Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing.
Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing.
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DOI：
10.1186/1471-2164-14-30
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发表时间：
2013-01-16
期刊：
影响因子：
4.4
通讯作者：
Montoro P
中科院分区：
文献类型：
--
作者：
Duan C;Argout X;Gébelin V;Summo M;Dufayard JF;Leclercq J;Kuswanhadi;Piyatrakul P;Pirrello J;Rio M;Champion A;Montoro P
橡胶(橡胶树)乳管是天然橡胶的来源。橡胶生产依赖于内源和外源乙烯(乙烯利)。AP2/ERF转录因子，尤其是乙烯反应因子，在植物发育和对生物和非生物胁迫的响应中起着至关重要的作用。本研究利用下一代测序技术对在不同组织中表达的转录产物进行测序，并鉴定橡胶树中的AP2/ERF超家族。利用454测序技术获得了5个组织类型的转录库(叶、树皮、胶乳、胚性组织和根)。所有文库的读物都被汇集和重组，以增加mRNA的长度并产生一个全球文库。根据来自全球文库的AP2保守结构域的氨基酸序列，通过电子分析鉴定了173个AP2/ERF重叠群。142个具有完整AP2结构域的重叠群被分为3个主要家族(20个AP2成员，115个ERF成员分为11个组，4个RAV成员)和3个SOLIST成员。在乳胶中发现59个AP2/ERF转录本。除了已经在植物中描述的microRNA172，还预测了另外11个microRNAs可以抑制橡胶树AP2/ERF转录本。橡胶树具有与其他双子叶植物相似的AP2/ERF基因数量。我们将比对和分类方法应用于来自下一代测序技术的数据，以提供可靠的信息。我们观察到ERF家族的几个特定特征。三名HbSoloist成员在橡胶树上组成一个团体。一些在胶乳中高表达的AP2/ERF基因表明它们在橡胶树中具有特定的功能。对橡胶树AP2/ERF转录本的分析为研究胶乳生产对非生物胁迫和胶乳细胞分化的分子调控提供了基础。
Rubber tree (Hevea brasiliensis) laticifers are the source of natural rubber. Rubber production depends on endogenous and exogenous ethylene (ethephon). AP2/ERF transcription factors, and especially Ethylene-Response Factors, play a crucial role in plant development and response to biotic and abiotic stresses. This study set out to sequence transcript expressed in various tissues using next-generation sequencing and to identify AP2/ERF superfamily in the rubber tree. The 454 sequencing technique was used to produce five tissue-type transcript libraries (leaf, bark, latex, embryogenic tissues and root). Reads from all libraries were pooled and reassembled to improve mRNA lengths and produce a global library. One hundred and seventy-three AP2/ERF contigs were identified by in silico analysis based on the amino acid sequence of the conserved AP2 domain from the global library. The 142 contigs with the full AP2 domain were classified into three main families (20 AP2 members, 115 ERF members divided into 11 groups, and 4 RAV members) and 3 soloist members. Fifty-nine AP2/ERF transcripts were found in latex. Alongside the microRNA172 already described in plants, eleven additional microRNAs were predicted to inhibit Hevea AP2/ERF transcripts. Hevea has a similar number of AP2/ERF genes to that of other dicot species. We adapted the alignment and classification methods to data from next-generation sequencing techniques to provide reliable information. We observed several specific features for the ERF family. Three HbSoloist members form a group in Hevea. Several AP2/ERF genes highly expressed in latex suggest they have a specific function in Hevea. The analysis of AP2/ERF transcripts in Hevea presented here provides the basis for studying the molecular regulation of latex production in response to abiotic stresses and latex cell differentiation.
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影响因子：
14.9
作者：
Dai X;Zhao PX
通讯作者：
Zhao PX
影响因子：
4.4
作者：
Argout, Xavier;Fouet, Olivier;Wincker, Patrick;Gramacho, Karina;Legavre, Thierry;Sabau, Xavier;Risterucci, Ange Marie;Da Silva, Corinne;Cascardo, Julio;Allegre, Mathilde;Kuhn, David;Verica, Joseph;Courtois, Brigitte;Loor, Gaston;Babin, Regis;Sounigo, Olivier;Ducamp, Michel;Guiltinan, Mark J.;Ruiz, Manuel;Alemanno, Laurence;Machado, Regina;Phillips, Wilberth;Schnell, Ray;Gilmour, Martin;Rosenquist, Eric;Butler, David;Maximova, Siela;Lanaud, Claire
通讯作者：
Lanaud, Claire
DOI：
10.1093/bioinformatics/btp024
发表时间：
2009-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gouzy J;Carrere S;Schiex T
通讯作者：
Schiex T
影响因子：
6.9
作者：
Chow, Keng-See;Wan, Kiew-Lian;Yeang, Hoong-Yeet
通讯作者：
Yeang, Hoong-Yeet
影响因子：
6.9
作者：
Chow KS;Mat-Isa MN;Bahari A;Ghazali AK;Alias H;Mohd-Zainuddin Z;Hoh CC;Wan KL
通讯作者：
Wan KL