Phylogenetic analysis of the Iranian Leek yellow stripe virus isolate from garlic host based on CP and CI Regions
2022
Entezari, Azadeh | Mehrvar, Mohsen | Zakiaghl, Mohammad
Abstract Leek yellow stripe virus (LYSV) (Potyvirus, Potyviridae), is one of the most important and prevalent viral pathogens of garlic (Allium sativum) causing significant yield losses worldwide. In this study, in order to identify LYSV, sampling was performed from Shushtar in Khuzestan province. For this purpose, 28 garlic leaf samples with chlorosis, mosaic and deformity were collected. Preliminary evaluation of the infection was performed using potyvirus-degenerate primers related to each of the CI (Cylindrical Inclusion) and NIb (Nuclear Inclusion body) genomic regions using RT-PCR test. Electrophoresis of PCR product on 1% agarose gel showed the presence of 700 and 350 bp fragments in 15 samples out of 28 collected samples, respectively. However, the results of nucleotide sequencing only confirmed the contamination of 3 samples out of 15 samples with LYSV. To complete the study, an isolate called LYSV-AE65 was selected and tested using two specific primer pairs for the complete sequence of CI and CP (Coat Protein) genes. The PCR product of each genome fragment was sequenced following cloning in the plasmid vector pTG19-T. In the phylogenetic analysis based on the nucleotide sequence of each of the CI and CP genes separately, no clear correlation was found between LYSV isolates similarities, their geographical origins and host range. Moreover, recombination analysis by RDP4 revealed that no potential recombination event/s happened between LYSV-AE65 from Iran with their respective isolates from NCBI in CI and CP genes. This study is the first molecular study of LYSV in Iran.
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