A global assembly of cotton ESTs

Genome Research

Volumn 16, Issue 3, 2006, Pages 441-450

  Udall, Joshua A ^a   Swanson, Jordan M ^a   Haller, Karl ^b   Rapp, Ryan A ^a   Sparks, Michael E ^a   Hatfield, Jamie ^b   Yu, Yeisoo ^b   Wu, Yingru ^c   Dowd, Caitriona ^c   Arpat, Aladdin B ^d   Sickler, Brad A ^d   Wilkins, Thea A ^d   Jin, Ying Guo ^e   Xiao, Ya Chen ^e   Scheffler, Jodi ^f   Taliercio, Earl ^f   Turley, Ricky ^f   McFadden, Helen ^c   Payton, Paxton ^g   Klueva, Natalya ^h   Allen, Randell ^h   Zhang, Deshui ⁱ   Haigler, Candace ⁱ   Wilkerson, Curtis ^j   Suo, Jinfeng ^k   Schulze, Stefan R ^l   Pierce, Margaret L ^m   Essenberg, Margaret ^m   Kim, HyeRan ^b   Llewellyn, Danny J ^c   Dennis, Elizabeth S ^c   Kudrna, David ^b   Wing, Rod ^b   Paterson, Andrew H ^l   Soderlund, Cari ^b   Wendel, Jonathan F ^a   more..

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c CSIRO   (Australia)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^f AGRICULTURAL RESEARCH SERVICE   (United States)

^g AGRICULTURAL RESEARCH SERVICE   (United States)

^h TEXAS TECH UNIVERSITY   (United States)

ⁱ NORTH CAROLINA STATE UNIVERSITY   (United States)

^j MICHIGAN STATE UNIVERSITY   (United States)

^k INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^l UNIVERSITY OF GEORGIA   (United States)

^m OKLAHOMA STATE UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CONTIG; NUCLEOTIDE;

ALLOPOLYPLOIDY; ARTICLE; BIOINFORMATICS; COTTON; DIPLOIDY; DNA LIBRARY; DROUGHT; EXPRESSED SEQUENCE TAG; GENE CONSTRUCT; GENE LIBRARY; GENE SEQUENCE; GENETIC CODE; GENOME; GENOMICS; GOSSYPIUM ARBOREUM; GOSSYPIUM HIRSUTUM; GOSSYPIUM RAIMONDII; NONHUMAN; NUCLEOTIDE SEQUENCE; ORGAN; PATHOGENESIS; PLANT GENETICS; PRIORITY JOURNAL; STRESS; TISSUE; UNINDEXED SEQUENCE;

DIPLOIDY; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENOME, PLANT; GOSSYPIUM; MOLECULAR SEQUENCE DATA; POLYPLOIDY; SEQUENCE ANALYSIS, DNA;

GOSSYPIUM; GOSSYPIUM ARBOREUM; GOSSYPIUM HIRSUTUM; GOSSYPIUM RAIMONDII;

EID: 33644657327     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4602906     Document Type: Article

References (68)

