中国热带农业科学院机构知识库

RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo for Subsequent Functional Genomics Approaches

收藏
分享
全文链接

文献类型：外文期刊

作者： Fan, Haikuo ¹ ; Xiao, Yong ² ; Yang, Yaodong ² ; Xia, Wei ² ; Mason, Annaliese S. ⁴ ; Xia, Zhihui ⁶ ; Qiao, Fei ³ ; Zhao, ¹ ;

作者机构： 1.Sichuan Agr Univ, Coll Hort, Yaan, Sichuang Provin, Peoples R China

2.Chinese Acad Trop Agr Sci, Hainan Key Lab Trop Oil Crops Biol, Coconut Res Inst, Wenchang, Hainan, Peoples R China

3.Chinese Acad Trop Agr Sci, Trop Corps Genet Resources Inst, Key Lab Crop Gene Resources & Germplasm Enhanceme, Danzhou, Hainan Province, Peoples R China

4.Univ Queensland, Sch Agr & Food Sci, Brisbane, Qld, Australia

5.Univ Queensland, Ctr Integrat Legume Res, Brisbane, Qld, Australia

6.Hainan Univ, Coll Agr

期刊名称：PLOS ONE （影响因子：3.24；五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2013 年 8 卷 3 期

页码：

收录情况： SCI

摘要： Background: 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. Methodology/Principal Findings: 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. Conclusions/Significance: 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.

相关文献

作者其他论文更多>>

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

作者：Li, Jing;Guo, Shukuan;Min Htwe, Yin;Sun, Xiwei;Zhou, Lixia;Wang, Fangyuan;Zeng, Chunru;Chen, Shuangyan;Iqbal, Amjad;Yang, Yaodong;Chen, Shuangyan;Iqbal, Amjad

关键词：MYBs; genome-wide analysis; color; RNA-seq; qPCR; coconut
Molecular cloning, expression profiles, characterization and function of a novel arginine decarboxylase gene (HbADC2) in Hevea brasiliensis

作者：Deng, Zhi;Hou, Lanfei;Dai, Longjun;Li, Dejun;Deng, Zhi;Hou, Lanfei;Dai, Longjun;Li, Dejun;Deng, Zhi;Deng, Zhi;Hou, Lanfei;Dai, Longjun;Li, Dejun;Hou, Lanfei;Men, Zhonghua;Xia, Zhihui;Li, Yao;Li, Dejun

关键词：Arginine decarboxylase (ADC); Rubber tree; Polyamine; MV-induced oxidative stress; Putrescine (Put)
Integrated transcriptomics and metabolomics analyses of the effects of bagging treatment on carotenoid biosynthesis and regulation of Areca catechu L.

作者：Zheng, Xin;Huang, Liyun;Fan, Benyi;Peng, Chunlin;Iqbal, Amjad;Zhang, Yujie;Ye, Jianqiu;Yang, Yaodong;Zheng, Xin;Fan, Benyi;Iqbal, Amjad;Chen, Hongman

关键词：Areca catechu L.; bagging; carotenoid; metabolomics; transcriptomics
Integrated transcriptomic and metabolomic data reveal the cold stress responses molecular mechanisms of two coconut varieties

作者：Li, Jing;Wang, Fangyuan;Sayed, Md. Abu;Shen, Xiaojun;Zhou, Lixia;Liu, Xiaomei;Sun, Xiwei;Chen, Shuangyan;Wu, Yi;Lu, Lilan;Gong, Shufang;Iqbal, Amjad;Yang, Yaodong;Chen, Shuangyan;Iqbal, Amjad

关键词：coconut; varieties; cold stress; transcriptome; metabolome
Widely targeted metabolomics combined with E-tongue and E-nose reveal dynamic changes of tender coconut water in responses to the infection of Ceratocystis paradoxa

作者：Shen, Xiaojun;Niu, Xiaoqing;Yang, Yaodong;Yang, Dejie;Li, Jing;Yu, Fengyu;Sun, Xiwei;Meng, Xiuli;Niu, Xiaoqing;Yang, Dejie;Yu, Fengyu;Meng, Xiuli

关键词：Cocos nucifera L.; Postharvest disease; Liquid endosperm; Flavor; Electronic sensing evaluation
Comparative Transcriptome Analysis Provides Insights into the Effect of Epicuticular Wax Accumulation on Salt Stress in Coconuts

作者：Sun, Xiwei;Feng, Yalan;Zhong, Yazhu;Dou, Yajing;Kaleri, Ghulam Abid;Mu, Zhihua;Yang, Zhuang;Xu, Hang;Zhou, Junjie;Luo, Jie;Xiao, Yong

关键词：coconut; transcriptome; salt tolerance
Bark transcriptome analyses reveals molecular mechanisms involved in tapping panel dryness occurrence and development in rubber tree (Hevea brasiliensis)

作者：Yue, Yifan;Deng, Zhi;Wang, Difei;Li, Dejun;Wang, Xuncheng;Xia, Zhihui;Li, Yao;Yin, Han;Yue, Yifan;Wang, Difei;Li, Dejun

关键词：Tapping panel dryness (TPD); Hevea brasiliensis; Molecular mechanisms; Transcriptome analyses; TPD-related genes

RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo for Subsequent Functional Genomics Approaches

作者其他论文更多>>

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Molecular cloning, expression profiles, characterization and function of a novel arginine decarboxylase gene (HbADC2) in Hevea brasiliensis

Integrated transcriptomics and metabolomics analyses of the effects of bagging treatment on carotenoid biosynthesis and regulation of Areca catechu L.

Integrated transcriptomic and metabolomic data reveal the cold stress responses molecular mechanisms of two coconut varieties

Widely targeted metabolomics combined with E-tongue and E-nose reveal dynamic changes of tender coconut water in responses to the infection of Ceratocystis paradoxa

Comparative Transcriptome Analysis Provides Insights into the Effect of Epicuticular Wax Accumulation on Salt Stress in Coconuts

Bark transcriptome analyses reveals molecular mechanisms involved in tapping panel dryness occurrence and development in rubber tree (Hevea brasiliensis)

意见箱

RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo for Subsequent Functional Genomics Approaches

作者其他论文 更多>>

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Molecular cloning, expression profiles, characterization and function of a novel arginine decarboxylase gene (HbADC2) in Hevea brasiliensis

Integrated transcriptomics and metabolomics analyses of the effects of bagging treatment on carotenoid biosynthesis and regulation of Areca catechu L.

Integrated transcriptomic and metabolomic data reveal the cold stress responses molecular mechanisms of two coconut varieties

Widely targeted metabolomics combined with E-tongue and E-nose reveal dynamic changes of tender coconut water in responses to the infection of Ceratocystis paradoxa

Comparative Transcriptome Analysis Provides Insights into the Effect of Epicuticular Wax Accumulation on Salt Stress in Coconuts

Bark transcriptome analyses reveals molecular mechanisms involved in tapping panel dryness occurrence and development in rubber tree (Hevea brasiliensis)

意 见 箱

作者其他论文更多>>

意见箱