Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Xie, Fuliang ^a   Sun, Guiling ^a   Stiller, John W ^a   Zhang, Baohong ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; MICRORNA; PROTEIN KINASE; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; COTTON; EXPRESSED SEQUENCE TAG; GENOME ANALYSIS; GRAPE; INDEL MUTATION; INTERNET; NONHUMAN; PLANT DEVELOPMENT; PLANT FIBER; PLANT GENE; PLANT GENOME; PLANT METABOLISM; PLANT STRESS; PREDICTION; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; CONTIG MAPPING; GENETIC ASSOCIATION; GENETIC DATABASE; GENETICS; GENOMICS; GOSSYPIUM; METHODOLOGY; MUTATION;

GOSSYPIUM HIRSUTUM; VITACEAE;

CONTIG MAPPING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GOSSYPIUM; INTERNET; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSCRIPTOME;

EID: 80555154263     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026980     Document Type: Article

References (45)

1. IAC (1996) Cotton: Review of World Situation, Monogram by International Advisory Committee. Washington, D.C.
2. Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, et al. (2007) Identification of cotton microRNAs and their targets. Gene 397: 26-37.
3. Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang T, et al. (2007) Toward sequencing cotton (Gossypium) genomes. Plant Physiol 145: 1303-1310.
4. Hendrix B, Stewart JM, (2005) Estimation of the nuclear DNA content of gossypium species. Ann Bot 95: 789-797.
5. Seki M, Hayashida N, Kato N, Yohda M, Shinozaki K, (1997) Rapid construction of a transcription map for a cosmid contig of Arabidopsis thaliana genome using a novel cDNA selection method. Plant J 12: 481-487.
6. Hattori J, Ouellet T, Tinker NA, (2005) Wheat EST sequence assembly facilitates comparison of gene contents among plant species and discovery of novel genes. Genome 48: 197-206.
7. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, et al. (2006) A global assembly of cotton ESTs. Genome Res 16: 441-450.
8. Pearson CE, Sinden RR, (1998) Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA. Curr Opin Struct Biol 8: 321-330.
9. Zeng S, Xiao G, Guo J, Fei Z, Xu Y, et al. (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics 11: 94.
10. Sanchez de la Hoz MP, Davila JA, Loarce Y, Ferrer E, (1996) Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley. Genome 39: 112-117.
11. Varshney RK, Graner A, Sorrells ME, (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55.
12. Bozhko M, Riegel R, Schubert R, Muller-Starck G, (2003) A cyclophilin gene marker confirming geographical differentiation of Norway spruce populations and indicating viability response on excess soil-born salinity. Mol Ecol 12: 3147-3155.
13. Park YH, Alabady MS, Ulloa M, Sickler B, Wilkins TA, et al. (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics 274: 428-441.
14. Wang S, Sha Z, Sonstegard TS, Liu H, Xu P, et al. (2008) Quality assessment parameters for EST-derived SNPs from catfish. BMC Genomics 9: 450.
15. Krawczak M, (1999) Informativity assessment for biallelic single nucleotide polymorphisms. Electrophoresis 20: 1676-1681.
16. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888.
17. Zhang J, Lu Y, Yuan Y, Zhang X, Geng J, et al. (2009) Map-based cloning and characterization of a gene controlling hairiness and seed coat color traits in Brassica rapa. Plant Mol Biol 69: 553-563.
18. Schneider K, Kulosa D, Soerensen TR, Mohring S, Heine M, et al. (2007) Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theor Appl Genet 115: 601-615.
19. Li F, Kitashiba H, Inaba K, Nishio T, (2009) A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits. DNA Res 16: 311-323.
20. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
21. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, et al. (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320: 1185-1190.
22. Voinnet O, (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
23. Zhang B, Pan X, Anderson TA, (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580: 3753-3762.
24. Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, et al. (2007) Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 581: 1464-1474.
25. Wang HC, Moore MJ, Soltis PS, Bell CD, Brockington SF, et al. (2009) Rosid radiation and the rapid rise of angiosperm-dominated forests. Proceedings of the National Academy of Sciences of the United States of America 106: 3853-3858.
26. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, (2008) miRBase: tools for microRNA genomics. Nucleic Acids Research 36: D154-D158.
27. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA, (2006) Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences 63: 246-254.
28. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, et al. (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517-527.
29. Guo HS, Xie Q, Fei JF, Chua NH, (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell 17: 1376-1386.
30. Sunkar R, Kapoor A, Zhu JK, (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18: 2051-2065.
31. Aukerman MJ, Sakai H, (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741.
32. An C, Saha S, Jenkins JN, Ma DP, Scheffler BE, et al. (2008) Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping. Theor Appl Genet 116: 1015-1026.
33. Kantartzi SK, Ulloa M, Sacks E, Stewart JM, (2009) Assessing genetic diversity in Gossypium arboreum L. cultivars using genomic and EST-derived microsatellites. Genetica 136: 141-147.
34. Chen YA, Lin CC, Wang CD, Wu HB, Hwang PI, (2007) An optimized procedure greatly improves EST vector contamination removal. Bmc Genomics 8: 11.
35. Jurka J, (1998) Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 8: 333-337.
36. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
37. Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
38. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
39. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29.
40. Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 28: 27-30.
41. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA, (2006) Conservation and divergence of plant microRNA genes. Plant J 46: 243-259.
42. Venne LS, Anderson TA, Zhang B, Smith LM, McMurry ST, (2008) Organochlorine pesticide concentrations in sediment and amphibian tissue in playa wetlands in the Southern High Plains, USA. Bulletin of Environmental Contamination and Toxicology 80: 497-501.
43. Xie F, Frazier TP, Zhang B, (2010) Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232: 417-434.
44. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA, (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Research 15: 336-360.
45. Rychlik W, (1995) Selection of primers for polymerase chain reaction. Mol Biotechnol 3: 129-134.