1. Adams, K.L., Cronn, R., Percifield, R., and Wendel, J.F. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. 100: 4649-4654.
2. Adams, K.L., Percifield, R., and Wendel, J.F. 2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217-2226.
3. Alba, R., Fei, Z., Payton, P., Liu, Y., Moore, S.L., Debbie, P., Cohn, J., D'Ascenzo, M., Gordon, J.S., Rose, J.K.C., et al. 2004. ESTs, cDNA microarrays, and gene expression profiling: Tools for dissecting plant physiology and development. Plant J. 39: 697-714.
4. Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. 2004. UniProt: The universal protein knowledgebase. Nucleic Acids Res. 32: D115-D119.
5. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
6. Arpat, A., Waugh, M., Sullivan, J.P., Gonzales, M., Frisch, D., Main, D., Wood, T., Leslie, A., Wing, R., and Wilkins, T. 2004. Functional genomics of cell elongation in developing cotton fibers. Plant Mol. Biol. 54: 911-929.
7. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al. 2000. Gene Ontology: Tool for the unification of biology. Nat. Genet. 25: 25-29.
8. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32: D138-D141.
9. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., and Apweiler, R. 2004. The Gene Ontology Annotation (GOA) database: Sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32: D262-D266.
10. Cedroni, M.L., Cronn, R.D., Adams, K.L., Wilkins, T.A., and Wendel, J.F. 2003. Evolution and expression of MYB genes in diploid and polyploid cotton. Plant Mol. Biol. 51: 313-325.
11. Chou, H.H. and Holmes, M.H. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
12. Chou, H.-H., Hsia, A.-P., Mooney, D.L., and Schnable, P.S. 2004. Picky: Oligo microarray design for large genomes. Bioinformatics 20: 2893-2902.
13. Claverie, J.-M. 1999. Computational methods for the identification of differential and coordinated gene expression. Hum. Mol. Genet. 8: 1821-1832.
14. Close, T.J., Wanamaker, S.I., Caldo, R.A., Turner, S.M., Ashlock, D.A., Dickerson, J.A., Wing, R.A., Muehlbauer, G.J., Kleinhofs, A., and Wise, R.P. 2004. A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol. 134: 960-968.
15. Cronn, R.C., Small, R.L., Haselkorn, T., and Wendel, J.F. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am. J. Bot. 89: 707-725.
16. Dowd, C., Wilson, I.W., and McFadden, H. 2004. Gene expression profile changes in cotton root and hypocotyl tissues in response to infection with Fusarium oxysporum f. sp. vasinfectum. Mol. Plant Microbe Inter. 17: 654-667.
17. Edgar, R.C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
18. Endrizzi, J.E., Turcotte, E.L., and Kohel, R.J. 1985. Genetics, cytology, and evolution of Gossypium. Adv. Genet. 23: 271-375.
19. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
20. Ewing, R.M., Kahla, A.B., Poirot, O., Lopez, F., Audic, S., and Claverie, J.-M. 1999. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9: 950-959.
21. Felsenstein, J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Department of Genome Sciences, University of Washington, Seattle, http://evolution.genetics.washington.edu/phylip.html.
22. Fulton, T.M., Van der Hoeven, R., Eannetta, N.T., and Tanksley, S.D. 2002. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467.
23. Greller, L.D. and Tobin, F.L. 1999. Detecting selective expression of genes and proteins. Genome Res. 9: 282-296.
24. Haigler, C.H., Zhang, D., and Wilkerson, C.G. 2005. Biotechnological improvement of cotton fibre maturity. Physiol. Plant. 124: 285-294.
25. Huang, X. and Madan, A. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877.
26. Hughes, A. and Friedman, R. 2004. Expression patterns of duplicate genes in the developing root in Arabidopsis thaliana. J. Mol. Evol. 60: 247-256.
