title: RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: College of Horticulture, Sichuan Agricultural University, Ya'an, Sichuang province, P.R. China.
authors.forename: Haikuo
authors.initials: H
authors.lastname: Fan
authors.forename: Yong
authors.initials: Y
authors.lastname: Xiao
authors.forename: Yaodong
authors.initials: Y
authors.lastname: Yang
authors.forename: Wei
authors.initials: W
authors.lastname: Xia
authors.forename: Annaliese S
authors.initials: AS
authors.lastname: Mason
authors.forename: Zhihui
authors.initials: Z
authors.lastname: Xia
authors.forename: Fei
authors.initials: F
authors.lastname: Qiao
authors.forename: Songlin
authors.initials: S
authors.lastname: Zhao
authors.forename: Haoru
authors.initials: H
authors.lastname: Tang
mesh_terms: D003059:Cocos / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018076:DNA, Complementary
references.citation: Genome Res. 2009 Dec;19(12):2324-33
references.pmid: 19767417
references.citation: PLoS One. 2012;7(5):e36940
references.pmid: 22615851
references.citation: Bioinformatics. 2009 Aug 1;25(15):1966-7
references.pmid: 19497933
references.citation: Nature. 2009 Jan 22;457(7228):413-20
references.pmid: 19158787
references.citation: PLoS One. 2012;7(2):e30646
references.pmid: 22347394
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Science. 1991 Jun 21;252(5013):1651-6
references.pmid: 2047873
references.citation: BMC Genomics. 2010 Jun 24;11:400
references.pmid: 20573269
references.citation: Plant Mol Biol. 2011 Oct;77(3):299-308
references.pmid: 21811850
references.citation: Nat Biotechnol. 2011 May 29;29(6):521-7
references.pmid: 21623354
references.citation: Genome Res. 2009 Jun;19(6):1117-23
references.pmid: 19251739
references.citation: Proc Int Conf Intell Syst Mol Biol. 1999;:138-48
references.pmid: 10786296
references.citation: PLoS One. 2012;7(8):e41150
references.pmid: 22905098
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: Science. 2005 Sep 2;309(5740):1527-8
references.pmid: 16141063
references.citation: Nat Biotechnol. 2011 May 15;29(7):644-52
references.pmid: 21572440
references.citation: BMC Genomics. 2012 Jan 13;13:19
references.pmid: 22244270
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references.pmid: 16845012
references.citation: Nature. 2008 Nov 27;456(7221):470-6
references.pmid: 18978772
references.citation: PLoS One. 2011;6(6):e21220
references.pmid: 21731678
references.citation: Genome Biol. 2008;9(12):R175
references.pmid: 19087247
references.citation: Mol Biol Evol. 2009 Dec;26(12):2731-44
references.pmid: 19706727
references.citation: Bioinformatics. 2009 Nov 1;25(21):2872-7
references.pmid: 19528083
references.citation: Nat Rev Genet. 2001 Dec;2(12):919-29
references.pmid: 11733745
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Genome Res. 2010 Feb;20(2):265-72
references.pmid: 20019144
references.citation: Nat Biotechnol. 2010 May;28(5):421-3
references.pmid: 20458303
references.citation: Nat Biotechnol. 2010 May;28(5):503-10
references.pmid: 20436462
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9
references.pmid: 19208812
references.citation: Lipids. 1987 Jun;22(6):417-20
references.pmid: 3112486
references.citation: Bioinformatics. 2012 Apr 15;28(8):1086-92
references.pmid: 22368243
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):27-30
references.pmid: 10592173
references.citation: Nat Protoc. 2009;4(3):333-40
references.pmid: 19229198
references.citation: BMC Genomics. 2005 May 03;6:60
references.pmid: 15869710