Population genetic analysis of potato virus X based on the CP gene sequence

Hajizadeh, Mohammad Reza; Sokhandan-Bashir, Nemat

doi:10.1007/s13337-017-0362-z

Cited by 10 publications

(10 citation statements)

References 42 publications

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“…The phylogeny of the large population composed of 370 non-rec sequences both confirmed earlier phylogenetic analyses of the smaller selection of sequences available then [42,43,100] and added to it. Both the 370 concat and 488 CP sequences were placed in two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups.…”

Section: Discussionsupporting

confidence: 69%

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

Fuentes

Gibbs

Hajizadeh

et al. 2021

Viruses

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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.

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Section: Discussionsupporting

confidence: 69%

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

Fuentes

Gibbs

Hajizadeh

et al. 2021

Viruses

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“…These studies used European PVX strains such as Roth1, UK3, and X3, as well as the American strains CP, CP4, and HB. Molecular analysis of PVX strains in Asia has been performed more recently and some isolates appear to be more similar to European isolates, suggesting that PVX was introduced before there were strict quarantine measures (Hajizadeh & Sokhandan‐Bashir, 2017; Komatsu et al, 2005; Yu et al, 2010). Japanese strains of PVX inoculated to Solanum demissium were categorized into the “common group” and the “necrosis group”.…”

Section: Pvx Genetic Variability and Innate Immunity Against Pvxmentioning

confidence: 99%

Potato virus X: A global potato‐infecting virus and type member of the Potexvirus genus

Verchot

2021

Molecular Plant Pathology

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Taxonomy Potato virus X is the type‐member of the plant‐infecting Potexvirus genus in the family Alphaflexiviridae. Physical properties Potato virus X (PVX) virions are flexuous filaments 460–480 nm in length. Virions are 13 nm in diameter and have a helical pitch of 3.4 nm. The genome is approximately 6.4 kb with a 5′ cap and 3′ poly(A) terminus. PVX contains five open reading frames, four of which are essential for cell‐to‐cell and systemic movement. One protein encodes the viral replicase. Cellular inclusions, known as X‐bodies, occur near the nucleus of virus‐infected cells. Hosts The primary host is potato, but it infects a wide range of dicots. Diagnostic hosts include Datura stramonium and Nicotiana tabacum. PVX is transmitted in nature by mechanical contact. Useful website https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rna-viruses/w/alphaflexiviridae/1330/genus-potexvirus

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“…Consequently, there exists high genetic differentiation between the virus population of Pakistan and the virus population from Bangladesh, India, Mexico, America and Australia. Similar results based on the highest Fst (0.54) value between South America and Japanese populations using Potato virus X , CP gene sequences suggest infrequent gene flow attributed to the long distances between these geographic regions [ 58 ]. In Genetic differentiation assessment between PRSV full length genomic populations with the exception of Pakistan vs Asian population, all the Kst* values range between 0.015–0.25 and a bit higher than “0” supported by P values >0.05 suggesting that populations are not well differentiated.…”

Section: Discussionmentioning

confidence: 58%

Genetic variability and evolutionary dynamics of atypical Papaya ringspot virus infecting Papaya

et al. 2021

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Papaya ringspot virus biotype-P is a detrimental pathogen of economically important papaya and cucurbits worldwide. The mutation prone feature of this virus perhaps accounts for its geographical dissemination. In this study, investigations of the atypical PRSV-P strain was conducted based on phylogenetic, recombination and genetic differentiation analyses considering of it’s likely spread across India and Bangladesh. Full length genomic sequences of 38 PRSV isolates and 35 CP gene sequences were subjected to recombination analysis. A total of 61 recombination events were detected in aligned complete PRSV genome sequences. 3 events were detected in complete genome of PRSV strain PK whereas one was in its CP gene sequence. The PRSV-PK appeared to be recombinant of a major parent from Bangladesh. However, the genetic differentiation based on full length genomic sequences revealed less frequent gene flow between virus PRSV-PK and the population from America, India, Colombia, other Asian Countries and Australia. Whereas, frequent gene flow exists between Pakistan and Bangladesh virus populations. These results provided evidence correlating geographical position and genetic distances. We speculate that the genetic variations and evolutionary dynamics of this virus may challenge the resistance developed in papaya against PRSV and give rise to virus lineage because of its atypical emergence where geographic spread is already occurring.

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Population genetic analysis of potato virus X based on the CP gene sequence

Cited by 10 publications

References 42 publications

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

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

Potato virus X: A global potato‐infecting virus and type member of the Potexvirus genus

Genetic variability and evolutionary dynamics of atypical Papaya ringspot virus infecting Papaya

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