Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Pavy, Nathalie ^a   Paule, Charles ^b   Parsons, Lee ^b   Crow, John A ^b   Morency, Marie Josee ^c   Cooke, Janice ^a,e   Johnson, James E ^b   Noumen, Etienne ^a   Guillet Claude, Carine ^a   Butterfield, Yaron ^d   Barber, Sarah ^d   Yang, George ^d   Liu, Jerry ^d   Stott, Jeff ^d   Kirkpatrick, Robert ^d   Siddiqui, Asim ^d   Holt, Robert ^d   Marra, Marco ^d   Seguin, Armand ^c   Retzel, Ernest ^b   Bousquet, Jean ^a   MacKay, John ^a   more..

^a UNIVERSITÉ LAVAL   (Canada)

^b UNIVERSITY OF MINNESOTA   (United States)

^c LAURENTIAN FORESTRY CENTRE   (Canada)

^d BRITISH COLUMBIA CANCER AGENCY   (Canada)

^e UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANE PROTEIN; COMPLEMENTARY DNA; METHIONINE ADENOSYLTRANSFERASE; TRANSCRIPTION FACTOR; TUMOR PROTEIN; MESSENGER RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; ASPEN; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER PROGRAM; CONIFER; CONSENSUS SEQUENCE; DATA BASE; DNA LIBRARY; DNA MICROARRAY; DNA TRANSCRIPTION; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE IDENTIFICATION; GENE SEQUENCE; GENOME ANALYSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PINE; PLANT GENETICS; PROBABILITY; RICE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; WHITE SPRUCE; CELL WALL; CLUSTER ANALYSIS; CONTIG MAPPING; CYTOSKELETON; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC DATABASE; GENETICS; GENOMICS; METABOLISM; MULTIGENE FAMILY; PLANT GENE; PLANT GENOME; SPRUCE;

ARABIDOPSIS; CONIFEROPHYTA; PICEA; PICEA GLAUCA; POPULUS BALSAMIFERA SUBSP. TRICHOCARPA;

ARABIDOPSIS; CELL WALL; CLUSTER ANALYSIS; CONTIG MAPPING; CYTOSKELETON; DATABASES AS TOPIC; DATABASES, GENETIC; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENES, PLANT; GENOME, PLANT; GENOMICS; MULTIGENE FAMILY; ORYZA SATIVA; PICEA; RNA, MESSENGER; SOFTWARE;

EID: 27744527781     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-144     Document Type: Article

References (71)

