Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies

Plant Molecular Biology

Volumn 57, Issue 3, 2005, Pages 375-391

  Forment, J ^a   Gadea, J ^a   Huerta, L ^a   Abizanda, L ^a   Agusti, J ^b   Alamar, S ^c   Alos, E ^b   Andres, F ^b   Arribas, R ^a   Beltran, J P ^a   Berbel, A ^a   Blazquez, M A ^a   Brumos, J ^b   Canas, L A ^a   Cercos, M ^b   Colmenero Flores, J M ^b   Conesa, A ^b   Estables, B ^c   Gandia, M ^b   Garcia Martinez, J L ^a   Gimeno, J ^a   Gisbert, A ^a   Gomez, G ^a   Gonzalez Candelas, L ^c   Granell, A ^a   Guerri, J ^b   Lafuente, M T ^c   Madueno, F ^a   Marcos, J F ^c   Marques, M C ^a   Martinez, F ^b   Martinez Godoy, M A ^a   Miralles, S ^a   Moreno, P ^b   Navarro, L ^b   Pallas, V ^a   Perez Amador, M A ^a   Perez Valle, J ^a   Pons, C ^a   Rodrigo, I ^a   Rodriguez, P L ^a   Royo, C ^a   Serrano, R ^a   Soler, G ^b   Tadeo, F ^b   Talon, M ^b   Terol, J ^b   Trenor, M ^a   Vaello, L ^a   Vicente, O ^a   Vidal, Ch ^a   Zacarias, L ^c   Conejero, V ^a   more..

^a Universidad Politécnica de Valencia   (Spain)

^b INSTITUTO VALENCIANO DE INVESTIGACIONES AGRARIAS IVIA   (Spain)

^c INSTITUTO DE AGROQUÍMICA Y TECNOLOGÍA DE ALIMENTOS CSIC   (Spain)

Author keywords

Bioinformatics; Citrus; EST; Genomics; Microarray; Transcriptome

Indexed keywords

AGRONOMY; DNA; PROJECT MANAGEMENT; RNA; TISSUE;

CDNA MICROARRAYS; CITRUS GENOMES; GENE EXPRESSION; PUTATIVE UNIGENES;

GENES;

COMPLEMENTARY DNA; PLANT RNA;

ARTICLE; CHEMISTRY; CITRUS FRUIT; COMPARATIVE STUDY; DNA MICROARRAY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; GENOME; GENOMICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; REPRODUCIBILITY;

CITRUS; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME, PLANT; GENOMICS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, PLANT; SEQUENCE ANALYSIS, DNA;

AGRONOMY; GENES; NUCLEIC ACIDS; PLANNING; TISSUE;

ARABIDOPSIS; CITRUS; CITRUS CLEMENTINA;

EID: 20244377239     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-004-7926-1     Document Type: Article

References (38)

