoes and other solanaceous crops worldwide that infects various plant species, including Lactuca serriola , a species of the Asteraceae family (Kaliciak and Syller, 2009).…”

“…Only recombination events that were detected by at least four methods and that had significant phylogenetic support (data not shown) were considered credible evidence of recombination. Those sequences with evidence of recombination were excluded from the subsequent analyses, according to Gibbs et al (2017).…”

Prediction of antigenic epitopes for coat protein of Potato virus Y, Egypt

“…Potato virus Y (PVY) is the type-species of genus Potyvirus, which is a member of Potyviridae family (Pringle, 1999;Abdel-Shafi et al, 2017;Dupuis;Gibbs et al, 2017). This genus of Potyvirus forms one of the largest and most economically important groups of plant viruses.…”