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...
| Autores principales: | , , , , , , , , , |
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| Formato: | info:eu-repo/semantics/article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2435 https://doi.org/10.3390/v13040644 |
| _version_ | 1855028699954413568 |
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| author | Fuentes, Segundo Gibbs, Adrian J. Hajizadeh, Mohammad Perez, Ana Adams, Ian Patrick Fribourg, Cesar E. Kreuze, Jan Fox, Adrian Boonham, Neil Jones, Roger A. C. |
| author_browse | Adams, Ian Patrick Boonham, Neil Fox, Adrian Fribourg, Cesar E. Fuentes, Segundo Gibbs, Adrian J. Hajizadeh, Mohammad Jones, Roger A. C. Kreuze, Jan Perez, Ana |
| author_facet | Fuentes, Segundo Gibbs, Adrian J. Hajizadeh, Mohammad Perez, Ana Adams, Ian Patrick Fribourg, Cesar E. Kreuze, Jan Fox, Adrian Boonham, Neil Jones, Roger A. C. |
| author_sort | Fuentes, Segundo |
| collection | Repositorio INIA |
| description | 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. |
| format | info:eu-repo/semantics/article |
| id | INIA2435 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA24352024-11-29T03:57:38Z The phylogeography of potato virus X shows the fingerprints of its human vector Fuentes, Segundo Gibbs, Adrian J. Hajizadeh, Mohammad Perez, Ana Adams, Ian Patrick Fribourg, Cesar E. Kreuze, Jan Fox, Adrian Boonham, Neil Jones, Roger A. C. Potato Virus disease Potato virus X South America Andean crop domestication center Strain groups High-throughput sequencing Phylogenetics Population genetics Andean lineages Dating Interpretation Evolution Prehistory Biosecurity significance https://purl.org/pe-repo/ocde/ford#4.04.01 Potatoes Papa Potato virus X Virus X de la papa Strains Cepas High-throughput sequencing Secuenciación de alto rendimiento Phylogenetics Filogenética Population genetics Genética de poblaciones 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. This work was supported, in part, by the Bill & Melinda Gates Foundation [OPP1130216]. Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. In 2015–2019, the main sequencing component of this research was funded at the International Potato Center (CIP) by the CGIAR Research Program on Roots, Tubers and Bananas (RTB), CGIAR trust fund contributors (https://www.cgiar.org/funders/), the Peruvian Programa Nacional de Innovaciόn Agraria (PNIA, contract 029-2015-INIA-PNIA/UPMSI/IE), and the Bill and Melinda Gates Fund; and at Fera Science Ltd. (FS) by the UK Government’s Department of Environment Food and Rural Affairs (DEFRA) Future Proofing Plant Health Project under the Defra-Fera Science Ltd. long term services agreement, and via the EUPHRESCO Virus Curate project. 2024-02-26T15:24:13Z 2024-02-26T15:24:13Z 2021-09-09 info:eu-repo/semantics/article Fuentes, S.; Gibbs, A. J.; Hajizadeh, M.; Perez, A.; Adams, I. P.; Fribourg, C. E.; Kreuze, J.; Fox, A.; Boonham, N.; & Jones, R. A. (2021). The phylogeography of potato virus X shows the fingerprints of its human vector. Viruses, 13(4), 644. doi: 10.3390/v13040644 1999-4915 https://hdl.handle.net/20.500.12955/2435 https://doi.org/10.3390/v13040644 eng urn:issn:1999-4915 Viruses info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf MDPI CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Potato Virus disease Potato virus X South America Andean crop domestication center Strain groups High-throughput sequencing Phylogenetics Population genetics Andean lineages Dating Interpretation Evolution Prehistory Biosecurity significance https://purl.org/pe-repo/ocde/ford#4.04.01 Potatoes Papa Potato virus X Virus X de la papa Strains Cepas High-throughput sequencing Secuenciación de alto rendimiento Phylogenetics Filogenética Population genetics Genética de poblaciones Fuentes, Segundo Gibbs, Adrian J. Hajizadeh, Mohammad Perez, Ana Adams, Ian Patrick Fribourg, Cesar E. Kreuze, Jan Fox, Adrian Boonham, Neil Jones, Roger A. C. The phylogeography of potato virus X shows the fingerprints of its human vector |
| title | The phylogeography of potato virus X shows the fingerprints of its human vector |
| title_full | The phylogeography of potato virus X shows the fingerprints of its human vector |
| title_fullStr | The phylogeography of potato virus X shows the fingerprints of its human vector |
| title_full_unstemmed | The phylogeography of potato virus X shows the fingerprints of its human vector |
| title_short | The phylogeography of potato virus X shows the fingerprints of its human vector |
| title_sort | phylogeography of potato virus x shows the fingerprints of its human vector |
| topic | Potato Virus disease Potato virus X South America Andean crop domestication center Strain groups High-throughput sequencing Phylogenetics Population genetics Andean lineages Dating Interpretation Evolution Prehistory Biosecurity significance https://purl.org/pe-repo/ocde/ford#4.04.01 Potatoes Papa Potato virus X Virus X de la papa Strains Cepas High-throughput sequencing Secuenciación de alto rendimiento Phylogenetics Filogenética Population genetics Genética de poblaciones |
| url | https://hdl.handle.net/20.500.12955/2435 https://doi.org/10.3390/v13040644 |
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