Genomic characterisation and evolutionary relationships of groundnut rosette virus from the western highlands of Kenya
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Viral symptomatic groundnut (Arachis hypogaea L.) leaf samples were collected in the heterogeneous agro-ecosystem of the western highlands of Kenya. High throughput RNA sequencing (RNA-Seq) was carried out on total plant RNA using the Illumina HiSeq platform. Subsequently, de novo assembly and sequence similarity searches identified the complete genome of Groundnut rosette virus (GRV). The genome consisted of 4298 nucleotides, encoding three open reading frames (ORF1-ORF3) including an RNA-dependent RNA polymerase gene. A sequence similarity search against GenBank reference sequences matched with 84% identity to a Malawian isolate (Z69910). Bayesian evolutionary relationships using the ORF3 and ORF4 genomic regions clustered the Kenyan isolates within a distinct clade. This study provides the first complete genome of GRV from Kenya and provides a genomic resource for the development of molecular diagnostic tools.
KeywordsGroundnut rosette virus Tombusviridae Next-generation sequencing Sub-Saharan Africa
An Australian Award Scholarship by the Department of Foreign Affairs and Trade (DFAT) supports JW, and this work forms part of his PhD research. Fieldwork activities were coordinated through the Cassava Diagnostic project Kenyan node. A Rising Star grant from the Faculty of Science alumni at the University of Western Australia to LMB provided laboratory reagents and consumables. Pawsey Supercomputing Centre provided supercomputer resources for data analysis with funding from the Australian Government and the Government of Western Australia.
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