High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families.
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families.
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DOI：
10.1186/1471-2164-9-593
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发表时间：
2008-12-09
期刊：
影响因子：
4.4
通讯作者：
Dalmay T
中科院分区：
文献类型：
--
作者：
Szittya G;Moxon S;Santos DM;Jing R;Fevereiro MP;Moulton V;Dalmay T
高通量测序技术能够在植物物种中鉴定新的短RNA。我们使用Solexa测序在一种模式豆科植物中发现了新的microRNA，即桶形苜蓿（Medicago truncatula）。从两个单独的短RNA文库获得3，948，871个读段，所述两个单独的短RNA文库由从M. truncatula叶，代表1，563，959个不同的序列。将2，168，937个读段映射到可用的M. truncatula基因组对应于619，175个不同序列。代表25个保守miRNA家族的174，504个读段显示与已知miRNA完全匹配。我们还鉴定了26种可能由32个基因座产生的新型miRNA候选物。这些基因座中的9个产生了8个不同的序列，其中的miRNA* 序列也进行了测序。这些序列在其他植物物种中没有描述，并且通过北方印迹分析证实了这八种新的miRNAs的积累。预测了大多数保守和新的miRNAs的潜在靶基因。对M.蒺藜叶鉴定出8个新的miRNAs，表明豆科植物中存在特异性miRNAs。
High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatula). 3,948,871 reads were obtained from two separate short RNA libraries generated from total RNA extracted from M. truncatula leaves, representing 1,563,959 distinct sequences. 2,168,937 reads were mapped to the available M. truncatula genome corresponding to 619,175 distinct sequences. 174,504 reads representing 25 conserved miRNA families showed perfect matches to known miRNAs. We also identified 26 novel miRNA candidates that were potentially generated from 32 loci. Nine of these loci produced eight distinct sequences, for which the miRNA* sequences were also sequenced. These sequences were not described in other plant species and accumulation of these eight novel miRNAs was confirmed by Northern blot analysis. Potential target genes were predicted for most conserved and novel miRNAs. Deep sequencing of short RNAs from M. truncatula leaves identified eight new miRNAs indicating that specific miRNAs exist in legume species.
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