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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.

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