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Article

Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events

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Plant Pathology Laboratory, Institute of Olive Tree, Subtropical Plants & Viticulture, ELGO-DIMITRA, Karamanlis Ave. 167, Gr-73134 Chania, Greece
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Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Gr-54124 Thessaloniki, Greece
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INRAE, UMR BFP, University of Bordeaux, CS20032, CEDEX, 33882 Villenave d’Ornon, France
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Embrapa Uva e Vinho, 95.701-008, Bento Gonçalves, Rio Grande do Sul 96200, Brazil
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Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, ul. Wł. Węgorka 20, 60-318 Poznań, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Kazusato Ohshima
Plants 2021, 10(5), 917; https://doi.org/10.3390/plants10050917
Received: 5 April 2021 / Revised: 26 April 2021 / Accepted: 27 April 2021 / Published: 3 May 2021
A RT–PCR assay developed to amplify the full coat protein (CP) gene of apple stem pitting virus (ASPV) was evaluated using 180 Greek apple and pear samples and showed a broad detection range. This method was used to investigate the presence of ASPV in quince in Greece and showed a high incidence of 52%. The sequences of 14 isolates from various hosts with a distinct RFLP profile were determined. ASPV population genetics and the factors driving ASPV evolution were analyzed using the Greek ASPV sequences, novel sequences from Brazilian apple trees and Chinese botanical Pyrus species, and homologous sequences retrieved from GenBank. Fourteen variant types of Greek, Brazilian and botanical isolates, which differ in CP gene length and presence of indels, were identified. In addition, these analyses showed high intra- and inter-group variation among isolates from different countries and hosts, indicating the significant variability present in ASPV. Recombination events were detected in four isolates originating from Greek pear and quince and two from Brazilian apples. In a phylogenetic analysis, there was a tendency for isolates to cluster together based on CP gene length, the isolation host, and the detection method applied. Although there was no strict clustering based on geographical origin, most isolates from a given country tended to regroup in specific clusters. Interestingly, it was found that the phylogeny was correlated to the type, position, and pattern of indels, which represent hallmarks of specific lineages and indicate their possible role in virus diversification, rather than the CP size itself. Evidence of recombination between isolates from botanical and cultivated species and the clustering of isolates from botanical species and isolates from cultivated species suggest the existence of a possible undetermined transmission mechanism allowing the exchange of ASPV isolates between the cultivated and wild/ornamental hosts. View Full-Text
Keywords: ASPV; CP-specific RT–PCR; pome fruits; botanical pears; variants; CP variability; indels; recombination ASPV; CP-specific RT–PCR; pome fruits; botanical pears; variants; CP variability; indels; recombination
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MDPI and ACS Style

Mathioudakis, M.M.; Maliogka, V.I.; Candresse, T.; Nickel, O.; Fajardo, T.V.M.; Budzyńska, D.; Hasiów-Jaroszewska, B.; Katis, N.I. Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events. Plants 2021, 10, 917. https://doi.org/10.3390/plants10050917

AMA Style

Mathioudakis MM, Maliogka VI, Candresse T, Nickel O, Fajardo TVM, Budzyńska D, Hasiów-Jaroszewska B, Katis NI. Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events. Plants. 2021; 10(5):917. https://doi.org/10.3390/plants10050917

Chicago/Turabian Style

Mathioudakis, Matthaios M., Varvara I. Maliogka, Thierry Candresse, Osmar Nickel, Thor V.M. Fajardo, Daria Budzyńska, Beata Hasiów-Jaroszewska, and Nikolaos I. Katis. 2021. "Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events" Plants 10, no. 5: 917. https://doi.org/10.3390/plants10050917

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