1. A. Abbott L. Georgi D. Yvergniaux Y. Wang A. Blenda G. Reighard M. Inigo B. Sosinski 2002 Peach the model genome for Rosaceae Acta Hort. 575 145 155
2. M.D. Adams M.B. Soares A.R. Kerlavage C. Fields J.C. Venter 1993 Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library Nat. Genet. 4 373 380
3. S.F. Altschul W. Gish W. Miller E.W. Myers D.J. Lipman 1990 Basic Local Alignment Search Tool J. Mol. Biol. 215 403 410
4. H.C. Barrett A.M. Rhodes 1976 A numerical taxonomic study of the affinity relationships in cultivated Citrus and its close relatives Systematic Botany 1 105 136
5. M. Bausher R. Shatters J. Chaparro P. Dang V. Hunter R.. Niedz 2003 An expressed sequence tag (EST) set from Citrus sinensis L. Osbeck whole seedlings and the implications of further perennial source investigations Plant Sci. 165 415 422
6. E.D. Brenner D.W. Stevenson R.W. McCombie M.S. Katari S.A. Rudd K.F. Mayer P.M. Palenchar S.J. Runko R.W. Twigg G. Dai R.A. Martienssen P.N. Benfey G.M. Coruzzi 2003 Expressed sequence tag analysis in Cycas, the most primitive living seed plant Genome Biol. 4 R78
7. R.C. Bugos V.L. Chiang X.-H. Zhang E.R. Campbell G.K. Podila W.H. Campbell 1995 RNA isolation from plant tissues recalcitrant to extraction in guanidine BioTechniques 19 734 737
8. G.M. Church W. Gilbert 1984 Genomic sequencing Proc. Natl. Acad. Sci. USA 81 1991 1995
9. M.S. Clark Y.J.K. Edwards S. Peterson S.W. Clifton A.J. Thompson M. Sasaki Y. Suzuki K. Kikuchi S. Watabe K. Kawakami S. Sugano G. Elgar S.L. Johnson 2003 Fugu ESTs: news resources for transcription analysis and genome annotation Genome Res. 13 2747 2753
10. E. Emmanuel A.A. Levy 2002 Tomato mutants as tools for functional genomics Curr. Opin. Plant Biol. 5 112 117
11. E.M. Evertsz J. Au-Young M.V. Ruvolo A.C. Lim M.A. Reynolds 2001 Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays Biotechniques 31 1182 1192
12. B. Ewing P. Green 1998 Base-calling of automated sequencer traces using Phred. II. Error probabilities Genome Res. 8 186 194
13. B. Ewing L. Hillier M.C. Wendl P. Green 1998 Base-calling of automated sequencer traces using Phred. I. Accuracy assessment Genome Res. 8 175 185
14. T. Girke J. Todd S. Ruuska J. White Ch. Benning J. Ohlrogge 2000 Microarray analysis of developing Arabidopsis seed Plant Physiol. 124 1570 1581
15. D. Gordon C. Abajian P. Green 1998 Consed: a graphical tool for sequence finishing Genome Res. 8 195 202
16. D.P. Horvath R. Schaffer M. West E. Wisman 2003 Arabidopsis microarrays identify conserved and differentially expressed genes involved in shoot growth and development from distantly related plant species Plant J. 34 125 134
17. J. Kawai A. Shinagawa K. Shibata M. Yoshino M. Itoh Y. Ishii T. Arakawa A. Hara Y. Fukunishi H. Konno 2001 Functional annotation of a full-length mouse cDNA collection Nature 409 685 690
18. C.J. Lawrence Q. Dong M.L. Polacco T.E. Seigfred V. Brendel 2004 MaizeGDB, the community database for maize genetics and genomics Nucl. Acids Res. 32 Database issue D393 D397
19. E.C. McKinney N. Ali A. Traut K.A. Feldmann D.A. Belostotsky J.M. McDowell R.B. Meagher 1995 Sequence-based identification of T-DNA insertion mutations in Arabidopsis: actin mutants act2-1 and act4-1 Plant J. 8 613 622
20. K. Meyer M.P. Leube E. Grill 1994 A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana Science 264 1452 1455
21. Navarro, L., Pina, J.A., Juarez, J., Ballester-Olmos, J.F., Arregui, J.M., Ortega, C., Navarro, A, Duran-Vila, N., Guerri, J., Moreno, P., Cambra, M. and Zaragoza, S. 2002. The Citrus variety improvement program in Spain in the period 1975-2001. Proceedings of the 15th Conference of the International Organization for Citrus Virol, In: N. Duran-Vila, R.G. Milne and J.V. da Grača (Eds.), International Organization for Citrus Virology, Riverside, CA, pp. 306-316
22. A.J. Poustka D. Groth S. Hennig S. Thamm A. Cameron A. Beck R. Reinhardt R. Herwig G. Panopoulou H. Lehrach 2003 Generation, annotation, evolutionary analysis, and database integration of 20.000 unique sea urchin EST clusters Genome Res. 13 2736 2746
23. M.L. Rise K.R. von Schalburg G.D. Brown M.A. Mawer R.H. Devlin N. Kuipers M. Busby M. Beetz-Sargent R. Alberto A.R. Gibbs P. Hunt R. Shukin J.A. Zeznik C. Nelson S.R.M. Jones D.E. Smailus S.J.M. Jones J.E. Schein M.A. Marra Y.S.N. Butterfield J.M. Stott S.H.S. Ng W.S. Davidson B.F. Koop 2004 Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics Genome Res. 14 478 490
24. Y. Ruan J. Gilmore T. Conner 1998 Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays Plant J. 15 821 833
25. R. Schaffer J. Landgraf M. Accerbi V.V. Simon M. Larson E. Wisman 2001 Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis Plant Cell 13 113 123
26. M. Schena D. Shalon R.W. Davis P.O. Brown 1995 Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 467 470
27. T. Shimada M. Kita T. Endo H. Fujii T. Ueda T. Moriguchi M. Omura 2003 Expressed sequence tags of ovary tissue cDNA library in Citrus unshiu Marc Plant Sci. 165 167 168
28. The Arabidopsis Genome Initiative (AGI) 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796 815
29. G.T. Tusher R. Tibshirani G. Chu 2001 Significance analysis of microarrays applied to the ionizing radiation response Proc. Natl. Acad. Sci. USA 98 5116 5121
30. A.L. Vettore F.R. da Silva E.L. Kemper G.M. Souza A.M. da Silva M.I.T. Ferro F. Henrique-Silva E.A. Giglioti M.V.F. Lemos L.L. Coutinho 2003 Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane Genome Res. 13 2725 2735
31. R. Whetten Y.H. Sun Y. Zhang R. Sederoff 2001 Functional genomics and cell wall biosynthesis in loblolly pine Plant Mol. Biol. 47 275 291
32. J.A. White J. Todd T. Newman N. Focks T. Girke O. Martinezde Ilarduya J.G. Jaworski J.B. Ohlrogge Benning Ch. 2000 A new set of Arabidopsis expressed sequence tags from developing seeds The metabolic pathway from carbohydrates to seed oil. Plant Physiol. 124 1582 1594
33. Ch.W. Whitfield M.R. Band M.F. Bonaldo Ch.G. Kumar L. Liu J.R. Pardinas H.M. Robertson M.B. Soares G.E. Robinson 2002 Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee Genome Res. 12 555 566
34. Y. Xue J. Li Z. Xu 2003 Recent highlights of the China Rice Functional Genomics Program Trends Genet. 19 390 394
35. K. Yamamoto T. Sasaki 1997 Large-scale EST sequencing in rice Plant Mol. Biol. 35 135 144
36. Y.H. Yang S. Dudoit P. Luu D.M. Lin V. Peng J. Ngai T.P. Speed 2002 Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res. 30 e15
37. J. Yazaki K. Kojima K. Suzuki N. Kishimoto S. Kikuchi 2004 The Rice PIPELINE: a unification tool for plant functional genomics Nucleic Acids Res. 32 Database issue D383 D387
38. H. Yue P.S. Eastman B.B. Wang J. Minor M.H. Doctolero R.L. Nuttall R. Stack J.W. Becker J.R. Montgomery M. Vainer R. Johnston 2001 An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression Nucleic Acids Res. 29 e41