Molecular and Pathobiological Characterization of Sixty One Potato mop-top virus full-length cDNAs Reveals Great Variability of the Virus in the Center of Potato Domestication, Novel Genotypes and Evidence for Recombination (original) (raw)
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Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes
Plant Disease, 2021
Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe, and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato’s Andean domestication center in Peru and of eight historical or recent isolates from Europe. When the principal open reading frames of these genomic sequences together with those of nine previously published genomic sequences were analyzed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 nonrecombinant open reading frame sequences showed that the PVV population had two major phylogroups, one of which formed three minor phylogroups (A1 to A3) of isolates, all of which are found only in the Andean region of South America (Peru and Colombia), and the other formed two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This sugg...
Phytopathology®, 2021
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-likel...
Global genetic diversity and evolutionary patterns among Potato leafroll virus populations
Frontiers in Microbiology
Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently det...
Genetic structure and molecular variability of potato virus M
2014
Cucumber mosaic virus (CMV) has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L.) in the Midwest and Northeastern United States. Virus diversity leading to emergence of new strains is often considered a significant factor in virus epidemics. In addition to epidemics, new disease phenotypes arising from genetic exchanges or mutation can compromise effectiveness of plant disease management strategies. Here, we captured a snapshot of genetic variation of 32 CMV isolates collected from different regions of the U.S including new field as well as historic isolates. Nucleotide diversity (p) was low for U.S. CMV isolates. Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB. Furthermore, phylogenetic analysis suggests likely reassortment between subgroups IA and IB within five CMV isolates. Based on phylogenetic and computational analysis, recombination between subgroups I and II as well as IA and IB in RNA 3 was detected. This is the first report of recombination between CMV subgroups I and II. Neutrality tests illustrated that negative selection was the major force operating upon the CMV genome, although some positively selected sites were detected for all encoded proteins. Together, these data suggest that different regions of the CMV genome are under different evolutionary constraints. These results also delineate composition of the CMV population in the US, and further suggest that recombination and reassortment among strain subgroups does occur but at a low frequency, and point towards CMV genomic regions that differ in types of selection pressure.
The Phylogeography of Potato Virus X Shows the Fingerprints of Its Human Vector
Viruses
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 cont...
Archives of Virology, 2012
An isolate of the Andean strain of potato virus S (PVS), named BB-AND, was detected for the first time in a Brazilian potato crop, fully sequenced and analyzed. A comparison of BB-AND with other PVS isolates (Andean and Ordinary) showed that BB-AND is quite distinct. The lowest amino acid sequence identity to the only other fully sequenced Andean isolate was found in ORF 1 (82%) and ORF 6 (87%). Recombination analysis showed that the isolate Vltava (AJ863510), from Germany, is a recombinant between PVS O and PVS A isolates, with the recombination event located between nucleotides 6125 and 8324.
Inter and Intra Variation of Potato Yellow Vein Virus in Three Potato Species From Colombia
Revista Facultad Nacional de Agronomía, 2015
Potato yellow vein virus (PYVV), (family Closteroviridae, genus Crinivirus) is a re-emergent virus in Andean countries. Low inter-isolate variation has been reported for PYVV CP gene, but there are no reports for intra-isolate variation. Inter- and intra-isolate variability in CP from a population of PYVV was studied. Samples of 216 symptomatic potato plants (115 Solanum tuberosum subsp. andigena (STA), 100 Solanum phureja (SPH) and 1 Solanum chaucha (SCH)) were collected in five Colombian departments. Viral isolates were amplified by RT-PCR and the amplicons were analyzed by single-strand conformation polymorphism (SSCP). Six different migration SSCP patterns (A to F) with different complexities were observed among the population. Pattern A was detected in the five departments in 66% of the isolates. Pattern E was found only in the department of Cundinamarca with a frequency of 0.09%. Patterns B, C, D and F were found in similar proportions of from 13% to 5.6% and were present in t...
The complete nucleotide sequence of potato virus T
Archives of Virology, 2009
Potato virus T (PVT), a member of an unassigned species in the family Flexiviridae, has a genome 6,539 nt in size with three ORFs coding for replication-associated proteins (185 kDa, ORF 1), movement protein (40 kDa, ORF 2) and coat protein (24 kDa, ORF 3), respectively. PVT differs from the type members of all genera of the family Flexiviridae with a 30K-type movement protein and is phylogenetically distant from all of these viruses, least so from grapevine virus A (GVA, genus Vitivirus), with which it groups in all trees. The viral genome resembles that of trichoviruses but is smaller and does not contain the 3' terminal fourth ORF found in some members of this genus. PTV may represent a new genus of plant viruses for which the provisional name of Andesvirus is proposed.