Identification of a viroid-like RNA in a lychee Transcriptome Shotgun Assembly
Identification of a viroid-like RNA in a lychee Transcriptome Shotgun Assembly
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荔枝转录组霰弹枪组装中类病毒 RNA 的鉴定
DOI：
10.1016/j.virusres.2017.07.012
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发表时间：
2017-08-15
期刊：
影响因子：
5
通讯作者：
Li, Shifang
中科院分区：
文献类型：
--
作者：
Jiang, Jihong;Zhang, Zhixiang;Li, Shifang
在对植物转录组数据进行系统筛选的过程中，在最近的中国荔枝转录组鸟枪组装（TSA）中的四个重叠群中鉴定出一种新的类病毒RNA序列。该序列的部分与Apscavioid属成员中存在的中央保守区（CCR）和末端保守区（TCR）密切相关，这些序列是类病毒分类的重要标准。用两个不同的相邻引物进行RT-PCR，扩增出该病毒样RNA的304个核苷酸的全序列，该病毒样RNA可以折叠成杆状二级结构，这是阳性病毒科中病毒样的典型特征。Northern印迹杂交变性聚丙烯酰胺凝胶电泳（sPAGE）和连续显示存在的环状和线性形式的类病毒样RNA在荔枝叶组织。系统发育分析表明，该RNA与Apscaviroid属已知成员的最大成对序列同一性<62%。田间调查显示，这种类病毒RNA的存在下，在中国收集的大多数荔枝样品，但是，它没有被发现在荔枝种质资源收集，起源于广泛的其他国家的加入。通过农杆菌接种和RNA接种，测试的四种草本宿主和一种木本宿主都不容易感染荔枝类病毒样RNA。拟将该种暂定名为荔枝类病毒样RNA（LVD样RNA）。
In the course of a systematic screen of plant transcriptomic data, the sequence of a novel viroid-like RNA was identified in four contigs in a recent Transcriptome Shotgun Assembly (TSA) from lychee in China. Portions of this sequence are closely related to the central conserved region (CCR) and terminal conserved region (TCR) present in members of the genus Apscaviroid, sequences that are important criteria for viroid classification. RT-PCR with two divergent adjacent primers amplified the full 304 nucleotide sequence of this viroid-like RNA which can be folded into the-rod-like secondary structure that is a typical feature of viroids in the family Pospiviroidae. Northern-blot hybridization following denaturing PAGE and sequential polyacrylamide gel electrophoresis (sPAGE) revealed the presence of both circular and linear forms of the viroid-like RNA in lychee leaf tissue. Phylogenetic analysis indicates that this RNA groups with known members of the genus Apscaviroid with a maximum pairwise sequence identity of < 62%. Field surveys revealed the presence of this viroid-like RNA in most lychee samples collected in China; however, it was not found in the accessions in a germplasm collection of lychees that originated from a wide range of other countries. None of the four herbaceous hosts and one woody host tested were susceptible to infection with the lychee viroid-like RNA via agroinoculation and RNA inoculation. The provisional name lychee viroid-like RNA (LVd-like RNA) is proposed for this tentative new species in the genus Apscaviroid.