Obonyo, D and Ouma, G and Ikawa, R and Odeny, D A (2024) Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus. Virology, 593. pp. 1-11. ISSN 0042-6822
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Abstract
Background Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses. Methods We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X. Results Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported. Conclusion Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : East & Southern Africa |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | RNA viruses, Arachis hypogaea, GRD, CaMV, CPPV2, Meta-transcriptomics, GRAV, GRV, PeMOV |
| Subjects: | Mandate crops > Groundnut Others > Genetics and Genomics Others > Plant Virology |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 31 Jul 2025 09:30 |
| Last Modified: | 31 Jul 2025 09:30 |
| URI: | http://oar.icrisat.org/id/eprint/13251 |
| Official URL: | https://www.sciencedirect.com/science/article/pii/... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | The authors are greatly indebted to the ICRISAT field officers in Gem, Siaya County and Matayos, Busia County, Kenya, and all the farmers in the two sub-counties for their warm welcome and permission to collect groundnut leaf samples from their fields. We are sincerely thankful to Accadius Lunayo for his useful contributions to the discussions of this manuscript and Samuel Manthi for technical assistance with the laboratory work. |
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