Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Aoki, Koh ^a   Yano, Kentaro ^b   Suzuki, Ayako ^b   Kawamura, Shingo ^b   Sakurai, Nozomu ^a   Suda, Kunihiro ^a   Kurabayashi, Atsushi ^a   Suzuki, Tatsuya ^c   Tsugane, Taneaki ^c   Watanabe, Manabu ^c   Ooga, Kazuhide ^a   Torii, Maiko ^a   Narita, Takanori ^d   Shin i, Tadasu ^d   Kohara, Yuji ^d   Yamamoto, Naoki ^b   Takahashi, Hideki ^e   Watanabe, Yuichiro ^f   Egusa, Mayumi ^g   Kodama, Motoichiro ^g   Ichinose, Yuki ^h   Kikuchi, Mari ⁱ   Fukushima, Sumire ⁱ   Okabe, Akiko ⁱ   Arie, Tsutomu ⁱ   Sato, Yuko ^j   Yazawa, Katsumi ^j   Satoh, Shinobu ^j   Omura, Toshikazu ^j   Ezura, Hiroshi ^j   Shibata, Daisuke ^a   more..

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b MEIJI UNIVERSITY   (Japan)

^c Chiba Prefectural Agriculture and Forestry Research Center 1762   (Japan)

^d NATIONAL INSTITUTE OF GENETICS   (Japan)

^e TOHOKU UNIVERSITY   (Japan)

^f UNIVERSITY OF TOKYO   (Japan)

^g TOTTORI UNIVERSITY   (Japan)

^h OKAYAMA UNIVERSITY   (Japan)

ⁱ TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^j UNIVERSITY OF TSUKUBA   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; NUCLEOTIDE; PLANT DNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; BASE MISPAIRING; CHIMERA; CONTROLLED STUDY; CULTIVAR; DNA SEQUENCE; EXON; FUNCTIONAL GENOMICS; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT BREEDING; PLANT GENE; PREDICTION; RICE; TOMATO; UNINDEXED SEQUENCE; GENE LIBRARY; GENETICS;

ARABIDOPSIS; LYCOPERSICON ESCULENTUM; SOLANACEAE;

DNA, COMPLEMENTARY; DNA, PLANT; GENE LIBRARY; GENOMICS; LYCOPERSICON ESCULENTUM;

EID: 77950400977     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-210     Document Type: Article

References (43)

