RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
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DOI：
10.1371/journal.pone.0059997
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Tang H
中科院分区：
文献类型：
--
作者：
Fan H;Xiao Y;Yang Y;Xia W;Mason AS;Xia Z;Qiao F;Zhao S;Tang H
椰子（Cocos nucifera）是棕榈科（Arecaceae）的一员，是一种在热带地区种植的具有重要经济价值的木本棕榈。尽管它在农学上具有重要性，但以往的种质评估研究仅仅依赖于形态学和农艺性状。分子生物学技术很少用于椰子遗传资源的评估以及重要农艺和品质性状的改良，这主要是由于缺乏可用的序列信息。
为了给椰子的分子育种和进一步的分子生物学分析提供基础信息，我们应用RNA - seq技术和从头组装，从混合组织样本中获得椰子转录组的全局概况。利用Illumina测序，我们获得了5490万个短读段，并进行从头组装，得到57304个单基因，平均长度为752个碱基对。组装的单基因与已发布的椰子和油棕（Elaeis guineensis）的cDNA序列之间的比对表明，组装的序列质量较高。与已发布的椰子EST序列相比，大约99.9%的单基因是新的。利用BLASTX，68.2%的单基因基于Genbank非冗余（Nr）蛋白质数据库成功注释。然后，利用基因本体论（GO）、直系同源簇（COG）和京都基因与基因组百科全书（KEGG）数据库对注释的单基因进一步分类。
我们的研究为椰子提供了大量新的遗传信息。这些信息将成为椰子进一步分子遗传学研究和育种以及分离和鉴定这一重要热带作物物种中不同生化途径所涉及的功能基因的宝贵资源。
Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.
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影响因子：
12.3
作者：
Denoeud F;Aury JM;Da Silva C;Noel B;Rogier O;Delledonne M;Morgante M;Valle G;Wincker P;Scarpelli C;Jaillon O;Artiguenave F
通讯作者：
Artiguenave F
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
4.4
作者：
Feng C;Chen M;Xu CJ;Bai L;Yin XR;Li X;Allan AC;Ferguson IB;Chen KS
通讯作者：
Chen KS
DOI：
10.1093/bioinformatics/bts094
发表时间：
2012-04-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Schulz MH;Zerbino DR;Vingron M;Birney E
通讯作者：
Birney E
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun