Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
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Insights into factors affecting synonymous codon usage in apple mosaic virus and its host adaptability

  • Pourrahim, R. (Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO)) ;
  • Farzadfar, Sh. (Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO))
  • Received : 2021.12.13
  • Accepted : 2022.01.24
  • Published : 2022.03.31
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Abstract

The genetic variability and population structure of apple mosaic virus (ApMV) have been studied; however, synonymous codon usage patterns influencing the survival rates and fitness of ApMV have not been reported. Based on phylogenetic analyses of 52 ApMV coat protein (CP) sequences obtained from apple, pear, and hazelnut, ApMV isolates were clustered into two groups. High molecular diversity in GII may indicate their recent expansion. A constant and conserved genomic composition of the CP sequences was inferred from the low codon usage bias. Nucleotide composition and relative synonymous codon usage (RSCU) analysis indicated that the ApMV CP gene is AU-rich, but G- and U-ending codons are favored while coding amino acids. This unequal use of nucleotides together with parity rule 2 and the effective number of codon (ENC) plots indicate that mutation pressure together with natural selection drives codon usage patterns in the CP gene. However, in this combination, selection pressure plays a more crucial role. Based on principal component analysis plots, ApMV seems to have originated from apple trees in Europe. However, according to the relative codon deoptimization index and codon adaptation index (CAI) analyses, ApMV exhibited the greatest fitness to hazelnut. As inferred from the results of the similarity index analysis, hazelnut has a major role in shaping ApMV RSCU patterns, which is consistent with the CAI analysis results. This study contributes to the understanding of plant virus evolution, reveals novel information about ApMV evolutionary fitness, and helps find better ApMV management strategies.

Keywords

Acknowledgement

We gratefully thank to Dr. Hassan Ebrahimi, Department of Advanced Technology Fusion, Graduate School of Science and Engineering, Saga University, 1 Honjo-Machi, Saga 840-8502, Japan, for kindly supporting CodonW analysis and mathematical equations in this research.

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