1. Knapp S. Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae. J Exp Bot 2002, 53:2001-2022. 10.1093/jxb/erf068, 12324525.
2. Giovannoni JJ. Genetic regulation of fruit development and ripening. Plant Cell 2004, 16(Suppl):S170-180. 10.1105/tpc.019158, 2643394, 15010516.
3. Pedley KF, Martin GB. Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. Annu Rev Phytopathol 2003, 41:215-243. 10.1146/annurev.phyto.41.121602.143032, 14527329.
4. Mueller LA, Tanksley SD, Giovannoni JJ, van Eck J, Stack S, Choi D, Kim BD, Chen M, Cheng Z, Li C, et al. The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics 2005, 6:153-158. 10.1002/cfg.468, 2447522, 18629226.
5. Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, et al. The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 2005, 138:1310-1317. 10.1104/pp.105.060707, 1176404, 16010005.
6. Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S. Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 2002, 14:1441-1456. 10.1105/tpc.010478, 150698, 12119366.
7. Alba R, Fei Z, Payton P, Liu Y, Moore SL, Debbie P, Cohn J, D'Ascenzo M, Gordon JS, Rose JK, et al. ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant J 2004, 39:697-714. 10.1111/j.1365-313X.2004.02178.x, 15315633.
8. Fei Z, Tang X, Alba RM, White JA, Ronning CM, Martin GB, Tanksley SD, Giovannoni JJ. Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant J 2004, 40:47-59. 10.1111/j.1365-313X.2004.02188.x, 15361140.
9. Yamamoto N, Tsugane T, Watanabe M, Yano K, Maeda F, Kuwata C, Torki M, Ban Y, Nishimura S, Shibata D. Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars. Gene 2005, 356:127-134. 10.1016/j.gene.2005.04.026, 15975739.
10. Yano K, Watanabe M, Yamamoto N, Tsugane T, Aoki K, Sakurai N, Shibata D. MiBASE: a database of a miniature tomato cultivar Micro-Tom. Plant Biotechnol 2006, 23:195-198.
11. Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V. Comparative plant genomics resources at PlantGDB. Plant Physiol 2005, 139:610-618. 10.1104/pp.104.059212, 1255980, 16219921.
12. D'Agostino N, Aversano M, Frusciante L, Chiusano ML. TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species. Nucleic Acids Res 2007, 35:D901-905. 10.1093/nar/gkl921, 1669777, 17142232.
13. Scott JW, Harbaugh BK. Micro-Tom-a miniature dwarf tomato. Florida Agr Expt Sta Circ 1989, 370:1-6.
14. Meissner R, Jacobson Y, Melamed S, Levyatuv S, Shalev G, Ashri A, Elkind Y, Levy AA. A new model system for tomato genetics. Plant J 1997, 12:1465-1472.
15. Shibata D. Genome sequencing and functional genomics approaches in tomato. J Gen Plant Pathol 2005, 71:1-7.
16. Matsukura C, Aoki K, Fukuda N, Mizoguchi T, Asamizu E, Saito T, Shibata D, Ezura H. Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom. Curr Genomics 2008, 9:436-443. 10.2174/138920208786241225, 2691670, 19506732.
17. Kato S, Ohtoko K, Ohtake H, Kimura T. Vector-capping: a simple method for preparing a high-quality full-length cDNA library. DNA Res 2005, 12:53-62. 10.1093/dnares/12.1.53, 16106752.
18. Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, et al. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 1996, 37:327-336. 10.1006/geno.1996.0567, 8938445.
19. He S, Liu C, Skogerbo G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R. NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 2008, 36:D170-172. 10.1093/nar/gkm1011, 2238973, 18000000.
20. Gouzy J, Carrere S, Schiex T. FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics 2009, 25:670-671. 10.1093/bioinformatics/btp024, 2647831, 19153134.
21. Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res 2005, 33:6494-6506. 10.1093/nar/gki937, 1298918, 16314312.
22. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003, 302:842-846. 10.1126/science.1088305, 14593172.
23. Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, et al. Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res 2008, 15:333-346. 10.1093/dnares/dsn024, 2608845, 18927222.
24. Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA. Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 2006, 60:69-85. 10.1007/s11103-005-2564-9, 16463100.
25. Ralph SG, Chun HJ, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJ, et al. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics 2008, 9:57. 10.1186/1471-2164-9-57, 2270264, 18230180.
26. Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J, Wang M, Zhang Y, Chen X, Zhang J, et al. Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J 2006, 48:710-727. 10.1111/j.1365-313X.2006.02905.x, 17076806.
27. Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB, et al. Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 2009, 69:179-194. 10.1007/s11103-008-9415-4, 2709227, 18937034.
28. Mignone F, Gissi C, Liuni S, Pesole G. Untranslated regions of mRNAs. Genome Biol 2002, 3:REVIEWS0004. 10.1186/gb-2002-3-3-reviews0004, 139023, 11897027.
29. Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K. Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res 2004, 32:5096-5103. 10.1093/nar/gkh845, 521658, 15452276.
30. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 2003, 301:376-379. 10.1126/science.1081288, 12869764.
31. Ner-Gaon H, Leviatan N, Rubin E, Fluhr R. Comparative cross-species alternative splicing in plants. Plant Physiol 2007, 144:1632-1641. 10.1104/pp.107.098640, 1914131, 17496110.
32. 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. 10.1186/1471-2105-4-25, 166152, 12820902.
33. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 2000, 290:2105-2110. 10.1126/science.290.5499.2105, 11118137.
34. Takahashi H, Shimizu A, Arie T, Rosmalawati S, Fukushima S, Kikuchi M, Hikichi Y, Kanda A, Takahashi A, Kiba A, et al. Catalog of Micro-Tom tomato responses to common fungal, bacterial, and viral pathogens. J Gen Plant Pathol 2005, 71:8-22.
35. Tsugane T, Watanabe M, Yano K, Sakurai N, Suzuki H, Shibata D. Expressed sequence tags of full-length cDNA clones from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom. Plant Biotechnol 2005, 22:161-165.
36. Iijima Y, Nakamura Y, Ogata Y, Tanaka K, Sakurai N, Suda K, Suzuki T, Suzuki H, Okazaki K, Kitayama M, et al. Metabolite annotations based on the integration of mass spectral information. Plant J 2008, 54:949-962. 10.1111/j.1365-313X.2008.03434.x, 2440531, 18266924.
37. Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987, 162:156-159. 10.1016/0003-2697(87)90021-2, 2440339.
38. 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.
39. Green P. Phrap documentation. 1996,
40. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
41. Mott R. EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput Appl Biosci 1997, 13:477-478.
42. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. InterProScan: protein domains identifier. Nucleic Acids Res 2005, 33:W116-120. 10.1093/nar/gki442, 1160203, 15980438.
43. Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res 2009, 37:D396-403. 10.1093/nar/gkn803, 2686469, 18957448.