Potato Virus A Isolates from Three Continents: Their Biological Properties, Phylogenetics, and Prehistory.

Forty-seven potato virus A (PVA) isolates from Europe, Australia, and South America's Andean region were subjected to high-throughput sequencing, and 46 complete genomes from Europe (n = 9), Australia (n = 2), and the Andes (n = 35) obtained. These and 17 other genomes gave alignments of 63 open reading frames 9,180 nucleotides long; 9 were recombinants. The nonrecombinants formed three tightly clustered, almost equidistant phylogroups; A comprised 14 Peruvian potato isolates; W comprised 37 from potato in Peru, Argentina, and elsewhere in the world; and T contained three from tamarillo in New Zealand. When five isolates were inoculated to a potato cultivar differential, three strain groups (= pathotypes) unrelated to phylogenetic groupings were recognized. No temporal signal was detected among the dated nonrecombinant sequences, but PVA and potato virus Y (PVY) are from related lineages and ecologically similar; therefore, "relative dating" was obtained using a single maximum-likelihood phylogeny of PVA and PVY sequences and PVY's well-supported 157 CE "time to most common recent ancestor". The PVA datings obtained were supported by several independent historical coincidences. The PVA and PVY populations apparently arose in the Andes approximately 18 centuries ago, and were taken to Europe during the Columbian Exchange, radiating there after the mid-19th century potato late blight pandemic. PVA's phylogroup A population diverged more recently in the Andean region, probably after new cultivars were bred locally using newly introduced Solanum tuberosum subsp. tuberosum as a parent. Such cultivars became widely grown, and apparently generated the A × W phylogroup recombinants. Phylogroup A, and its interphylogroup recombinants, might pose a biosecurity risk.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Potato Virus Y Biological Strain Group YD: Hypersensitive Resistance Genes Elicited and Phylogenetic Placement.

Potato virus Y (PVY) disrupts healthy seed potato production and causes tuber yield and quality losses globally. Its subdivisions consist of strain groups defined by potato hypersensitive resistance (HR) genes and whether necrosis occurs in tobacco, and phylogroups defined by sequencing. When PVY isolate PP was inoculated to potato cultivar differentials with HR genes, the HR phenotype pattern obtained resembled that caused by strain group PVYD isolate KIP1. A complete genome of isolate PP was obtained by high-throughput sequencing. After removal of its short terminal recombinant segment, it was subjected to phylogenetic analysis together with 30 complete nonrecombinant PVY genomes. It fitted within the same minor phylogroup PVYO3 subclade as KIP1. Putative HR gene Nd was proposed previously to explain the unique HR phenotype pattern that developed when differential cultivars were inoculated with PVYD. However, an alternative explanation was that PVYD elicits HR with HR genes Nc and Ny instead. To establish which gene(s) it elicits, isolates KIP1 and PP were inoculated to F1 potato seedlings from (i) crossing 'Kipfler' and 'White Rose' with 'Ruby Lou' and (ii) self-pollinated 'Desiree' and 'Ruby Lou', where 'Kipfler' is susceptible (S) but 'White Rose', 'Desiree', and 'Ruby Lou' develop HR. With both isolates, the HR:S segregation ratios obtained fitted 5:1 for 'Kipfler' × 'Ruby Lou', 11:1 for 'White Rose' × 'Ruby Lou', and 3:1 for 'Desiree'. Those for 'Ruby Lou' were 68:1 (isolate PP) and 52:0 (isolate KIP1). Because potato is tetraploid, these ratios suggest PVYD elicits HR with Ny from 'Ruby Lou' (duplex condition) and 'Desiree' (simplex condition) and Nc from 'White Rose' (simplex condition) but provide no evidence that Nd exists. Therefore, our differential cultivar inoculations and inheritance studies highlight that PVYD isolates elicit an HR phenotype in potato cultivars with either of two HR genes Nc or Ny, so putative gene Nd can be discounted. Moreover, phylogenetic analysis placed isolate PP within the same minor phylogroup PVYO3 subclade as KIP1, which constitutes the most basal divergence within overall major phylogroup PVYO.

Genetic Diversity of Nine Non-Recombinant Potato virus Y Isolates From Three Biological Strain Groups: Historical and Geographical Insights.

Potato virus Y (PVY) isolates from potato currently exist as a complex of six biologically defined strain groups all containing nonrecombinant isolates and at least 14 recombinant minor phylogroups. Recent studies on eight historical UK potato PVY isolates preserved since 1984 found only nonrecombinants. Here, four of five PVY isolates from cultivated potato or wild Solanum spp. collected recently in Australia, Mexico, and the U.S.A. were typed by inoculation to tobacco plants and/or serological testing using monoclonal antibodies. Next, these five modern isolates and four additional historical UK isolates belonging to biological strain groups PVYC, PVYZ, or PVYN obtained from cultivated potato in 1943 to 1984 were sequenced. None of the nine complete PVY genomes obtained were recombinants. Phylogenetic analysis revealed that the four historical UK isolates were in minor phylogroups PVYC1 (YC-R), PVYO-O (YZ-CM1), PVYNA-N (YN-M), or PVYEu-N (YN-RM), Australian isolate YO-BL2 was in minor phylogroup PVYO-O5, and both Mexican isolate YN-Mex43 and U.S.A. isolates YN-MT12_Oth288, YN-MT12_Oth295, and YN-WWAA150131G42 were in minor phylogroup PVYEu-N. When combined, these new findings and those from the eight historical UK isolates sequenced earlier provide important historical insights concerning the diversity of early PVY populations in Europe and the appearance of recombinants in that part of the world. They and four recent Australian isolates sequenced earlier also provide geographical insights about the geographical distribution and diversity of PVY populations in Australia and North America.

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

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.

A new strain group of common carp: The genetic differences and admixture events between Cyprinus carpio breeds.

Common carp (Cyprinus carpio) has an outstanding economic importance in freshwater aquaculture due to its high adaptive capacity to both food and environment. In fact, it is the third most farmed fish species worldwide according to the Food and Agriculture Organization. More than four million tons of common carp are produced annually in aquaculture, and more than a hundred thousand tons are caught from the wild. Historically, the common carp was also the first fish species to be domesticated in ancient China, and now, there is a huge variety of domestic carp strains worldwide. In the present study, we used double digestion restriction site-associated DNA sequencing to genotype several European common carp strains and showed that they are divided into two distinct groups. One of them includes central European common carp strains as well as Ponto-Caspian wild common carp populations, whereas the other group contains several common carp strains that originated in the Soviet Union, mostly as cold-resistant strains. We believe that breeding with wild Amur carp and subsequent selection of the hybrids for resistance to adverse environmental conditions was the attribute of the second group. We assessed the contribution of wild Amur carp inheritance to the common carp strains and discovered discriminating genes, which differed in allele frequencies between groups. Taken together, our results improve our current understanding of the genetic variability of common carp, namely the structure of natural and artificial carp populations, and the contribution of wild carp traits to domestic strains.