Metagenomic study for the identification of viruses infecting soybean in Pakistan

• Published in: Australasian plant pathology Vol. 52; no. 3; pp. 191 - 194
• Main Authors: Rahman, Saleem Ur, Domier, Leslie L., Raza, Ghulam, Ahmed, Nasim, McCoppin, Nancy K., Amin, Imran, Mansoor, Shahid
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.05.2023; Springer Nature B.V
• Subjects: Agriculture; Biomedical and Life Sciences; Cowpea mild mottle virus; Cowpeas; Deoxyribonucleic acid; DNA; DNA viruses; Ecology; Entomology; family; Gene sequencing; genus; leaf curling; Leaf-curl; leaves; Life Sciences; Metagenomics; Mungbean yellow mosaic India virus; Mungbean yellow mosaic virus; Pakistan; Plant diseases; Plant Pathology; Plant Sciences; Plant viruses; Research Note; Ribonucleic acid; RNA; RNA viruses; Soybeans; Torradovirus; Vigna unguiculata; Viruses; Pakistan; Metatranscriptomics; Soybean; Carlaviruses; Begomoviruses
• ISSN: 0815-3191; 1448-6032
• DOI: 10.1007/s13313-023-00909-9

In 2018, symptoms of multiple viruses were observed in a soybean field at Faisalabad, Pakistan. Symptomatic and asymptomatic leaf samples were collected, RNA was extracted, and cDNA was synthesized and characterized using high throughput RNA sequencing (RNAseq). The RNAseq results showed the presence of three strains of cowpea mild mottle virus, an RNA virus in the Carlavirus genus in the family Betaflexiviridae . Eight contigs of a putative member of the genus Torradovirus in the family Secoviridae were also observed, which was named soybean torradovirus-1. Multiple DNA viruses of the genus Begomovirus were also identified. These included mungbean yellow mosaic India virus, mungbean yellow mosaic virus and pedilanthus leaf curl virus. Among the RNA and DNA viruses, cowpea mild mottle virus and mungbean yellow mosaic virus were the most abundant.