Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach.
Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach.
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DOI：
10.1186/s12985-015-0332-2
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发表时间：
2015-07-07
期刊：
影响因子：
4.8
通讯作者：
Zhou X
中科院分区：
文献类型：
--
作者：
Su X;Fu S;Qian Y;Xu Y;Zhou X
下一代测序技术的出现使植物病毒的发现取得了重大进展，特别是在隐性病毒和以前未描述的病毒的鉴定方面。柑橘柠檬 Burm。 f. (C. limon) 是一种原产于亚洲的常绿小乔木，并且。中国是世界上最大的柠檬生产国。在这项工作中，柠檬样本是从中国西南部采集的，那里爆发了一场未知的疾病，给柠檬生产行业造成了巨大损失。利用高通量焦磷酸测序和小 RNA 的组装，我们发现柠檬叶样本中存在啤酒花矮化类病毒 (HSVd)。其中大部分是柠檬生产的主要农业品种啤酒花矮化类病毒衍生的siRNA (HSVd-siRNA)。柠檬的长度为21个核苷酸，来自正基因组RNA链的HSVd-siRNA的数量与来自互补链的HSVd-siRNA的数量几乎相等。观察到 HSVd-siRNA 偏向于以 5'-鸟嘌呤开头的序列。此外，热点分析表明大量的HSVd-siRNA源自HSVd基因组的中心域和变异域。我们的结果表明柠檬柠檬可以对啤酒花矮化类病毒建立小RNA介导的基因沉默反应。有趣的是，基于生物信息学分析，我们的结果还表明来自中央和变异域的大量HSVd-siRNA可能参与干扰宿主基因表达并影响症状发展。
The advent of next generation sequencing technology has allowed for significant advances in plant virus discovery, particularly for identification of covert viruses and previously undescribed viruses. The Citrus limon Burm. f. (C. limon) is a small evergreen tree native to Asia, and . China is the world’s top lemon-producing nation. In this work, lemon samples were collected from southwestern of China, where an unknown disease outbreak had caused huge losses in the lemon production industry. Using high-throughput pyrosequencing and the assembly of small RNAs, we showed that the Hop stunt viroid (HSVd) was present in C. limon leaf sample. The majority of it is a main lemon producing agricultural cultivarHop stunt viroid derived siRNAs (HSVd-siRNAs) in C. limon were 21 nucleotides in length, and nearly equal amount of HSVd-siRNAs originated from the plus-genomic RNA strand as from the complementary strand. A bias of HSVd-siRNAs toward sequences beginning with a 5′-Guanine was observed. Furthermore, hotspot analysis showed that a large amount of HSVd-siRNAs derived from the central and variant domains of the HSVd genome. Our results suggest that C. limon could set up a small RNA-mediated gene silencing response to Hop stunt viroid, Interestingly, based on bioinformatics analysis, our results also suggest that the large amounts of HSVd-siRNAs from central and variant domains might be involved in interference with host gene expression and affect symptom development.
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发表时间：
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期刊：
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