27. International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. 436: 793-800.
28. Iseli, C., Jongeneel, C.V., and Bucher, P. 1999. ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequence. Proc. Int. Conf. Intell. Syst. Mol. Biol. 138: 48.
29. Ji, S.-J., Lu, Y.-C., Feng, J.-X., Wei, G., Li, J., Shi, Y.-H., Fu, Q., Liu, D., Luo, J.-C., and Zhu, Y.-X. 2003. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. Nucleic Acids. Res. 31: 2534-2543.
30. Jiang, C., Wright, R.J., El-Zik, K.M., and Paterson, A.H. 1998. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc. Natl. Acad. Sci. 95: 4419-4424.
31. Kalyanaraman, A., Aluru, S., Kothari, S., and Brendel, V. 2003. Efficient clustering of large EST data sets on parallel computers. Nucleic Acids Res. 31: 2963-2974.
32. Kawasaki, S., Borchert, C., Deyholos, M., Wang, H., Brazille, S., Kawai, K., Galbraith, D., and Bohnert, H.J. 2001. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13: 889-906.
33. Kim, H.J., William, M.Y., and Triplett, B.A. 2002. A novel expression assay system for fiber-specific promoters in developing cotton fibers. Plant Mol. Biol. Rep. 20: 7-18.
34. Lacape, J.-M., Nguyen, T.-B., Courtois, B., Belot, J.-L., Giband, M., Gourlot, J.-P., Gawryziak, G., Roques, S., and Hau, B. 2005. QTL analysis of cotton fiber quality using multiple Gossypium hirsutum x Gossypium barbadense backcross generations. Crop Sci. 45: 123-140.
35. Lazo, G.R., Chao, S., Hummel, D.D., Edwards, H., Crossman, C.C., Lui, N., Matthews, D.E., Carollo, V.L., Hane, D.L., You, F.M., et al. 2004. Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. Genetics 168: 585-593.
36. Li, X.-B., Cai, L., Cheng, N.-H., and Liu, J.-W. 2002. Molecular characterization of the cotton GhTUB1 gene that is preferentially expressed in fiber. Plant Physiol. 130: 666-674.
37. Lottaz, C., Iseli, C., Jongeneel, C.V., and Bucher, P. 2003. Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 19: ii103-ii112.
38. Meyers, B.C., Galbraith, D.W., Nelson, T., and Agrawal, V. 2004. Methods for transcript profiling in plants. Be fruitful and replicate. Plant Physiol. 135: 637-652.
39. Michalek, W., Weschke, W., Pleissner, K.-P., and Graner, A. 2002. EST analysis in barley defines a unigene set comprising 4,000 genes. Theor. Appl. Genet. 104: 97-103.
40. Mochida, K., Yamazaki, Y., and Ogihara, Y. 2003. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol. Gen. Genomics 270: 371-377.
41. Orford, S.J. and Timmis, J.N. 1998. Specific expression of an expansin gene during elongation of cotton fibers. Biochem. Biophys. Acta 1398: 342-346.
42. Orford, S.J., Carney, T.J., Olenicky, N.S., and Timmis, J.N. 1999. Characterization of a cotton gene expressed late in fibre cell elongation. Theor. Appl. Genet. 98: 757-764.
43. Pavy, N., Laroche, J., Bousquet, J., and Mackay, J. 2005. Large-scale statistical analysis of secondary xylem ESTs in pine. Plant Mol. Biol. 57: 203-224.
44. Rabinowicz, P.D., Citek, R., Budiman, M.A., Numberg, A., Bedell, J.A., Lakey, N., O'Shaughnessy, A.L., Nacimiento, L.U., McCombie, W.R., and Martienssen, R.A. 2005. Differential methylation of genes and repeats in land plants. Genome Res. 15: 1431-1440.
45. Rong, J., Abbey, C., Bowers, J.E., Brubaker, C.L., Chang, C., Chee, P.W., Delmonte, T.A., Ding, X., Garza, J.J., Marler, B.S., et al. 2004. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166: 389-417.
46. Ronning, C.M., Stegalkina, S.S., Ascenzi, R.A., Bougri, O., Hart, A.L., Utterbach, T.R., Vanaken, S.E., Riedmuller, S.B., White, J.A., Cho, J., et al. 2003. Comparative analyses of potato expressed sequence tag libraries. Plant Physiol. 131: 419-429.
47. Schlueter, J.A., Dixon, P., Granger, C., Grant, D., Clark, L., Doyle, J., and Shoemaker, R. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47: 868-876.
