Molecular characterization and Phylogenetic Analysis of Viruses Associated with Garlic and Onion in Punjab, India

Author: Irfan Khan and Abhishek Sharma

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Abstract

Garlic and onion grown in Punjab, India are generally infected with several viruses, including the common alliumviruses of the genera Allexivirus, Potyvirus and Carlavirus, and these were responsible for drastic yield losses. Onion Yellow Dwarf Virus (OYDV), Shallot Latent Virus (SLV) and Garlic Virus D (GarV-D) were identified by RT-PCR assay using virus-specific primer sets. BLASTn analysis of sequences confirmed the presence of OYDV and GarV-D, SLV in infected onion and garlic samples, respectively. During BLASTn analysis, OYDV isolate (KP862051) shared 98-99% identity with OYDV isolates (KP862053, KP862052) from Ludhiana and 97% similarity with OYDV isolate (FR833734) from New Delhi. Whereas in the case of garlic viruses, SLV (KR074209) had 91% similarity to SLV isolate (EF600902) from New Delhi, and GarV-D isolate (KR045606) showed a maximum resemblance of 99% with GarV-D isolate (HQ724840) from Spain. OYDV isolate (KP862051) shared 79% nt identity with Rajasthan isolate (EU045556), and 72.9% with New Delhi isolate (FR873734), GarV-D isolates (KR045606) shared a maximum 99.5% nt similarity with Spain isolate (HQ724840) and SLV isolate (KR074209) shared 90.8 nt similarities with New Delhi isolate (EF600902). Phylogenetic analysis of nucleotide sequences revealed that Indian isolates of OYDV and GarV-D have the closest phylogenetic relationship with Indian and abroad isolates; however, SLV isolate (KR074209) was found to be significantly divergent from abroad isolates. Phylogenetic analysis confirms the evolutionary origin of OYDV and SLV from Indian ancestors and GarV-D origin from Spain isolates. Present investigation unravels the virus diversity, subgrouping, and evolutionary history within the alliumviruses in India.

Keywords

Alliumviruses, Characterization, Phylogenetic, Onion and Garlic

Conclusion

GarV-D, OYDV, and SLV have been identified as the viruses associated with samples of garlic and onions based on their closest phylogenetic relationships and highest nucleotide identities. Phylogenetic analysis confirms the evolutionary origin of OYDV and SLV from Indian ancestors and GarV-D origin from Spain isolates. Phylogenetic analysis of the Indian isolates provided updating on viral species subgrouping and evolutionary process. Present investigation unravels the virus diversity, subgrouping, evolutionary history within the allium viruses in India.

References

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How to cite this article

Irfan Khan and Abhishek Sharma (2023). Molecular characterization and Phylogenetic Analysis of Viruses Associated with Garlic and Onion in Punjab, India. Biological Forum – An International Journal, 15(2): 285-290.