title: Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database.
abstract: A total of 28,432 unique contigs (25,371 in consensus contigs and 3,061 as singletons) were assembled from all 268,786 cotton ESTs currently available. Several in silico approaches [comparative genomics, Blast, Gene Ontology (GO) analysis, and pathway enrichment by Kyoto Encyclopedia of Genes and Genomes (KEGG)] were employed to investigate global functions of the cotton transcriptome. Cotton EST contigs were clustered into 5,461 groups with a maximum cluster size of 196 members. A total of 27,956 indel mutants and 149,616 single nucleotide polymorphisms (SNPs) were identified from consensus contigs. Interestingly, many contigs with significantly high frequencies of indels or SNPs encode transcription factors and protein kinases. In a comparison with six model plant species, cotton ESTs show the highest overall similarity to grape. A total of 87 cotton miRNAs were identified; 59 of these have not been reported previously from experimental or bioinformatics investigations. We also predicted 3,260 genes as miRNAs targets, which are associated with multiple biological functions, including stress response, metabolism, hormone signal transduction and fiber development. We identified 151 and 4,214 EST-simple sequence repeats (SSRs) from contigs and raw ESTs respectively. To make these data widely available, and to facilitate access to EST-related genetic information, we integrated our results into a comprehensive, fully downloadable web-based cotton EST database (www.leonxie.com).
authors.affiliation: Department of Biology, East Carolina University, Greenville, North Carolina, United States of America.
authors.forename: Fuliang
authors.initials: F
authors.lastname: Xie
authors.forename: Guiling
authors.initials: G
authors.lastname: Sun
authors.forename: John W
authors.initials: JW
authors.lastname: Stiller
authors.forename: Baohong
authors.initials: B
authors.lastname: Zhang
mesh_terms: D020451:Contig Mapping; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D003368:Gossypium / Q000235:genetics*; D020407:Internet; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome / Q000235:genetics*
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3853-8
references.pmid: 19223592
references.citation: BMC Genomics. 2007 Nov 13;8:416
references.pmid: 17997864
references.citation: Cell. 2009 Feb 20;136(4):669-87
references.pmid: 19239888
references.citation: Bull Environ Contam Toxicol. 2008 Jun;80(6):497-501
references.pmid: 18498007
references.citation: Electrophoresis. 1999 Jun;20(8):1676-81
references.pmid: 10435431
references.citation: Bioinformatics. 2003 Mar 22;19(5):651-2
references.pmid: 12651724
references.citation: Curr Opin Struct Biol. 1998 Jun;8(3):321-30
references.pmid: 9666328
references.citation: Plant J. 1997 Aug;12(2):481-7
references.pmid: 9301097
references.citation: Mol Genet Genomics. 2005 Nov;274(4):428-41
references.pmid: 16187061
references.citation: Trends Biotechnol. 2005 Jan;23(1):48-55
references.pmid: 15629858
references.citation: Plant J. 2006 Apr;46(2):243-59
references.pmid: 16623887
references.citation: Genome. 1996 Feb;39(1):112-7
references.pmid: 8851800
references.citation: Science. 2008 May 30;320(5880):1185-90
references.pmid: 18483398
references.citation: Plant Mol Biol. 2009 Mar;69(5):553-63
references.pmid: 19039665
references.citation: Gene. 2007 Aug 1;397(1-2):26-37
references.pmid: 17574351
references.citation: Genome Res. 1999 Sep;9(9):868-77
references.pmid: 10508846
references.citation: PLoS Genet. 2010 Apr 01;6(4):e1000888
references.pmid: 20369019
references.citation: Theor Appl Genet. 2007 Sep;115(5):601-15
references.pmid: 17622508
references.citation: Plant Cell. 2005 May;17(5):1376-86
references.pmid: 15829603
references.citation: Cell Mol Life Sci. 2006 Jan;63(2):246-54
references.pmid: 16395542
references.citation: Plant Physiol. 2007 Dec;145(4):1303-10
references.pmid: 18056866
references.citation: Plant Cell. 2006 Aug;18(8):2051-65
references.pmid: 16861386
references.citation: Ann Bot. 2005 Apr;95(5):789-97
references.pmid: 15701660
references.citation: Mol Biotechnol. 1995 Apr;3(2):129-34
references.pmid: 7620973
references.citation: BMC Genomics. 2010 Feb 08;11:94
references.pmid: 20141623
references.citation: BMC Genomics. 2008 Sep 30;9:450
references.pmid: 18826589
references.citation: FEBS Lett. 2007 Apr 3;581(7):1464-74
references.pmid: 17367786
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Plant Cell. 2003 Nov;15(11):2730-41
references.pmid: 14555699
references.citation: Genome Res. 2006 Mar;16(3):441-50
references.pmid: 16478941
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
references.pmid: 17991681
references.citation: Planta. 2010 Jul;232(2):417-34
references.pmid: 20461402
references.citation: Theor Appl Genet. 2008 May;116(7):1015-26
references.pmid: 18338155
references.citation: Mol Ecol. 2003 Nov;12(11):3147-55
references.pmid: 14629393
references.citation: FEBS Lett. 2006 Jun 26;580(15):3753-62
references.pmid: 16780841
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Cell Res. 2005 May;15(5):336-60
references.pmid: 15916721
references.citation: Genetica. 2009 May;136(1):141-7
references.pmid: 18853261
references.citation: DNA Res. 2009 Dec;16(6):311-23
references.pmid: 19884167
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):27-30
references.pmid: 10592173
references.citation: Curr Opin Struct Biol. 1998 Jun;8(3):333-7
references.pmid: 9666329
references.citation: Cell. 2004 Jan 23;116(2):281-97
references.pmid: 14744438
references.citation: Genome. 2005 Apr;48(2):197-206
references.pmid: 15838541
references.citation: Dev Cell. 2005 Apr;8(4):517-27
references.pmid: 15809034