CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, Saint-Pierre, 97410, France.
Sci Rep. 2019 Sep 3;9(1):12716. doi: 10.1038/s41598-019-49134-9.
Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.
主要在非洲及其周边岛屿发现，非洲条纹病毒（AfSV）代表了已知最多的马斯特罗病毒群。在已知感染栽培或野生禾本科植物物种的 13 种 AfSV 物种中，有 6 种已在留尼汪岛被发现。为了更好地描述该岛的 AfSV 多样性，我们使用了一种新的基于宏基因组学的方法，对一个小的农业生态系统进行了调查，该方法涉及滚环扩增与随机 PCR 扩增标记（RCA-RA-PCR）、高通量测序（Illumina HiSeq）以及使用系统发育定位对马斯特罗病毒读段进行分类。发现了可能属于三个新物种的马斯特罗病毒，并通过 Sanger 测序确定了这些病毒的全基因组序列。本研究中应用的专注于双生病毒的宏基因组学方法在检测已知和新型马斯特罗病毒方面都非常有用。研究结果证实，留尼汪岛确实是 AfSV 多样性的热点地区，而且许多马斯特罗病毒物种可能已经多次被引入。在其他自然和农业环境中应用类似的方法，应该可以详细了解双生病毒群落的组成和多样性，从而推动我们对这一重要病毒群的生态学和进化历史的理解取得重大进展。
