The Phylogeography of Potato Virus X Shows the Fingerprints of Its Human Vector

Abstract

Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop′s main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed. Only 18 of them were recombinants, 17 of them Peruvian. A phylogeny of the non-recombinant sequences found two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups, which included 12 statistically supported clusters. Analysis of 488 coat protein (CP) gene sequences, including 128 published previously, gave a completely congruent phylogeny. Among the minor phylogroups, I-2 and II-3 only contained Andean isolates, I-1 and II-2 were of both Andean and other isolates, but all of the three II-1 isolates were European. I-1, I-2, II-1 and II-2 all contained biologically typed isolates. Population genetic and dating analyses indicated that PVX emerged after potato’s domestication 9000 years ago and was transported to Europe after the 15th century. Major clusters A–D probably resulted from expansions that occurred soon after the potato late-blight pandemic of the mid-19th century. Genetic comparisons of the PVX populations of different Peruvian Departments found similarities between those linked by local transport of seed potato tubers for summer rain-watered highland crops, and those linked to winter-irrigated crops in nearby coastal Departments. Comparisons also showed that, although the Andean PVX population was diverse and evolving neutrally, its spread to Europe and then elsewhere involved population expansion. PVX forms a basal Potexvirus genus lineage but its immediate progenitor is unknown. Establishing whether PVX′s entirely Andean phylogroups I-2 and II-3 and its Andean recombinants threaten potato production elsewhere requires future biological studies.

Translating virome analyses to support biosecurity, on-farm management, and crop breeding

“…Monitoring viromes in farms and regionally could provide advance warning of virus incidence and potential disease outbreaks for farm managers and phytosanitary agencies. Understanding the phylogenetics and phylogeography of each virus locally, regionally, and globally will allow for a better understanding of how viruses were disseminated or introduced ( Fuentes et al., 2019 ; Fuentes et al., 2021a ; Fuentes et al., 2021b ; Fuentes et al., 2022 ). Effective management of seed degeneration in vegetatively propagated crops can be achieved through the integration of seed health assessments and pest risk evaluations ( Thomas-Sharma et al., 2017 ).…”

A global analysis of the Rubus virome using public transcriptome data

“…PVX was detected in R. idaeus datasets from New Zealand (Jibran et al, 2019) at abundances between 0.04-2.41 RPM. A mixed assembly resulted in a scaffold comprising about 59% of the expected genome size about 96.8% identical to members of Eurasian PVX clade (Fuentes et al, 2021 andVerchot, 2022), (Supp. data) The Carlavirus HdCMV was detected in R. argutus datasets from China (Wu et al, 2022) at abundances between 0.05 and 23.5 RPMs, and sequence assembly resulted in a scaffold comprising 98% of the expected genome size with 96.7-98.9% nucleotide identities to available HdCMV isolates (Supp.…”

Plant-Based Production of Metabolites and Nanoparticles Using Potyvirus Vectors

“…encoding MPs involved in cell-to-cell movement, and lastly the CP gene at the 3' end (Fuentes et al, 2021;He et al, 2022). Studies on PVX structure, replication and spread have advanced its utilization for diverse biomedical and agricultural applications (Scholthof et al, 2011).…”