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:: Volume 14, Issue 2 (12-2020) ::
Iran J Virol 2020, 14(2): 44-51 Back to browse issues page
Molecular Detection of Beet Curly Top Iran Becurtovirus in Insect Vector (Circulifer Haematocpes) and Analysis of Synonymous Codon Usage Bias
Shirin Farzadfar *, Mohammad Reza Rezapanah, Reza Pourrahim
Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran.
Abstract:   (67 Views)
Background and Aims: Beet curly top Iran virus is a member of the genus Becurtovirus in the family Geminiviradae, and is a major pathogen of sugar beet in Iran. BCTIV is transmitted by beet leafhopper Circulifer haematocpes in a persistent manner. The primary objective of the work was to monitor the occurrence and incidence of BCTIV in vector leafhoppers, which provides useful information on the potential risk to other economically important hosts. A secondary objective was to analysis of CUB using CP gene sequences available in Genbank. This information will further our understanding of the importance of the beet leafhopper in diseases affecting sugar beet and other host crops. In addition, CUB analyses reveal novel information about the evolutionary fitness of BCTD.
Materials and Methods: Total nucleic acid was extracted from 10 leafhoppers individually, which were collected from West Iran. The partial coat protein (CP) genes were amplified using specific primers. For molecular analysis, CP sequences of 164 isolates worldwide, including BCTIV (n=53), and BCTV (n=111) isolates obtained from the GenBank database, were used for codon usage bias -CUB analysis. To clarify the genetic diversity of BCTIV and BCTV, CP sequences were aligned using CLUSTALX2. The CodonW 1.4.2 package was used for assessing of 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.
Results: After polymerase chain reaction (PCR) an expected DNA band of about 600bp was amplified, which confirmed the infection of six leafhoppers with BCTIV. 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 A/U ended optimal codon. This unequal use of nucleotides composition, effective number of codons (ENC), and principal component analysis (PCA) 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.
Conclusion: Our PCR method would be useful in monitoring and detection of BCTIV in this important insect vector, and the data regarding viruliferous vectors can be applied in disease forecasting and management. In addition, our findings showed that overall codon usage bias within BCT CP genes is slightly biased. The evolution of BCT 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 andeal the novel information about their evolutionary fitness.
Keywords: BCT viruses, insect vector, beet leafhopper, PCR, codon usage patterns
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Type of Study: Original article | Subject: Special
Received: 2022/08/2 | Accepted: 2020/12/10 | Published: 2020/12/10
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Farzadfar S, Rezapanah M R, Pourrahim R. Molecular Detection of Beet Curly Top Iran Becurtovirus in Insect Vector (Circulifer Haematocpes) and Analysis of Synonymous Codon Usage Bias. Iran J Virol. 2020; 14 (2) :44-51
URL: http://journal.isv.org.ir/article-1-481-en.html

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