Phylogenetic Relationship of Alfalfa Mosaic Virus (AMV) Isolate Identified in Bingöl Province of Turkey

Abstract

Alfalfa mosaic virus (AMV) is one of the most important viral diseases of alfalfa plant among the forage crop, causing significant annual economic losses. The agent is also of potential importance to other cultivars such as tomatoes, potatoes, and peppers in most cases. The identification and phylogenetic relationships of AMV were carried out by reverse-transcription polymerase chain reaction (RT-PCR), following by bacterial cloning. The cDNA of alfalfa samples (12) were subjected to RT-PCR tests using primer pairs, specific for the capsid protein gene (CP) of AMV, resulting in a DNA fragment of approximately 700 bp as expected. The amplicons were directly cloned and then resulting sequences were deposited in GenBank (Acc. No: MW962977, MW962976). The BLASTn analysis of both sequences demonstrated that AMV virus isolates from alfalfa were highly similar to other AMV isolates from various crops in the world, with nucleotide identity ranging from 97 to 99.37%. The results of phylogenetic dendrogram based on CP gene sequences clearly suggested that our isolates are closely related to four AMV isolates from alfalfa in Turkey. To our knowledge, this study is the first report of molecular phylogeny and AMV presence in alfalfa exhibiting yellowing, mottling, and leaves abnormalities in Bingöl province, Turkey.

Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes

“…In addition, the partial CP gene of Bingöl AMV isolates (MW962977 and MW962976) from alfalfa was found to contain 700 bp nucleotides. The phylogenetic tree related these isolates to other Turkish isolates from Van and Iğdır provinces with 3 major groups (Güller et al, 2022). Topkaya (2022) reported the presence of AMV by PCR amplification based on the CP gene from potato plants in the Tokat province, Türkiye.…”

“…AMV-infected pepper plants were reported in Samsun by Arli-Sökmen et al (2005), in Adana by Çetinkıran and Baloğlu (2011), and in Kahramanmaraş by Demir (2005). In addition, the presence of AMV in Türkiye was molecularly shown with RT-PCR in parsley in Konya , potato in Tokat (Topkaya, 2022), and alfalfa in Bingöl and Van (Usta and Güller, 2020;Güller et al, 2022). AMV was also reported in the provinces of Manisa, Balıkesir, and Burdur from different plant origins Kılıç and Yardımcı, 2015).…”

“…Viral RNA was reverse transcribed using random primers, and then subjected to polymerase chain reaction (PCR) using sense and antisense primers. PCR was performed using an Eppendorf Mastercycler (Germany) with a total of 25 µl of reaction volume under the same reaction mixture and temperature conditions as previously described by Güller et al (2022). For the identification of pathogens identified during preliminary testing, an alfalfa AMV isolate was utilized as a positive control.…”

“…For the determination of the molecular mechanism of action of phytocompounds in connection to viral protein targets, molecular docking research on essential oils was carried out in silico with the help of the Auto Dock Vina software (http://vina.scripps.edu/). The term "in silico analysis" relates to the practice of conducting scientific research using computer simulations, modeling, and analysis, as opposed to empirical experiments (Korkmaz et al, 2022). This methodology is used to save costs, optimize the use of time, and sometimes in situations where experimentation is challenging or dangerous has the potential to provide a valid alternative (Cairns et al, 2016;Usta et al, 2023, Demirel, 2021.…”