Molecular analysis of prune dwarf virus reveals divergence within non-Turkish and Turkish viral populations

dc.authoridSantosa, Adyatma Irawan/0000-0002-2826-5444
dc.authoridGlasa, Miroslav/0000-0002-8495-7971
dc.authoridULUBAS SERCE, CIGDEM/0000-0001-5337-5883
dc.authoridCELIK, Ali/0000-0002-5836-8030
dc.contributor.authorSantosa, Adyatma Irawan
dc.contributor.authorCelik, Ali
dc.contributor.authorGlasa, Miroslav
dc.contributor.authorUlubas Serce, Cigdem
dc.contributor.authorErtunc, Filiz
dc.date.accessioned2024-11-07T13:35:05Z
dc.date.available2024-11-07T13:35:05Z
dc.date.issued2023
dc.departmentNiğde Ömer Halisdemir Üniversitesi
dc.description.abstractPrune dwarf virus (PDV) infection affects the production of stone fruits (Prunus spp.) around the world, including in Turkey. In this study, we analyzed the available nucleotide (nt) and amino acid (aa) sequences of P1, P2, movement protein (MP), and coat protein (CP) genes to assess the molecular variability and structure of non-Turkish and Turkish PDV populations. Global isolates were clustered into three major groups in nt-based phylogenetic trees of MP and CP. Comparison of geographically different isolates showed that the MP aa sequences were more conserved than the CP aa sequences. The major aa changes in MP and CP showed the most effect on group 3 isolates. MP and CP-based analyses revealed the lowest number of variable sites (S), total number of mutations (eta), average number of nt differences between sequences (k), and nt diversity (per site) (pi) values in group 3 isolates, indicating high genomic similarities. The Turkish isolates manifested the highest S and eta, and the second highest k and pi values were observed in the comparison with CP, confirmed the high intra-group divergence of the Turkish isolates belonging to the three phylogroups. A stronger purifying selection pressure was observed in the MP region than in the CP region. Neutrality tests deduced negative values for all the MP and CP phylogroups and positive values for the P1, P2, Bulgarian, and Polish populations. MP and CP comparisons showed the divergence of the three phylogroups, as revealed by the results of the K-S*, K-ST*, Z*, and S-nn permutation statistical tests. The fixation index (F-ST) values suggested that non-Turkish PDV isolates had a higher genetic distance compared with Turkish isolates from group 3 and the Turkish isolates from the other two groups.
dc.description.sponsorshipFaculty of Agriculture, Universitas Gadjah Mada [3612/UN1/PN/PN/PT.01.03/2022]; Scientific Grant Agency of the Ministry of Education and Slovak Academy of Sciences [VEGA 2/0030/20]
dc.description.sponsorshipAIS was supported by the grant (3612/UN1/PN/PN/PT.01.03/2022) from the Faculty of Agriculture, Universitas Gadjah Mada. MG was supported by the grant (VEGA 2/0030/20) from the Scientific Grant Agency of the Ministry of Education and Slovak Academy of Sciences.
dc.identifier.doi10.1007/s42161-023-01412-2
dc.identifier.endpage954
dc.identifier.issn1125-4653
dc.identifier.issn2239-7264
dc.identifier.issue3
dc.identifier.scopus2-s2.0-85160637203
dc.identifier.scopusqualityQ2
dc.identifier.startpage943
dc.identifier.urihttps://doi.org/10.1007/s42161-023-01412-2
dc.identifier.urihttps://hdl.handle.net/11480/16327
dc.identifier.volume105
dc.identifier.wosWOS:000999638100005
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.language.isoen
dc.publisherSpringer
dc.relation.ispartofJournal of Plant Pathology
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.snmzKA_20241106
dc.subjectIdentity percentages
dc.subjectIlarvirus
dc.subjectGenetic linkage
dc.subjectMolecular variation
dc.subjectPopulation structure
dc.subjectSelection pressure
dc.titleMolecular analysis of prune dwarf virus reveals divergence within non-Turkish and Turkish viral populations
dc.typeArticle

Dosyalar