Department of Plant Pathology, University of Florida, Gainesville, FL, USA.
Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
Sci Rep. 2020 Jul 21;10(1):12043. doi: 10.1038/s41598-020-68654-3.
A growing number of metagenomics-based approaches have been used for the discovery of viruses in insects, cultivated plants, and water in agricultural production systems. In this study, sixteen blueberry root transcriptomes from eight clonally propagated blueberry plants of cultivar 'Emerald' (interspecific hybrid of Vaccinium corymbosum and V. darrowi) generated as part of a separate study on varietal tolerance to soil salinity were analyzed for plant viral sequences. The objective was to determine if the asymptomatic plants harbored the latent blueberry red ringspot virus (BRRV) in their roots. The only currently known mechanism of transmission of BRRV is through vegetative propagation; however, the virus can remain latent for years with some plants of 'Emerald' never developing red ringspot symptoms. Bioinformatic analyses of 'Emerald' transcriptomes using de novo assembly and reference-based mapping approaches yielded eight complete viral genomes of BRRV (genus Soymovirus, family Caulimoviridae). Validation in vitro by PCR confirmed the presence of BRRV in 100% of the 'Emerald' root samples. Sequence and phylogenetic analyses showed 94% to 97% nucleotide identity between BRRV genomes from Florida and sequences from Czech Republic, Japan, Poland, Slovenia, and the United States. Taken together, this study documented the first detection of a complete BRRV genome from roots of asymptomatic blueberry plants and in Florida through in silico analysis of plant transcriptomes.
越来越多的基于宏基因组学的方法被用于在昆虫、栽培植物和农业生产系统中的水中发现病毒。在这项研究中，分析了 16 个蓝莓根转录组，这些转录组来自 8 株经无性繁殖的‘Emerald’蓝莓植株（Vaccinium corymbosum 和 V. darrowi 的种间杂种），这是一项关于品种对土壤盐度耐受性的单独研究的一部分。目的是确定无症状植株的根中是否潜伏着蓝莓红环斑病毒（BRRV）。BRRV 目前已知的唯一传播机制是通过营养繁殖；然而，该病毒可以潜伏多年，一些‘Emerald’植株从未出现红环斑症状。使用从头组装和基于参考的映射方法对‘Emerald’转录组进行生物信息学分析，得到了 8 个完整的 BRRV 病毒基因组（属 Soymovirus，家族 Caulimoviridae）。体外 PCR 验证证实了 100%的‘Emerald’根样本中存在 BRRV。序列和系统发育分析显示，来自佛罗里达州和来自捷克共和国、日本、波兰、斯洛文尼亚和美国的 BRRV 基因组之间的核苷酸同一性为 94%至 97%。总之，这项研究通过对植物转录组的计算机分析，首次从无症状蓝莓植株的根中以及从佛罗里达州检测到了完整的 BRRV 基因组。
