Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation.
Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation.
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大豆 microRNA 及其靶标的全基因组鉴定揭示了它们的器官特异性和对磷酸盐饥饿的反应
DOI：
10.1186/1471-2164-14-66
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发表时间：
2013-01-31
期刊：
影响因子：
4.4
通讯作者：
Liao H
中科院分区：
文献类型：
--
作者：
Xu F;Liu Q;Chen L;Kuang J;Walk T;Wang J;Liao H
磷(P)在植物生长发育中起着重要作用。已经在拟南芥和水稻中发现了参与磷信号传导的microrna，但对大豆叶片和根系中磷响应的microrna及其靶点知之甚少。结果利用高通量合成测序（SBS）技术，在全基因组水平上分别对磷（Pi）充足（+Pi）和缺磷（-Pi）条件下生长的叶片和根中的4个小RNA文库和缺磷（-Pi）条件下生长的1个RNA降解文库进行了测序。每个文库生成了~ 2145 ~ 2863万个短序列，产生了~ 2056 ~ 2708万干净读取。从这些序列中，计算预测了总共126个mirna，其中包含154个基因靶点。这包括92个新的候选miRNA，具有20-23个核苷酸，与glycine maxgenome 1.0完全匹配，其中70个属于21个miRNA家族，其余22个miRNA未分配到miRBase 18.0中任何现有的miRNA家族。在+Pi和-Pi条件下，126个mirna中有112个（89%）在叶片和根中均有表达。在+Pi条件下，检测到12个叶片特异性mirna和2个根特异性mirna；而在- pi条件下，鉴定出10个叶片特异性mirna和4个根特异性mirna。结果表明，Pi饥饿诱导了25个mirna，抑制了11个mirna。然后，茎环实时PCR证实了四个选定的p响应miRNAs的表达，RLM-5 ' RACE证实了PHO2和GmPT5（一个含有kelch结构域的蛋白）和Myb转录因子分别是miR399、miR2111和miR159e-3p的靶标。最后，在全基因组范围内分析了大豆miRNA基因启动子区域的p响应元件。结论大豆叶片和根系特异性mirna以及p响应性mirna在全基因组范围内得到了鉴定。通过降解组测序和计算分析，共预测了154个mirna靶基因。确定了miR399、miR2111和miR159e-3p的靶点。综上所述，我们的研究揭示了mirna在P信号传导中的重要作用，并为解读大豆中microRNA/靶模块的功能提供了线索。
BackgroundPhosphorus (P) plays important roles in plant growth and development. MicroRNAs involved in P signaling have been identified in Arabidopsis and rice, but P-responsive microRNAs and their targets in soybean leaves and roots are poorly understood.ResultsUsing high-throughput sequencing-by-synthesis (SBS) technology, we sequenced four small RNA libraries from leaves and roots grown under phosphate (Pi)-sufficient (+Pi) and Pi-depleted (-Pi) conditions, respectively, and one RNA degradome library from Pi-depleted roots at the genome-wide level. Each library generated ∼21.45−28.63 million short sequences, resulting in ∼20.56−27.08 million clean reads. From those sequences, a total of 126 miRNAs, with 154 gene targets were computationally predicted. This included 92 new miRNA candidates with 20-23 nucleotides that were perfectly matched to theGlycine maxgenome 1.0, 70 of which belong to 21 miRNA families and the remaining 22 miRNA unassigned into any existing miRNA family in miRBase 18.0. Under both +Pi and -Pi conditions, 112 of 126 total miRNAs (89%) were expressed in both leaves and roots. Under +Pi conditions, 12 leaf- and 2 root-specific miRNAs were detected; while under -Pi conditions, 10 leaf- and 4 root-specific miRNAs were identified. Collectively, 25 miRNAs were induced and 11 miRNAs were repressed by Pi starvation in soybean. Then, stem-loop real-time PCR confirmed expression of four selected P-responsive miRNAs, and RLM-5’ RACE confirmed that a PHO2 and GmPT5, a kelch-domain containing protein, and a Myb transcription factor, respectively are targets of miR399, miR2111, and miR159e-3p. Finally, P-responsivecis-elements in the promoter regions of soybean miRNA genes were analyzed at the genome-wide scale.ConclusionsLeaf- and root-specific miRNAs, and P-responsive miRNAs in soybean were identified genome-wide. A total of 154 target genes of miRNAs were predicted via degradome sequencing and computational analyses. The targets of miR399, miR2111, and miR159e-3p were confirmed. Taken together, our study implies the important roles of miRNAs in P signaling and provides clues for deciphering the functions for microRNA/target modules in soybean.
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影响因子：
14.9
作者：
Chen C;Ridzon DA;Broomer AJ;Zhou Z;Lee DH;Nguyen JT;Barbisin M;Xu NL;Mahuvakar VR;Andersen MR;Lao KQ;Livak KJ;Guegler KJ
通讯作者：
Guegler KJ
影响因子：
2.9
作者：
Kulcheski, Franceli Rodrigues;Marcelino-Guimaraes, Francismar Correa;Margis, Rogerio
通讯作者：
Margis, Rogerio
影响因子：
9.2
作者：
Addo-Quaye, Charles;Eshoo, Tifani W.;Axtell, Michael J.
通讯作者：
Axtell, Michael J.
影响因子：
11.6
作者：
Lelandais-Briere, Christine;Naya, Loreto;Crespi, Martin
通讯作者：
Crespi, Martin
影响因子：
5.8
作者：
Addo-Quaye, Charles;Miller, Webb;Axtell, Michael J.
通讯作者：
Axtell, Michael J.