Large-scale EST sequencing in rice

Plant Molecular Biology

Volumn 35, Issue 1-2, 1997, Pages 135-144

  Yamamoto, Kimiko ^a   Sasaki, Takuji ^b  

^a Rice Genome Research Program (RGP)   (Japan)

^b NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

cDNA; EST; Random cloning; Rice

Indexed keywords

ANIMALIA; JAPONICA;

EID: 0031239046     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-94-011-5794-0_13     Document Type: Article

References (39)

1. Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, et al.: Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377: 3-174 (1995).
2. Akagi H, Baba T, Shimada H, FujimuraT: Nucleotide sequence of a stearoyl-acyl carrier protein desaturase cDNA from developing seeds of rice. Plant Physiol 108: 845-846 (1995).
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 215: 403-410 (1990).
4. Alvarez AM, Fukuhara E, Nakase M, Adachi T, Aoki T, Nakamura R, Matsuda T: Four rice seed cDNA clones belonging to the alpha-amylase/trypsin inhibitor gene family encode potential rice allergens. Biosci Biotechnol Biochem 59: 1304-1308 (1995).
5. Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-218 (1991).
6. Breviario D, Giani S, Meoni C: Three rice cDNA clones encoding defferent beta-tubulin isotypes. Plant Physiol 108: 823-824 (1995).
7. Cooke R, Raynal M, Laudi Ä M, Grellet F, Delseny M, et al.: Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J 9: 101-124 (1996).
8. Eun My: Korea Rice Genome Research Program. Abstracts of Plant genome IV p18 (1996).
9. Hashimoto H, Nishi R, Umeda M, Uchimiya H, Kato A: Isolation and characterization of rice cDNA clone encoding ATP/ADP translocator. Plant Mol Biol 22: 163-164 (1993).
10. Hashimoto J, Hirabayashi T, Hayano Y, Hata S, Ohashi Y, Suzuka I, Utsugi T, Toh-e A, Kikuchi Y: Isolation and characterization of cDNA clones encoding cdc2 homologues from Oryza sativa: a functional homologue and cognate variants. Mol Gen Genet 233: 10-16 (1992).
11. Hodgkin J, Plasterk RH, Waterston RH: The nematode Caenorhabditis elegans and its genome. Science 270: 410-414 (1995).
12. Hofte H, Desprez T, Amselem J, Chiapello H, Rouze P, Caboche M, Moisan A, Jourjon MF, Charpenteau JL, Berthomieu P, Guerrier D, Giraudat J, Quigley F, Thomas F, Yu DY, Mache R, Raynal M, Cooke R, Grellet F, Delsent M, Parmentier Y, Marcillac G, Gigot C, Fleck J, Philipps G, Axelos M, Bardet C, Tremousaygue D, Lescure B: An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana Plant J 4: 1051-1061 (1993).
13. Kim HU, Yun CH, Cho WS, Kang SK, Chung TY: Nucleotide sequence of rice cDNA that encodes a ubiquitin protein and a 79-amino acid protein. Plant Physiol 108: 865 (1995).
14. Koga-Ban Y, Niki T, Nagamura Y, Sasaki T, Minobe Y: cDNA sequences of three kinds of beta-tubulins from rice. DNA Res. 2: 21-26 (1995).
15. Kurata N, Nagamura Y, Yamamoto K, Harushima H, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin SY, Inoue T, Fukuda A, Shimano T, Kuboki Y, Toyama T, Miyamoto Y, Kirihara T, Hayasaka K, Miyao A, Monna L, Zhong HS, Tamura Y, Wang ZX, Momma T, Umehara Y, Yano M, Sasaki T, Minobe Y: A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nature Genet 8: 365-372 (1994).
16. Lee YL, Chang PF, Yeh KW, Jinn TL, Kung CC, Lin WC, Chen YM, Lin CY: Cloning and characterization of a cDNA encoding an 18.0-kDa class-L low-molecular-weight heat-shock protein from rice. Gene 165: 223-227 (1995).
17. Liu J, Hara C, Umeda M, Zhao Y, Okita TW, Uchimiya H: Analysis of randomly isolated cDNAs from developing endosperm of rice (Oryza sativa L.): evaluation of expressed sequence tags, and expression levels of mRNAs. Plant Mol Biol 29: 685-689 (1995).
18. McCombie WR, Adams MD, Kelley JM, FitzGerald MG, Utterback TR, Khan M, Dubnick M, Kerlavage AR, Venter JC, Fields C: Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genet 1: 124-131 (1992).
19. Nahm BH: Random sequencing analysis of rice immature seed cDNA and database network. Abstracts of Plant Genome IV p19 (1996).
