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Fuentes S, Gibbs AJ, Adams IP, Wilson C, Botermans M, Fox A, Kreuze J, Boonham N, Kehoe MA, Jones RAC. Potato Virus A Isolates from Three Continents: Their Biological Properties, Phylogenetics, and Prehistory. PHYTOPATHOLOGY 2021; 111:217-226. [PMID: 33174824 DOI: 10.1094/phyto-08-20-0354-fi] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
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.
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Affiliation(s)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center (CIP), La Molina, Lima, Peru
| | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT, Australia
| | | | - Calum Wilson
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tasmania, Australia
| | - Marleen Botermans
- National Reference Centre of Plant Health, Dutch National Plant Protection Organization Service, Wageningen, The Netherlands
| | - Adrian Fox
- Fera Science Ltd., Sand Hutton, York, U.K
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), La Molina, Lima, Peru
| | - Neil Boonham
- Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne, U.K
| | - Monica A Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Roger A C Jones
- Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
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Madroñero J, Corredor Rozo ZL, Escobar Pérez JA, Velandia Romero ML. Next generation sequencing and proteomics in plant virology: how is Colombia doing? ACTA BIOLÓGICA COLOMBIANA 2019. [DOI: 10.15446/abc.v24n3.79486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Crop production and trade are two of the most economically important activities in Colombia, and viral diseases cause a high negative impact to agricultural sector. Therefore, the detection, diagnosis, control, and management of viral diseases are crucial. Currently, Next-Generation Sequencing (NGS) and ‘Omic’ technologies constitute a right-hand tool for the discovery of novel viruses and for studying virus-plant interactions. This knowledge allows the development of new viral diagnostic methods and the discovery of key components of infectious processes, which could be used to generate plants resistant to viral infections. Globally, crop sciences are advancing in this direction. In this review, advancements in ‘omic’ technologies and their different applications in plant virology in Colombia are discussed. In addition, bioinformatics pipelines and resources for omics data analyses are presented. Due to their decreasing prices, NGS technologies are becoming an affordable and promising means to explore many phytopathologies affecting a wide variety of Colombian crops so as to improve their trade potential.
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