Department of Biotechnology, University of Eldoret, Kenya, P.O Box 1125-30100, Eldoret, Kenya; Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya.
Institute for Climate Change and Adaptation, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya.
Virology. 2024 May;593:110011. doi: 10.1016/j.virol.2024.110011. Epub 2024 Feb 6.
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.
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.
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.
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.
落花生（Arachis hypogaea L.）是全球第 13 大重要作物，种植于热带和亚热带地区。落花生生产的主要限制因素之一是病毒，病毒也是豆科作物中最重要和最丰富的经济病原体。仅有少数研究报告了在肯尼亚西部种植的落花生中 RNA 病毒的特征，其中大多数采用了检测已知病毒的经典方法。
我们从肯尼亚西部农民田间的 21 个有症状和 3 个无症状落花生叶片样本中采集了样本。从样品中提取总 RNA，然后在 Illumina HiSeq 2500 平台上进行第一链 cDNA 合成和测序。去除宿主和 rRNA 序列后，使用公共可用的 NCBI 病毒数据库对高质量的病毒 RNA 序列进行从头组装和病毒基因组注释。使用 MEGA X 进行多序列比对和系统发育分析。
使用低至约 350 万条读数的生物信息学分析，产生了花椰菜花叶病毒（CaMV）、豇豆花叶病毒 2 （CPPV2）、落花生卷叶辅助病毒（GRAV）、落花生卷叶病毒（GRV）、落花生卷叶病毒卫星 RNA（satRNA）和花生斑驳病毒（PeMoV）的完整和部分基因组，这些病毒均符合种间区分标准。这是世界上首次报道 CaMV 和 CPPV2 在落花生宿主上的报道。通过与已发表的高度相似病毒一起进行系统发育分析，进一步验证了所检测病毒的存在。PeMoV 是唯一报道的种传病毒。
我们的研究结果表明，下一代测序技术在发现和鉴定落花生中的新型病毒方面具有强大的能力。新病毒的检测表明，落花生病毒病的复杂性，这需要在未来的研究中更加关注，以确定病毒作为单一或混合感染对作物的影响。从马拉维起源的 PeMoV 的检测表明，种子认证和跨界种子健康测试的重要性。
