Expressed sequence tags: Alternative or complement to whole genome sequences?

Trends in Plant Science

Volumn 8, Issue 7, 2003, Pages 321-329

  Rudd, Stephen ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA;

EID: 0042232552     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1360-1385(03)00131-6     Document Type: Article

References (56)

1. Putney, S.D. et al. (1983) A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature 302, 718-721
2. Brenner, S. (1990) The human genome: the nature of the enterprise. CIBA Found. Symp. 149, 6-17
3. Adams, M.D. et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651-1656
4. Boguski, M.S. et al. (1993) dbEST - database for 'expressed sequence tags'. Nat. Genet. 4, 332-333
5. Gress, T.M. et al. (1992) Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues. Mamm. Genome 3, 609-619
6. Van der Hoeven, R. et al. (2002) 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 14, 1441-1456
7. Obermayer, R. et al. (2002) Nuclear DNA C-values in 30 species double the familial representation in pteridophytes. Ann. Bot. 90, 209-217
8. Gaut, B.S. et al. (2000) Maize as a model for the evolution of plant nuclear genomes. Proc. Natl. Acad. Sci. U. S. A. 97, 7008-7015
9. Heslop-Harrison, J.S. (2000) Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12, 617-636
10. Bennetzen, J.L. (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115, 29-36
11. Carels, N. et al. (1995) The gene distribution of the maize genome. Proc. Natl. Acad. Sci. U. S. A. 92, 11057-11060
12. Barakat, A. et al. (1997) The distribution of genes in the genomes of Gramineae. Proc. Natl. Acad. Sci. U. S. A. 94, 6857-6861
13. Hoskins, R.A. et al. (2002) Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 3, RESEARCH0085.1-0085.16
14. Kent, W.J. and Haussler, D. (2001) Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11, 1541-1548
15. Raizada, M.N. et al. (2001) Somatic and germinal mobility of the RescueMu transposon in transgenic maize. Plant Cell 13, 1587-1608
16. Rabinowicz, P.D. et al. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat. Genet. 23, 305-308
17. Mayer, K. and Mewes, H.W. (2002) How can we deliver the large plant genomes? Strategies and perspectives. Curr. Opin. Plant Biol. 5, 173-177
18. Stoesser, G. et al. (2003) The EMBL nucleotide sequence database: major new developments. Nucleic Acids Res. 31, 17-22
19. Daly, D.C. et al. (2001) Plant systematics in the age of genomics. Plant Physiol. 127, 1328-1333
20. Pryer, K.M. et al. (2002) Deciding among green plants for whole genome studies. Trends Plant Sci. 7, 550-554
21. Herwig, R. et al. (2002) Construction ofa 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes. Plant J. 32, 845-857
22. Bonaldo, M.F. et al. (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 6, 791-806
23. Hillier, L.D. et al. (1996) Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6, 807-828
24. Curry, J. and Glickman, B.W. (1997) Moloney murine leukemia reverse transcriptase suspect in the production of multiple misincorporations during hprt cDNA synthesis. Mutat. Res. 374, 145-148
25. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194
26. Seki, M. et al. (1998) High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. Plant J. 15, 707-720
27. Heumann, K. and Mewes, H.W. (1996) The hashed position tree (HPT): a suffix tree variant for large data sets stored on slow mass storage devices. In Proceedings of the Third South American Workshop on String Processing (Ziviani, N. et al., eds), pp. 101-115, Carlton University Press
28. Gordon, D. et al. (1998) Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202
29. Huang, X. and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res. 9, 868-877
30. Rudd, S. et al. (2003) Sputnik: a database platform for comparative plant genomics. Nucleic Acids Res. 31, 128-132
31. Ronning, C.M. et al. (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol. 131, 419-429
32. Fulton, T.M. et al. (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14, 1457-1467
33. The Arabidopsis Genome Initiative, (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815
34. Goff, S.A. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100
35. Ewing, R. et al. (1999) Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets. In Silico Biol. 1, 197-213
36. Theodorides, K. et al. (2002) Comparison of EST libraries from seven beetle species: towards a framework for phylogenomics of the Coleoptera. Insect Mol. Biol. 11, 467-475
37. Shrager, J. et al. (2003) Chlamydomonas reinhardtii genome project. A guide to the generation and use of the cDNA information. Plant Physiol. 131, 401-408
38. Yu, J. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92
39. Stormo, G.D. (2000) Gene-finding approaches for eukaryotes. Genome Res. 10, 394-397
40. Mathe, C. et al. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30, 4103-4117
41. Reese, M.G. et al. (2000) Genome annotation assessment in Drosophila melanogaster. Genome Res. 10, 483-501
42. Haas, B.J. et al. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol. 3, RESEARCH0029.1-0029.12
43. Brendel, V. and Zhu, W. (2002) Computational modeling of gene structure in Arabidopsis thaliana. Plant Mol. Biol. 48, 49-58
44. Zhu, W. et al. Refined annotation of the Arabidopsis thaliana genome by complete EST mapping. Plant Physiol. (in press)
45. Burke, J. et al. (1998) Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Res. 8, 276-290
46. Schoof, H. and Karlowski, W. (2003) Comparison of rice and Arabidopsis annotation. Curr. Opin. Plant Biol. 6, 1-7
47. Ewing, R.M. et al. (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9, 950-959
48. MacIntosh, G.C. et al. (2001) Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol. 127, 765-776
49. Lisacek, F.C. et al. (2001) Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting. Proteomics 1, 186-193
50. Eujayl, I. et al. (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor. Appl. Genet. 104, 399-407
51. Picoult-Newberg, L. et al. (1999) Mining SNPs from EST databases. Genome Res. 9, 167-174
52. Brown, G.R. et al. (2001) Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 159, 799-809
53. Chandler, V.L. and Brendel, V. (2002) The maize genome sequencing project. Plant Physiol. 130, 1594-1597
54. Wheeler, D.L. et al. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res. 31, 28-33
55. Quackenbush, J. et al. (2001) The TIGR gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29, 159-164
56. Lamblin, A.F. et al. (2003) MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome. Nucleic Acids Res. 31, 196-201