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

Fan, Haikuo, Xiao, Yong, Yang, Yaodong, Xia, Wei, Mason, Annaliese S., Xia, Zhihui, Qiao, Fei, Zhao, Songlin and Tang, Haoru (2013) RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo for Subsequent Functional Genomics Approaches. PLoS One, 8 3: e59997.1-e59997.10. doi:10.1371/journal.pone.0059997

Author Fan, Haikuo
Xiao, Yong
Yang, Yaodong
Xia, Wei
Mason, Annaliese S.
Xia, Zhihui
Qiao, Fei
Zhao, Songlin
Tang, Haoru
Title RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo for Subsequent Functional Genomics Approaches
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2013-03
Year available 2013
Sub-type Article (original research)
DOI 10.1371/journal.pone.0059997
Open Access Status DOI
Volume 8
Issue 3
Start page e59997.1
End page e59997.10
Total pages 10
Place of publication San Francisco, CA United States
Publisher Public Library of Science
Collection year 2014
Language eng
Formatted abstract
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.
Keyword Kyoto Encyclopedia
Noncoding Rna
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Agriculture and Food Sciences
Official 2014 Collection
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Citation counts: TR Web of Science Citation Count  Cited 27 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 28 times in Scopus Article | Citations
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Created: Sun, 26 May 2013, 00:38:53 EST by System User on behalf of School of Agriculture and Food Sciences