Genome-wide Functional Analysis of the Cotton Transcriptome by Creating an Integrated EST Database

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2011 Nov 17

PMID 22087239

Citations 54

Authors

Fuliang Xie

Guiling Sun

John W Stiller

Baohong Zhang

Affiliations

Soon will be listed here.

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).

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References

Wang H, Moore M, Soltis P, Bell C, Brockington S, Alexandre R . Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc Natl Acad Sci U S A. 2009; 106(10):3853-8. PMC: 2644257. DOI: 10.1073/pnas.0813376106. View

Chen Y, Lin C, Wang C, Wu H, Hwang P . An optimized procedure greatly improves EST vector contamination removal. BMC Genomics. 2007; 8:416. PMC: 2194723. DOI: 10.1186/1471-2164-8-416. View

Voinnet O . Origin, biogenesis, and activity of plant microRNAs. Cell. 2009; 136(4):669-87. DOI: 10.1016/j.cell.2009.01.046. View

Venne L, Anderson T, Zhang B, Smith L, McMurry S . Organochlorine pesticide concentrations in sediment and amphibian tissue in playa wetlands in the southern high plains, USA. Bull Environ Contam Toxicol. 2008; 80(6):497-501. DOI: 10.1007/s00128-008-9457-y. View

Krawczak M . Informativity assessment for biallelic single nucleotide polymorphisms. Electrophoresis. 1999; 20(8):1676-81. DOI: 10.1002/(SICI)1522-2683(19990101)20:8<1676::AID-ELPS1676>3.0.CO;2-D. View

Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S . TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 2003; 19(5):651-2. DOI: 10.1093/bioinformatics/btg034. View

Pearson C, Sinden R . Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA. Curr Opin Struct Biol. 1998; 8(3):321-30. DOI: 10.1016/s0959-440x(98)80065-1. View

Seki M, Hayashida N, Kato N, Yohda M, Shinozaki K . Rapid construction of a transcription map for a cosmid contig of Arabidopsis thaliana genome using a novel cDNA selection method. Plant J. 1997; 12(2):481-7. DOI: 10.1046/j.1365-313x.1997.12020481.x. View

Park Y, Alabady M, Ulloa M, Sickler B, Wilkins T, Yu J . Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics. 2005; 274(4):428-41. DOI: 10.1007/s00438-005-0037-0. View

10.

Varshney R, Graner A, Sorrells M . Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005; 23(1):48-55. DOI: 10.1016/j.tibtech.2004.11.005. View

11.

Zhang B, Pan X, Cannon C, Cobb G, Anderson T . Conservation and divergence of plant microRNA genes. Plant J. 2006; 46(2):243-59. DOI: 10.1111/j.1365-313X.2006.02697.x. View

12.

Sanchez de la Hoz M, Davila J, Loarce Y, Ferrer E . Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley. Genome. 1996; 39(1):112-7. DOI: 10.1139/g96-015. View

13.

Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Y Yamamoto Y, Sieburth L . Widespread translational inhibition by plant miRNAs and siRNAs. Science. 2008; 320(5880):1185-90. DOI: 10.1126/science.1159151. View

14.

Zhang J, Lu Y, Yuan Y, Zhang X, Geng J, Chen Y . Map-based cloning and characterization of a gene controlling hairiness and seed coat color traits in Brassica rapa. Plant Mol Biol. 2008; 69(5):553-63. DOI: 10.1007/s11103-008-9437-y. View

15.

Zhang B, Wang Q, Wang K, Pan X, Liu F, Guo T . Identification of cotton microRNAs and their targets. Gene. 2007; 397(1-2):26-37. DOI: 10.1016/j.gene.2007.03.020. View

16.

Huang X, Madan A . CAP3: A DNA sequence assembly program. Genome Res. 1999; 9(9):868-77. PMC: 310812. DOI: 10.1101/gr.9.9.868. View

17.

Nicolae D, Gamazon E, Zhang W, Duan S, Dolan M, Cox N . Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 2010; 6(4):e1000888. PMC: 2848547. DOI: 10.1371/journal.pgen.1000888. View

18.

Schneider K, Kulosa D, Rosleff Soerensen T, Mohring S, Heine M, Durstewitz G . Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theor Appl Genet. 2007; 115(5):601-15. DOI: 10.1007/s00122-007-0591-4. View

19.

Guo H, Xie Q, Fei J, Chua N . MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell. 2005; 17(5):1376-86. PMC: 1091761. DOI: 10.1105/tpc.105.030841. View

20.

Zhang B, Pan X, Cox S, Cobb G, Anderson T . Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci. 2006; 63(2):246-54. PMC: 11136112. DOI: 10.1007/s00018-005-5467-7. View