BACKGROUND Publicly available transcriptomic datasets have become a valuable tool for the discovery of new pathogens, particularly viruses. In this study, several coding-complete viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the NCBI Sequence Read Archive. METHODS Publicly available Medicago spp. transcriptomic datasets were retrieved from the NCBI SRA database. The raw reads were first mapped to the reference genomes of Medicago sativa and Medigago truncatula followed by the alignment of the unmapped reads to the NCBI viral genome database and de novo assembly using the SPAdes tool. When possible, assemblies were experimentally confirmed using 5'/3' RACE and RT-PCRs. RESULTS Twenty three different viruses were identified in the analyzed datasets, of which several represented emerging viruses not reported in alfalfa prior to this study. Among them were two strains of cnidium vein yellowing virus, lychnis mottle virus and Cactus virus X, for which coding-complete genomic sequences were obtained by a de novo assembly. CONCLUSIONS The results improve our knowledge of the diversity and host range of viruses infecting alfalfa, provide essential tools for their diagnostics and characterization and demonstrate the utility of transcriptomic datasets for the discovery of new pathogens.

中文翻译：

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苜蓿（Medicago sativa L.）转录组数据集中新兴病毒基因组的鉴定。


背景技术公开的转录组数据集已成为发现新病原体，特别是病毒的有价值的工具。在这项研究中，从 NCBI 序列读取档案中检索到的植物数据集中鉴定了以前在苜蓿中未发现或实验证实的几种编码完整病毒基因组。方法 公开的苜蓿属植物。转录组数据集取自 NCBI SRA 数据库。首先将原始读数映射到苜蓿和蒺藜苜蓿的参考基因组，然后将未映射的读数与 NCBI 病毒基因组数据库进行比对，并使用 SPAdes 工具从头组装。如果可能，使用 5'/3' RACE 和 RT-PCR 进行实验确认组装。结果 在分析的数据集中发现了二十三种不同的病毒，其中几种代表了本研究之前在苜蓿中未报告的新出现的病毒。其中有蛇床子静脉黄化病毒、地衣斑驳病毒和仙人掌X病毒两个毒株，通过从头组装获得了其编码完整基因组序列。结论这些结果提高了我们对感染苜蓿的病毒多样性和宿主范围的了解，为其诊断和表征提供了必要的工具，并证明了转录组数据集在发现新病原体方面的实用性。