First complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasus

Birol Akbaş; Ali Ferhan Morca; Sevgi Coşkan; Adyatma Irawan Santosa; Handan Çulal-Kılıç; Ali Çelik

doi:10.1007/s13205-023-03746-1

First complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasus

3 Biotech. 2023 Oct;13(10):332. doi: 10.1007/s13205-023-03746-1. Epub 2023 Sep 5.

Authors

Birol Akbaş¹, Ali Ferhan Morca¹, Sevgi Coşkan¹, Adyatma Irawan Santosa², Handan Çulal-Kılıç³, Ali Çelik⁴

Affiliations

¹ Directorate of Plant Protection Central Research Institute, Gayret Mah. Fatih Sultan Mehmet Bulv., 06172 Yenimahalle, Ankara Turkey.
² Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jl. Flora No. 1, Sleman, 55281 Yogyakarta, Indonesia.
³ Department of Plant Protection, Faculty of Agriculture, Isparta University of Applied Sciences, 32000 Isparta, Turkey.
⁴ Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, 14030 Bolu, Turkey.

PMID: 37681114
PMCID: PMC10480364 (available on 2024-10-01)
DOI: 10.1007/s13205-023-03746-1

Abstract

The complete genome of plum pox virus strain T isolates from five different Prunus spp., including almond (P. dulcis) and sour cherry (P. ceracus) isolates, was fully sequenced using the primer pairs designed in this study. The five isolates were aligned with other 50 PPV-T isolates whose complete genome sequences were available in GenBank and then subjected to phylogenetic and diversity analyses. Recombination analysis showed no significant signal detected in the five newly sequenced isolates while confirming four recombinant isolates reported in a previous study. Nucleotide and amino acid phylogenetic trees clustered the tested isolates into three major groups: Balkan 1, 2, and 3. Strain T isolates shared high nucleotide and amino acid identities among them. Diversity analysis applied different parameters to found that the sequences of P3 and 6K1 genes were more conserved over other genes. In accordance, the highly variable P1 and CP genes were found to experience weaker purifying pressures, ω = 0.127 and 0.219, respectively, than other genes. The three neutrality tests gave negative values to all genes, suggesting that strain T populations have expanding or bottleneck selections. Genetic make-up of the only known sour cherry isolate is highly identical to isolates from other Prunus spp. Therefore, this study has updated our knowledge of T strain diversity in new hosts and provided a clear picture of genetic variation and host relationships.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-023-03746-1.

Keywords: Diversity and polymorphism analyses; Neutrality tests; Phylogenetic analysis; RT-PCR; Recombination analysis.

© King Abdulaziz City for Science and Technology 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.