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. 1994 Dec;106(4):1241–1255. doi: 10.1104/pp.106.4.1241

Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones.

T Newman 1, F J de Bruijn 1, P Green 1, K Keegstra 1, H Kende 1, L McIntosh 1, J Ohlrogge 1, N Raikhel 1, S Somerville 1, M Thomashow 1, et al.
PMCID: PMC159661  PMID: 7846151

Abstract

High-throughput automated partial sequencing of anonymous cDNA clones provides a method to survey the repertoire of expressed genes from an organism. Comparison of the coding capacity of these expressed sequence tags (ESTs) with the sequences in the public data bases results in assignment of putative function to a significant proportion of the ESTs. Thus, the more than 13,400 plant ESTs that are currently available provide a new resource that will facilitate progress in many areas of plant biology. These opportunities are illustrated by a description of the results obtained from analysis of 1500 Arabidopsis ESTs from a cDNA library prepared from equal portions of poly(A+) mRNA from etiolated seedlings, roots, leaves, and flowering inflorescences. More than 900 different sequences were represented, 32% of which showed significant nucleotide or deduced amino acid sequences similarity to previously characterized genes or proteins from a wide range of organisms. At least 165 of the clones had significant deduced amino acid sequence homology to proteins or gene products that have not been previously characterized from higher plants. A summary of methods for accessing the information and materials generated by the Arabidopsis cDNA sequencing project is provided.

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Selected References

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  1. Adams M. D., Dubnick M., Kerlavage A. R., Moreno R., Kelley J. M., Utterback T. R., Nagle J. W., Fields C., Venter J. C. Sequence identification of 2,375 human brain genes. Nature. 1992 Feb 13;355(6361):632–634. doi: 10.1038/355632a0. [DOI] [PubMed] [Google Scholar]
  2. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991 Jun 21;252(5013):1651–1656. doi: 10.1126/science.2047873. [DOI] [PubMed] [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  4. Appel R. D., Bairoch A., Hochstrasser D. F. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem Sci. 1994 Jun;19(6):258–260. doi: 10.1016/0968-0004(94)90153-8. [DOI] [PubMed] [Google Scholar]
  5. Boguski M. S., Lowe T. M., Tolstoshev C. M. dbEST--database for "expressed sequence tags". Nat Genet. 1993 Aug;4(4):332–333. doi: 10.1038/ng0893-332. [DOI] [PubMed] [Google Scholar]
  6. Gibson S., Somerville C. Isolating plant genes. Trends Biotechnol. 1993 Jul;11(7):306–313. doi: 10.1016/0167-7799(93)90019-6. [DOI] [PubMed] [Google Scholar]
  7. Green P., Lipman D., Hillier L., Waterston R., States D., Claverie J. M. Ancient conserved regions in new gene sequences and the protein databases. Science. 1993 Mar 19;259(5102):1711–1716. doi: 10.1126/science.8456298. [DOI] [PubMed] [Google Scholar]
  8. Hunkapiller T., Kaiser R. J., Koop B. F., Hood L. Large-scale and automated DNA sequence determination. Science. 1991 Oct 4;254(5028):59–67. doi: 10.1126/science.1925562. [DOI] [PubMed] [Google Scholar]
  9. Höfte H., Desprez T., Amselem J., Chiapello H., Rouzé P., Caboche M., Moisan A., Jourjon M. F., Charpenteau J. L., Berthomieu P. An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J. 1993 Dec;4(6):1051–1061. doi: 10.1046/j.1365-313x.1993.04061051.x. [DOI] [PubMed] [Google Scholar]
  10. Keith C. S., Hoang D. O., Barrett B. M., Feigelman B., Nelson M. C., Thai H., Baysdorfer C. Partial sequence analysis of 130 randomly selected maize cDNA clones. Plant Physiol. 1993 Jan;101(1):329–332. doi: 10.1104/pp.101.1.329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Palazzolo M. J., Hamilton B. A., Ding D. L., Martin C. H., Mead D. A., Mierendorf R. C., Raghavan K. V., Meyerowitz E. M., Lipshitz H. D. Phage lambda cDNA cloning vectors for subtractive hybridization, fusion-protein synthesis and Cre-loxP automatic plasmid subcloning. Gene. 1990 Mar 30;88(1):25–36. doi: 10.1016/0378-1119(90)90056-w. [DOI] [PubMed] [Google Scholar]
  12. Patanjali S. R., Parimoo S., Weissman S. M. Construction of a uniform-abundance (normalized) cDNA library. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1943–1947. doi: 10.1073/pnas.88.5.1943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Reiter R. S., Williams J. G., Feldmann K. A., Rafalski J. A., Tingey S. V., Scolnik P. A. Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1477–1481. doi: 10.1073/pnas.89.4.1477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Sasaki T., Song J., Koga-Ban Y., Matsui E., Fang F., Higo H., Nagasaki H., Hori M., Miya M., Murayama-Kayano E. Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J. 1994 Oct;6(4):615–624. doi: 10.1046/j.1365-313x.1994.6040615.x. [DOI] [PubMed] [Google Scholar]
  15. Waterston R., Martin C., Craxton M., Huynh C., Coulson A., Hillier L., Durbin R., Green P., Shownkeen R., Halloran N. A survey of expressed genes in Caenorhabditis elegans. Nat Genet. 1992 May;1(2):114–123. doi: 10.1038/ng0592-114. [DOI] [PubMed] [Google Scholar]

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