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黄瓜绿斑驳花叶病毒全球分离物的基因组和系统进化分析及高灵敏度 RT-qPCR 检测方法的验证。

Genome and Phylogenetic Analysis of Cucumber Green Mottle Mosaic Virus Global Isolates and Validation of a Highly Sensitive RT-qPCR Assay.

机构信息

Department of Plant Pathology, University of California, Davis, CA 95616.

California Department of Food and Agriculture, Sacramento, CA 95832.

出版信息

Plant Dis. 2022 Jun;106(6):1713-1722. doi: 10.1094/PDIS-10-21-2263-RE. Epub 2022 May 9.

Abstract

The last two decades have seen exponential growth in the international movement of seeds for annual food crops, from a gross U.S. import value of $349 million in 1999 to $1.05 billion in 2019. This has led to the proportionate growth of seedborne pathogens dispersed with seed stocks. One such viral pathogen is cucumber green mottle mosaic virus (CGMMV), a tobamovirus that infects cucurbit crops such as melon, watermelon, cucumber, pumpkin, and squash. The first CGMMV introduction to California occurred in 2013, with subsequent annual outbreaks or detections since then. Here, we describe the use of next-generation sequencing to characterize the full genomes of 25 CGMMV isolates collected between 2013 and 2020 in California, either from CGMMV field detections or seed lots identified as CGMMV positive. We sequenced an additional 31 CGMMV isolates collected in Europe, Israel, and southeast Asia that were provided by industry collaborators. We also performed an in silico nucleotide database search in GenBank for full genome CGMMV sequences to include in all in silico analyses. Based on conserved regions within the coat protein gene, we then developed a quantitative reverse-transcription PCR assay for the sensitive and specific detection of CGMMV in seed and plant samples. Finally, based on our sequence and phylogenetic analysis, our data support that CGMMV has been introduced multiple times into California.

摘要

在过去的二十年中,年度粮食作物种子的国际流通呈指数级增长,从 1999 年的 3.49 亿美元的进口总值增长到 2019 年的 10.5 亿美元。这导致了与种子库存一起传播的种子携带病原体的相应增长。其中一种病毒病原体是黄瓜绿斑驳花叶病毒(CGMMV),一种感染瓜类作物的烟草花叶病毒,如甜瓜、西瓜、黄瓜、南瓜和葫芦。CGMMV 首次传入加利福尼亚是在 2013 年,此后每年都会发生或检测到疫情。在这里,我们描述了使用下一代测序技术来描述 2013 年至 2020 年间在加利福尼亚州收集的 25 个 CGMMV 分离株的全基因组特征,这些分离株要么是从 CGMMV 田间检测中分离出来的,要么是从被确定为 CGMMV 阳性的种子批中分离出来的。我们还对来自欧洲、以色列和东南亚的 31 个由行业合作伙伴提供的 CGMMV 分离株进行了测序。我们还在 GenBank 中对全基因组 CGMMV 序列进行了核苷酸数据库搜索,以包括所有的计算机分析。根据外壳蛋白基因内的保守区域,我们随后开发了一种用于在种子和植物样本中灵敏和特异性检测 CGMMV 的定量逆转录 PCR 检测方法。最后,根据我们的序列和系统发育分析,我们的数据支持 CGMMV 已经多次传入加利福尼亚。

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