1. Ahuja MR: Recent advances in molecular genetics of forest trees. Euphytica 2001, 121:173-195.
2. Dhillon SS: DNA in tree species. In Cell and Tissue Culture in Forestry Volume 1. Edited by Bonga JM. and. Durzan DJ.: Martinus Nijhoff Publishers, Dordrecht; 1987:298-313.
3. Wakamiya I, Newton RJ, Price JS: Genome size and environmental factors in the genus Pinus. Am J Bot 1993, 80:1235-1241.
4. Rake AW, Miksche JP, Hall RB, Hanson KM: DNA reassociation kinetics for four conifers. Can J Genet Cytol 1980, 22:69-79.
5. Ohri D, Khoshoo TN: Genome size in gymnosperms. Plant Syst Evol 1986, 153:119-132.
6. Murray BG: Nuclear DNA amounts in gymnosperms. Ann Bot 1998, Suppl 82:3-15.
7. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J: The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 2001, 29:159-164.
8. Kirst M, Johnson AF, Baucom C, Ulrich E, Hubbard K, Staggs R, Paule C, Retzel E, Whetten R, Sederoff R: Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana. Proc Natl Acad Sci USA 2003, 100:7383-7388.
9. Pavy N, Laroche J, Bousquet J, Mackay J: Large-scale statistical analysis of secondary xylem ESTs in pine. Plant Mol Biol 2005, 57:203-224.
10. Guillet-Claude C, Isabel N, Pelgas B, Bousquet J: The evolutionary implications of knox-I gene duplications in conifers: correlated evidence from phylogeny, gene mapping, and analysis of functional divergence. Mol Biol Evol 2004, 21:2232-2245.
11. Allona I, Quinn M, Shoop E, Swope K, St Cyr S, Carlis J, Riedl J, Retzel E, Campbell M, Sederoff R, Whetten RW: Analysis of xylem formation in pine by cDNA sequencing. Proc Natl Acad Sci U S A 1998, 95:9693-9698.
12. Dendrome project [http://dendrome.ucdavis.edu/dfgp/about.html].
13. Treenomix project [http://www.treenomix.com].
14. Dubos C, Plomion C: Identification of water-deficit responsive genes in maritime pine (Pinus pinaster Ait.) roots. Plant Mol Biol 2003, 51:249-262.
15. Le Provost G, Paiva J, Pot D, Brach J, Plomion C: Seasonal variation in transcript accumulation in wood-forming tissues of maritime pine (Pinus pinaster Ait.) with emphasis on a cell wall glycine-rich protein. Planta 2003, 217:820-830.
16. Egertsdotter U, van Zyl LM, MacKay J, Peter G, Kirst M, Clark C, Whetten R, Sederoff R: Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes. Plant Biol 2004, 6:654-663.
17. van Zyl L, von Arnold S, Bozhkov P, Chen Y, Egertsdotter U, MacKay J, Sederoff R, Shen J, Zelena L, Clapham D: Heterologous array analysis in Pinaceae: Hybridization of high density arrays of Pinus taeda cDNA with cDNA from needles and embryogenic cultures of P. taeda, P. sylvestris or Picea abies. Function Compar Genomics 2002, 3:306-318.
18. Stasolla C, Belmonte MF, van Zyl L, Craig DL, Liu W, Yeung EC, Sederoff R: The effect of reduced glutathione on morphology and gene expression of white spruce (Picea glauca) somatic embryos. J Exp Bot 2004, 55:695-709.
19. Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlandsson R, Blomqvist K, Bhalerao R, Uhlen M, Teeri TT, Lundeberg J, Sundberg B, Nilsson P, Sandberg G: A transcriptional roadmap to wood formation. Proc Natl Acad Sci USA 2001, 98:14732-14737.
20. Yang J, Park S, Kamdem DP, Keathley DE, Retzel E, Paule C, Kapur V, Han KH: Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia. Plant Mol Biol 2003, 52:935-956.
21. Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J: Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol Biol 2004, 55:263-280.
22. Canadian Council of Forest Ministers [http://nfdp.ccfm.org/].
23. Florin R: The distribution of conifer and taxad genera in time and space. Acta Horti Bergiani 1963, 20:121-312.
24. Bouillé M, Bousquet J: Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): Implications for the long-term maintenance of genetic diversity in trees. Am J Bot 2005, 92:63-73.
25. Pelgas B, Bousquet J, Beauseigle S, Isabel N: A composite linkage map from two crosses for the species complex Picea mariana [Mill.] B.S.P × Picea rubens (Sarg.) and analysis of synteny with other Pinaceae. Theor Applied Genetics 2005, in press.
26. Neale DB, Savolainen O: Association genetics of complex traits in conifers. Trends Plant Sci 2004, 9:325-330.
27. Gene Ontology Consortium: Creating the gene ontology resource: design and implementation. Genome Res 2001, 11:1425-1433.
28. SpruceDB [http://ccgb.umn.edu/Pub_SpruceDB/].
29. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MI, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL, Nobrega MP, Carrer H, Franca SC, Bacci Junior M, Goldman MH, Gomes SL, Nunes LR, Camargo LE, Siqueira WJ, Van Sluys MA, Thiemann OH, Kuramae EE, Santelli RV, Marino CL, Targon ML, Ferro JA, Silveira HC, Marini DC, Lemos EG, Monteiro-Vitorello CB, Tambor JH, Carraro DM, Roberto PG, Martins VG, Goldman GH, de Oliveira RC, Truffi D, Colombo CA, Rossi M, de Araujo PG, Sculaccio SA, Angella A, Lima MM, de Rosa Junior VE, Siviero F, Coscrato VE, Machado MA, Grivet L, Di Mauro SM, Nobrega FG, Menck CF, Braga MD, Telles GP, Cara FA, Pedrosa G, Meidanis J, Arruda P. Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 2003, 13:2725-2735.
30. Forment J, Gadea J, Huerta L, Abizanda L, Agusti J, Alamar S, Alos E, Andres F, Arribas R, Beltran JP, Berbel A, Blazquez MA, Brumos J, Canas LA, Cercos M, Colmenero-Flores JM, Conesa A, Estables B, Gandia M, Garcia-Martinez JL, Gimeno J, Gisbert A, Gomez G, Gonzalez- Candelas L, Granell A, Guerri J, Lafuente MT, Madueno F, Marcos JF, Marques MC, Martinez F, Martinez-Godoy MA, Miralles S, Moreno P, Navarro L, Pallas V, Perez-Amador MA, Perez-Valle J, Pons C, Rodrigo I, Rodriguez PL, Royo C, Serrano R, Soler G, Tadeo F, Talon M, Terol J, Trenor M, Vaello L, Vicente O, Vidal Ch, Zacarias L, Conejero V: Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol 2005, 57:375-391.
31. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schonbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium.: Functional annotation of a full-length mouse cDNA collection. Nature 2001, 409:685-690.
32. Whitfield Ch.W, Band MR, Bonaldo MF, Kumar ChG, Liu L, Pardinas JR, Robertson HM, Soares MB, Robinson GE: Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res 2002, 12:555-566.
33. Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB: Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc Natl Acad Sci U S A 2004, 101:15255-15260.
34. Pot D, McMillan L, Echt C, Le Provost G, Gamier-Géré P, Cato S, Plomion C: Nucleotide variation in genes involved in wood formation in two pine species. New Phytologist 2005, 167:101-112.
35. Garcia-Gil MR, Mikkonen M, Savolainen O: Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol Ecol 2003, 12:1195-1206.
36. Crow J.A: Diogenes - Reliable prediction of protein-encoding regions in short genomic sequences. 2005 [http://analysis.ccgb.umn.edu/ diogenes].
37. PFAM database. [http://www.sanger.ac.uk/Software/Pfam/].
38. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam Protein Families Database. Nucleic Acids Res 2004, 32 Database issue:D138-D141.
39. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LL: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005, 33 Database Issue: D154-D159.
40. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P: The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 2003, 31:224-228.
41. Pine Gene Index PGI5.0 database. [http://www.tigr.org/tigr-scripts/tgi/T_index.cgi?species=pine].
42. Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E: AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 2003, 4:25.
43. Girke T, Lauricha J, Tran H, Keegstra K, Raikhel N: The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol 2004, 136:3003-3008.
44. Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W: Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol 2003, 133:1051-1071.
45. Li F, Zhang D, Fujise K: Characterization of fortilin, a novel antiapoptotic protein. J Biol Chem 2001, 276:47542-47549.
46. Pay A, Heberle-Bors E, Hirt H: An alfalfa cDNA encodes a protein with homology to translationally controlled human tumor protein. Plant Mol Biol 1992,19:501-503.
47. Sage-Ono K, Ono M, Harada H, Kamada H: Dark-induced accumulation of mRNA for a homolog of translationally controlled tumor protein (TCTP) in Pharbitis. Plant Cell Physiol 1998, 39:357-360.
48. Campbell M, Sederoff RR: Variation in lignin content and composition. Plant Physiol 1996, 110:3-13.
49. Peleman J, Saito K, Cottyn B, Engler G, Seurinck J, Van Montagu M, Inze D : Structure and expression analyses of the S-adenosylmethionine synthetase gene family in Arabidopsis thaliana. Gene 1989, 84:359-369.
50. Shen B, Li C, Tarczynski MC: High free-methionine and decreased lignin content result from a mutation in the Arabidopsis S-adenosyl-l-methionine synthetase 3 gene. Plant J 2002, 29:371-380.
51. Sanchez-Aguayo I, Rodriguez-Galan JM, Garcia R, Torreblanca J, Pardo JM: Salt stress enhances xylem development and expression of S-adenosyl-L-methionine synthase in lignifying tissues of tomato plants. Planta 2004, 220:278-285.
52. Espartero J, Pintor-Toro JA, Pardo JM: Differential accumulation of S-adenosylmethionine synthetase transcripts in response to salt stress. Plant Mol Biol 1994, 25:217-227.
53. Schröder G, Eichel J, Breining S, Schröder J: Three differentially expressed S-adenosylmethionine synthetase from Catharantus roseus: molecular and functional characterization. Plant Mol Biol 1997, 33:211-222.
54. Gramene database [http://www.gramene.org/].
55. Lindroth AM, Saarikoski P, Flygh G, Clapham D, Gronroos R, Thelander M, Ronne H, von Arnold S: Two S-adenosylmethionine synthetase-encoding genes differentially expressed during adventitious root development in Pinus contorta. Plant Mol Biol 2001, 46:335-346.
56. CCGB biodata database [http://ccgb.umn.edu/biodata/].
57. Lamblin AF, Crow JA, Johnson JE, Silverstein KA, Kunau TM, Kilian A, Benz D, Stromvik M, Endre G, VandenBosch KA, Cook DR, Young ND, Retzel EF: MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome. Nucleic Acids Res 2003, 31:196-201.
58. Arborea project [http://www.arborea.ulaval.ca/en].
59. Chang S, J Puryear J, Cairney J: A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 1993, 11:113-116.
60. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, 2nd ed. Plainview, NY: Cold Spring Harbor Laboratory Press; 1989.
61. Yang GS, Stott JM, Smailus D, Barber SA, Balasundaram M, Marra MA, Holt RA: High-throughput sequencing: a failure mode analysis. BMC Genomics 2005, 6:2.
62. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8:175-185.
63. Phrap software [http://www.phrap.org].
64. National Center for Biotechnology Information [http://www.ncbi.nlm.nih.gov/].
65. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
66. The Institute for Genomic Research [http://www.tigr.org/].
67. Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM: Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol 2003, 4: R78.
68. Sputnik database [http://sputnik.btk.fi/].
69. The Arabidopsis Information Resource [http://www.arabidopsis.org].
70. Rice Genome Annotation Database [http://www.tigr.org/tdb/e2k1/osa1/].
71. EMBOSS [http://emboss.sourceforge.net/].