Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
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DOI：
10.1111/j.0960-7412.2010.04208.x
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发表时间：
2010-06-01
期刊：
影响因子：
7.2
通讯作者：
Burgyan, Jozsef
中科院分区：
文献类型：
--
作者：
Pantaleo, Vitantonio;Szittya, Gyorgy;Burgyan, Jozsef
在植物中，microRNAs(MiRNAs)包括在转录后水平调节基因表达的三类小RNA之一。许多植物miRNAs是保守的，在发育、非生物胁迫反应或病原体反应中发挥作用。然而，一些miRNAs只在某些物种中被发现。在这里，我们使用深度测序、计算和分子方法来识别、分析和描述四个葡萄(Vitis Vinifera)组织中保守和非保守的miRNAs。在所有四种组织中共鉴定出24个保守的miRNA家族，还有26个已知但非保守的miRNAs。除了已知的miRNAs，我们还发现了21个新的葡萄特有的miRNAs及其星形链。我们还表明，几乎所有这些基因都起源于单基因。此外，还描述了另外21个可能的miRNA候选基因。我们发现许多已知的和新的miRNAs具有组织特异性表达。最后，通过对miRNA裂解的mRNAs进行基因组规模的高通量测序，鉴定了112个已知mRNAs的靶mRNAs和44个新的葡萄特异miRNAs的靶mRNAs。
P>In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post-transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep-sequencing, computational and molecular methods to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total of 24 conserved miRNA families were identified in all four tissues, and 26 known but non-conserved miRNAs were also found. In addition to known miRNAs, we also found 21 new grapevine-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNA candidates have been described. We have found that many known and new miRNAs showed tissue-specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.