Mosharaf, Nadia, Tabein, Saeid, Mehrabi-Koushki, Mehdi, Hemmati, Seyed Ali, Ghorbani, Abozar (2023). Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates. , 12(1), 1-13. doi: 10.48311/jcp.2023.1617
Nadia Mosharaf; Saeid Tabein; Mehdi Mehrabi-Koushki; Seyed Ali Hemmati; Abozar Ghorbani. "Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates". , 12, 1, 2023, 1-13. doi: 10.48311/jcp.2023.1617
Mosharaf, Nadia, Tabein, Saeid, Mehrabi-Koushki, Mehdi, Hemmati, Seyed Ali, Ghorbani, Abozar (2023). 'Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates', , 12(1), pp. 1-13. doi: 10.48311/jcp.2023.1617
Mosharaf, Nadia, Tabein, Saeid, Mehrabi-Koushki, Mehdi, Hemmati, Seyed Ali, Ghorbani, Abozar Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates. , 2023; 12(1): 1-13. doi: 10.48311/jcp.2023.1617

Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates

Journal of Crop Protection
Article 1, Volume 12, Issue 1, 2023, Pages 1-13    PDF (992.03 K)
Document Type: Original Research
DOI: 10.48311/jcp.2023.1617
Authors
Nadia Mosharaf1; Saeid Tabein* 1; Mehdi Mehrabi-Koushki1; Seyed Ali Hemmati1; Abozar Ghorbani2
1Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
2Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran.
Abstract
Hibiscus chlorotic ringspot virus (HCRSV), genus Betacarmovirus, family Tombusviridae, is a common pathogen of hibiscus plants in tropical and subtropical regions. During 2020-2021, leaf samples of Chinese hibiscus Hibiscus rosa-sinensis L. with mottling and chlorotic ring spot symptoms were collected from Ahvaz and Molasani Khuzestan province, southwestern Iran. Total RNA extracted from symptomatic samples was subjected to RT-PCR analysis to amplify the sequence of the coat protein gene (CP) (p38) of HCRSV. Complete (1038 bp) and partial (932 bp) p38 sequences were determined and deposited in the GenBank database. The consensus sequences obtained from CP were compared with those of known isolates using the nBLAST program and phylogenetic analysis. The phylogenetic tree constructed based on the p38 sequences showed different ancestors for Iranian isolates of HCRSV. Additionally, the isolates studied were grouped into clades regardless of their geographic distribution, suggesting that there is no differentiation of population based on location and that populations are interconnected. Recombination analysis based on p38 sequences predicted at least two acceptable recombinant isolates, Ahvaz (Iran) and Israel. In silico prediction of CP structures of isolates involved in recombination events showed low sequence to structure identity between HCRSV isolates. In addition to reporting two new HCRSV isolates from Iran, our work demonstrated that HCRSV exhibits a high genetic variation through recombination and that the classification criterion could be changed from low nucleotide sequence identity to a higher value, along with the structural analysis of betacarmovirus proteins.
Keywords
HCRSV; Coat Protein; Recombination; Tertiary structure
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