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Genetic Diversity of Coat Protein Gene of Peanut Stunt Virus (PSV); Its Evolution Governed by Mutation and Natural Selection
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Reza Pourrahim *   , Mohammad Reza Rezapanah , Shirin Farzadfar |
| Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran. |
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Abstract: (965 Views) |
Background and Aims: Peanut stunt virus is a member of the genus Cucumovirus in the family Bromoviridae, and causes economic yield losses mostly in legume plants worldwide. The synonymous codon usage patterns, which provide significant information about the evolutionary changes that influenced viral survival rates and fitness have not been reported for PSV.
Materials and Methods: The complete coat protein (CP) gene sequences of 73 PSV isolates worldwide, including Iranian isolates from the GenBank database were used for codon usage bias -CUB analysis. To clarify the genetic diversity of PSV, CP sequences were aligned using CLUSTALX2. Maximum Likelihood (ML) tree was reconstructed using 34 representatives of each group by MEGAX using the K2+G+I method with 1000 Bootstrap replicates. The CodonW 1.4.2 package was used for assessing the nucleotide mixtures at the 3rd codon position (A3, C3, T3, and G3%). The Emboss explorer (http://www.bioinformatics.nl/emboss-explorer/) was used for calculating GC content at the first, second, and third codon positions (GC1s, GC2s, GC3s), where the average of GC1 and GC2s is indicated by GC1,2s. The codon usage data for the different hosts were obtained from the codon usage database (available at https://hive.biochemistry.gwu.edu/review/codon).
Results: Phylogenetic analyses using CP sequences clustered the PSV isolates into two main groups (GI & GII), in which subgroups I to V isolates fell in GI however, a new subgroup VI isolates cluster in GII. High nucleotide diversity in the PSV CP gene of new subgroup VI may indicate the recent expansion of these isolates. The average of codon adaptation index (CAI) analyses shows that the host adaptation was highest for subgroup VI, followed by V, II, III, I, and IV subgroups, respectively. A constant and conserved genomic composition CP coding sequences were inferred by low codon usage bias. Nucleotide composition analysis indicates the frequency of amino acid coded by U/C ended optimal codon. This unequal use of nucleotides composition with parity rule 2 (PR2) and the effective number of codons (ENC) plots indicates that the combination of mutation pressure and natural selection are deriving the codon usage patterns in the CP gene but the role of selection pressure is more important. Principal component analysis (PCA) demonstrated that the majority of PSV isolates from subgroups I to V clustered near the origin, which might be due to these isolates being older with a common origin.
Conclusion: Our findings showed that overall codon usage bias within PSV CP gene sequences is slightly biased. The evolution of PSV perhaps reflects a dynamic process of mutation and natural selection to adapt their codon usage to different environments and hosts. This research makes an essential contribution to the understanding of plant virus evolution and reveals novel information about their evolutionary fitness. This study shows the high nucleotide diversity among CP gene sequences of PSV isolates and proposes a new subgroup VI. |
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| Keywords: PSV, codon usage patterns, mutation pressure, natural selection, host adaptation |
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Full-Text [PDF 583 kb]
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Type of Study: Original article |
Subject:
Special
Received: 2022/08/1 | Accepted: 2020/06/25 | Published: 2020/06/25
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