20. Newman T, de Bruijin FJ, Green P, Keegstra K, Kende H, McIntosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M, Retzel E, Somerville C: Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones Plant Physiol 106: 1241-1255 (1994).
21. Nocker S, Deveraux Q, Rechsteiner M, Vierstra RD: Arabidopsis MBP1 gene encodes a conserved ubiquitin recognition component of the 26S proteasome. Proc Natl Acad Sci USA 93: 856-860 (1996).
22. Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85: 2444-2448 (1988).
23. Sakamoto M, Shimada H, Fujimura T: Nucleotide sequence of a cDNA encoding a beta subunit of the mitochondrial ATPase from rice (Oryza sativa). Plant Mol Biol 20: 171-174 (1992).
24. Sasaki T, Song J, Koga-Ban Y, Matsui E, Fang F, Higo H, Nagasaki H, Hori M, Miya M, Maruyama-Kayano E, Takiguchi T, Takasuga A, Niki T, Ishimaru K, Ikeda H, Yamamoto Y, Mukai Y, Ohta I, Miyadera N, Havukkala I, Minobe Y: Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J 6: 615-624 (1994).
25. Sasaki T, Yano M, Kurata N, Yamamoto K: The Japanese Rice Genome Research Program. Genome Res 6: 661-666 (1996).
26. Schultes NP, Brutnell TP, Allen A, Dellaporta SL, Nelson T, Chen J: Leaf permeasel gene of maize is required for chloroplast development. Plant Cell 8: 463-475 (1996).
27. Shcherban TY, Shi J, Durachko DM, Guiltinan MJ, McQueen-Mason SJ, Shieh M, Cosgrove DJ: Molecular cloning and sequence analysis of expansions-a highly conserved, multigene family of proteins that mediate cell wall extension in plants. Proc Natl Acad Sci USA 92: 9245-9249 (1995).
28. Shen B, Carneiro N, Torres-Jerez I, Stevenson R, McGreery T, Helentjaris T, Baysdorfer C, Almira E, Ferl R, Habben J, Larkins B: Partial sequencing and mapping of clones from two maize cDNA libraries. Plant Mol Biol 26: 1085-101 (1994).
29. Sutton GG, White O, Adams MD, Kerlavage AR: TIGR assembler: a new tool for assembling large shotgun sequencing project. Genome Sci Technol 1: 9-19 (1995).
30. Takahashi N, Ko MS: Toward a whole cDNA catalog: construction of an equalized cDNA library from mouse embryos. Genomics 23: 202-210 (1994).
31. Takaiwa F, Oono K: Genomic DNA sequences of two new strage protein glutelin in rice. Jpn J Genet 66: 161-171 (1991).
32. Terada Y, Aoki H, Tanaka T, Morikawa H, Ida S: Cloning and nucleotide sequence of a leaf ferredoxin-nitrite reductase cDNA of rice. Biosci Biotechnol Biochem 59: 2183-2185 (1995).
33. Uchimiya H, Kidou S, Shimazaki T, Takamatsu S, Hashimoto H, Nishi R, Aotsuka S, Matsubayashi Y, Kidou N, Umeda M, Kato A: Random sequencing of cDNA libraries reveals a variety of expressed genes in cultured cells of rice (Oryza sativa L.). Plant J 2: 1005-1009 (1992).
34. Umehara Y, Inagaki A, Tanoue H, Yasukochi Y, Nagamura Y, Saji S, Otsuki Y, FujimuraT, Kurata N, Minobe Y: Construction and characterization of rice YAC library for physical mapping. Mol Breed 1: 79-89 (1995).
35. Umehara Y, Tanoue H, Kurata N, Ashikawa I, Minobe Y, Sasaki T: An ordered yeast artificial chromosome library covering half of rice chromosome 6. Genome Res, in press.
36. Vassarotti A, Goffeau A: Sequencing the yeast genome: the European effort. Trends Biotechnol 10: 15-18 (1992).
37. Waterston R, Martin C, Craxton M, Coulson A, Hillier L, Durbin R, Green P, Shownkeen R, Halloran N, Metzstein M, Hawkins T and Wilson R, Berks M, Du Z, Thomas K, Thierry-Mieg J, Sulston J: A survey of expressed genes in Caenorhabditis elegans. Nature Genetics 1: 114-123 (1992).
38. Wu J, Matsui E, Yamamoto K, Nagamura Y, Kurata N, Sasaki T, Minobe Y: Genomic organization of 57 ribosomal protein genes in rice (Oryza sativa L.) through RFLP mapping. Genome 38: 1189-1200 (1995).
39. Yoshiba Y, Yamaguchi-Shinozaki K, Shinozaki K, Harada Y: Characterization of a cDNA clone encoding 23 kDa polypeptide of the oxygen-evolving complex of photosystem II in rice. Plant Cell Physiol 36: 1677-1682 (1985).