48. Senchina, D.S., Alvarez, I., Cronn, R.C., Liu, B., Rong, J., Noyes, R.D., Paterson, A.H., Wing, R.A., Wilkins, T.A., and Wendel, J.F. 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol. Biol. Evol. 20: 633-643.
49. Skovsted, A. 1934. Cytological studies in cotton. II. Two interspecific hybrids between Asiatic and New World cottons. J. Genet. 28: 407-424.
50. Small, R.L. and Wendel, J.F. 2000a. Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae). Mol. Phylo. Evol. 16: 73-84.
51. _. 2000b. Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155: 1913-1926.
52. _. 2002. Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Mol. Biol. Evol. 19: 597-607.
53. Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G.R., Korf, I., Lapp, H., et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12: 1611-1618.
54. Stekel, D.J., Git, Y., and Falciani, F. 2000. The comparison of gene expression from multiple cDNA libraries. Genome Res. 10: 2055-2061.
55. Suo, J., Liang, X., Pu, L., Zhang, Y., and Xue, Y. 2003. Identification of GhMYB109 encoding a R2R3 MYB transcription factor that expressed specifically in fiber initials and elongating fibers of cotton (Gosspyium hirsutum L.). Biochem. Biophys. Acta 1630: 25-34.
56. USDA-FAS. 2005. Cotton: World markets and trade. United States Department of Agriculture Foreign Agricultural Service. FC-07-05, http://www.fas.usda.gov/ cotton/circular/2005/07/CottonWMT.pdf
57. Vettore, A.L., da Silva, F.R., Kemper, E.L., Souza, G.M., da Silva, A.M., Ferro, M.I.T., Henrique-Silva, F., Giglioti, E.A., Lemos, M.V.F., Coutinho, L.L., et al. 2003. Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res. 13: 2725-2735.
58. Wendel, J.F. 1995. Cotton. In Evolution of crop plants (eds. N. Simmonds and J. Smartt), pp. 358-366. Longman, London.
59. Wendel, J.F. and Cronn, R.C. 2003. Polyploidy and the evolutionary history of cotton. Adv. Agronomy 78: 139-186.
60. Whitfield, C.W., Band, M.R., Bonaldo, M.F., Kumar, C.G., Liu, L., Pardinas, J.R., Robertson, H.M., Soares, M.B., and Robinson, G.E. 2002. Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res. 12: 555-566.
61. Wilkins, T.A. and Smart, L.B. 1996. Isolation of RNA from plant tissue. In A laboratory guide to RNA: Isolation, analysis, and synthesis (ed. P.A. Krieg), pp. 21-41. Wiley-Liss, New York.
62. Wisman, E. and Ohlrogge, J. 2000. Arabidopsis microarray service facilities. Plant Physiol. 124: 1468-1471.
63. Wortman, J.R., Haas, B.J., Hannick, L.I., Smith Jr., R.K., Maiti, R., Ronning, C.M., Chan, A.P., Yu, C., Ayele, M., Whitelaw, C.A., et al. 2003. Annotation of the Arabidopsis genome. Plant Physiol. 132: 461-468.
64. Wright, R.J., Thaxton, P.M., El-Zik, K.M., and Paterson, A.H. 1998. D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel avenues for evolution. Genetics 149: 1987-1996.
65. Wu, Y., Llewellyn, D.J., and Dennis, E.S. 2002. A quick and easy method for isolating good-quality RNA from cotton (Gossypium hirsutum L.) tissues. Plant Mol. Biol. Rep. 20: 213-218.
66. Zhang, D., Hrmova, M., Wan, C.-H., Wu, C., Balzen, J., Cai, W., Wang, J., Densmore, L.D., Fincher, G.B., Zhang, H., et al. 2004. Members of a new group of chitinase-like genes are expressed preferentially in cotton cells with secondary walls. Plant Mol. Biol. 54: 353-372.
67. Zhao, G. and Liu, J. 2001. Isolation of a cotton RGP gene: A homolog of reversibly glycosylated polypeptide highly expressed during fiber development. Biochem. Biophys. Acta 1574: 370-374.
68. Zuo, K., Wang, J., Wu, W., Chai, Y., Sun, X., and Tang, K. 2005. Identification and characterization of differentially expressed ESTs of Gossypium barbadense infected by Verticillium dahliae with suppression of subtractive hybridization. Mol. Biol. 39: 191-199.