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Genomic characterisation of an isolate of Brassica Yellows Virus associated with Brassica weed in Tasmania

Citation

Umar, M and Farooq, T and Tegg, RS and Thangavel, T and Wilson, CR, Genomic characterisation of an isolate of Brassica Yellows Virus associated with Brassica weed in Tasmania, Plants, 11, (7) Article 884. ISSN 2223-7747 (2022) [Refereed Article]


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DOI: doi:10.3390/plants11070884

Abstract

Brassica yellows virus (BrYV), a tentative species in the genus Polerovirus, of the Solemoviridae family, is a phloem-restricted and aphid-transmitted virus with at least three genotypes (A, B, and C). It has been found across mainland China, South Korea, and Japan. BrYV was previously undescribed in Tasmania, and its genetic variability in the state remains unknown. Here, we describe a near-complete genome sequence of BrYV (genotype A) isolated from Raphanus raphanistrum in Tasmania using next-generation sequencing and sanger sequencing of RT-PCR products. BrYV-Tas (GenBank Accession no. OM469309) possesses a genome of 5516 nucleotides (nt) and shares higher sequence identity (about 90%) with other BrYV isolates. Phylogenetic analyses showed variability in the clustering patterns of the individual genes of BrYV-Tas. Recombination analysis revealed beginning and ending breakpoints at nucleotide positions 1922 to 5234 nt, with the BrYV isolate LC428359 and BrYV isolate KY310572 identified as major and minor parents, respectively. Results of the evolutionary analysis showed that the majority of the codons for each gene are evolving under purifying selection, though a few codons were also detected to have positive selection pressure. Taken together, our findings will facilitate an understanding of the evolutionary dynamics and genetic diversity of BrYV.

Item Details

Item Type:Refereed Article
Keywords:Brassica yellows virus, genome characterisation, recombination, Polerovirus, phylogenetic analysis, plant virus, NGS, biosecurity
Research Division:Agricultural, Veterinary and Food Sciences
Research Group:Crop and pasture production
Research Field:Crop and pasture protection (incl. pests, diseases and weeds)
Objective Division:Plant Production and Plant Primary Products
Objective Group:Horticultural crops
Objective Field:Field grown vegetable crops
UTAS Author:Umar, M (Mr Muhammad Umar)
UTAS Author:Tegg, RS (Dr Robert Tegg)
UTAS Author:Thangavel, T (Dr Tamil Thangavel)
UTAS Author:Wilson, CR (Professor Calum Wilson)
ID Code:149958
Year Published:2022
Deposited By:TIA - Research Institute
Deposited On:2022-05-03
Last Modified:2022-05-04
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