Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants.
Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants.
复制标题
分析番茄植株中两种马铃薯纺锤形块茎病毒变种的小 RNA 产生模式。
DOI：
10.1016/j.gdata.2015.08.008
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发表时间：
2015-12
期刊：
影响因子：
--
通讯作者：
Sano T
中科院分区：
文献类型：
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作者：
Adkar-Purushothama CR;Perreault JP;Sano T
为了分析类病毒感染植物后小RNA（sRNA）的产生，用马铃薯纺锤块茎类病毒（PSTVd）变种接种番茄植物（Solanum lycopersicum 品种 Rutgers）。接种后21天后，提取总RNA并使用Illumina HiSeq平台进行深度测序。对原始数据进行质量检查后，对引物进行修剪，仅过滤 21 至 24 nt 长的 sRNA。然后使用标准模式匹配算法将过滤后的 sRNA 群体映射到相应 PSTVd 变体的基因组 (+) 和反基因组 (-) 链。类病毒衍生的 sRNA (vd-sRNA) 分析表明，类病毒容易受到宿主 RNA 沉默机制的影响。与该项目相关的高通量序列数据已存储在基因表达综合 (GEO) 数据库中，登录号为 GSE69225。
In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Solanum lycopersicum cultivar Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of postinoculation, total RNA was extracted and subjected for deep-sequencing using Illumina HiSeq platform. The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data. The filtered sRNA population was then mapped against both the genomic (+) and antigenomic (−) strands of the respective PSTVd variants using standard pattern-matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism. High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.