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The Major Sources of Genetic Variation Among Grapevine Leafroll-Associated Virus 3 Isolates And Their Relation to Evolution
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Reza Pourrahim *    , Shirin Farzadfar |
| Iranian Research Institute of Plant Protection (IRIPP), Agricultural research, extension and education organization (AREEO) |
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Abstract: (353 Views) |
Background and Aims: The genetic variability and population structure of Grapevine leafroll-associated virus 3 (GLRaV-3) have not already been studied in mid-Eurasia Iran. The investigations will contribute to developing efficient and durable control strategies of latent and graft-transmissible virus.
Materials and Methods: During the winter of 2018-2019, a total of 229 dormant cutting samples were collected from 15 vineyards in West Azarbaijan province. All the samples were analyzed by serological and RT-PCR assays. The phylogenetic tree and two-dimensional nucleotide diversity plot were constructed using CP sequences by the SplitsTree4 v.4.12.6, and SDTv1.2 soft wares, respectively. Dnasp v.6.10.04 was used for genetic diversity and demographic analysis. We provide analyses of the codon usage and composition of GLRaV-3 based on 517 nucleotide sequences of the CP gene including 11 full CP sequences from Iran.
Results: Using serological assay 31.87% GLRaV-3 infection was detected. Neighbor-Net method analysis of the virus complete CP gene showed that the Iranian isolates fell into phylogroup I (GI) “as it is dominant in the rest of the world”. High haplotype diversities indicate the recent expansion of GLRaV-3. No clustering was found according to where the GLRaV-3 was isolated. Using dN/dS values it was found that the different populations of this virus is under negative (purifying) selection. The highest gene flow was determined between Europe and East Asia. Moderate or low genetic differentiation, and frequent gene flow (FST < 0.33 and Nm > 1) also confirmed with Ks*, Kst* Z, Z* and Snn statistics values. The frequency of amino acid coded by A/G ended optimal codon indicates the overlapping influences of natural selection and mutational pressure on the codon preferences in the CP gene. Codon bias of the CP gene was strongly affected by natural selection rather than mutation according to the effective number of codons-ENC vs. GC3s plot. Principal component plot analysis (PCA), illustrated the possible origin of GLRaV-3 in the Old World.
Conclusions: This analysis is the first demonstration of the population structuring of GLRaV-3 in mid-Eurasian Iran. Indeed, these consequences explain selectively driven codon bias in GLRaV-3 species; and reveal the potential importance of expression-mediated selection in shaping the genome evolution of this virus. |
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| Keywords: GLRaV-3, Iran, nucleotide diversity, codon usage bias |
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Full-Text [PDF 1248 kb]
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Type of Study: Original article |
Subject:
Special
Received: 2022/11/23 | Accepted: 2024/01/15 | Published: 2022/12/19
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