This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Castelli, V. Articles by Salanoubat, M. Search for Related Content PubMed PubMed Citation Articles by Castelli, V. Articles by Salanoubat, M. Social Bookmarking                   What's this?

Methods

Whole Genome Sequence Comparisons and "Full-Length" cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation

¹ Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique Unité Mixte de Recherche-3080, 91000 Evry, France ² Institut National de la Recherche Agronomique, Unité de Recherche en Génomique Végétale, 91000 Evry, France ³ Life Technologies, a Division of Invitrogen, Carlsbad, California 92008 USA

To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides evidence that the gene catalog of Arabidopsis is not yet complete, and that a number of these annotations require re-examination. To improve the Arabidopsis genome annotation further, we used a novel "full-length" enriched cDNA collection prepared from several tissues. An additional 1931 genes were covered by new "full-length" cDNA sequences, raising the number of annotated genes with a corresponding "full-length" cDNA sequence to about 14,000. Detailed comparisons between these "full-length" cDNA sequences and annotated genes show that this resource is very helpful in determining the correct structure of genes, in particular, those not yet supported by "full-length" cDNAs. In addition, a total of 326 genomic regions not included previously in the Arabidopsis genome annotation were detected by this cDNA resource, providing clues for new gene discovery. Because, as expected, the two data sets only partially overlap, their combination produces very useful information for improving the Arabidopsis genome annotation.

⁴ Present address: Intronn, Inc. Gaithersburg, MD 20878, USA.

⁵ Corresponding author.
E-MAIL salanou{at}genoscope.cns.fr; FAX 33-01-60-87-25-14.

[Supplemental material is available online at www.genome.org. The cDNA sequences have been released to the EMBL. The data produced during this analysis and accession nos. are available at http://www.genoscope.cns.fr/Arabidopsis/. The GSLT cDNA clones are available at Genoscope. The results can be visualized at http://www.genoscope.cns.fr/cgi-bin/ggb/ggb?source=Arabidopsis/.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				R. Muralla, E. Chen, C. Sweeney, J. A. Gray, A. Dickerman, B. J. Nikolau, and D. Meinke A Bifunctional Locus (BIO3-BIO1) Required for Biotin Biosynthesis in Arabidopsis Plant Physiology, January 1, 2008; 146(1): 60 - 73. [Abstract] [Full Text] [PDF]

				H. Yi and E. J. Richards A Cluster of Disease Resistance Genes in Arabidopsis Is Coordinately Regulated by Transcriptional Activation and RNA Silencing PLANT CELL, September 1, 2007; 19(9): 2929 - 2939. [Abstract] [Full Text] [PDF]

				D. Duy, G. Wanner, A. R. Meda, N. von Wiren, J. Soll, and K. Philippar PIC1, an Ancient Permease in Arabidopsis Chloroplasts, Mediates Iron Transport PLANT CELL, March 1, 2007; 19(3): 986 - 1006. [Abstract] [Full Text] [PDF]

				X. Hong, D. G. Scofield, and M. Lynch Intron Size, Abundance, and Distribution within Untranslated Regions of Genes Mol. Biol. Evol., December 1, 2006; 23(12): 2392 - 2404. [Abstract] [Full Text] [PDF]

				G. Thill, V. Castelli, S. Pallud, M. Salanoubat, P. Wincker, P. de la Grange, D. Auboeuf, V. Schachter, and J. Weissenbach ASEtrap: A biological method for speeding up the exploration of spliceomes Genome Res., June 1, 2006; 16(6): 776 - 786. [Abstract] [Full Text] [PDF]

				C. A. Hayden, T. J. Wheeler, and R. A. Jorgensen Evaluating and improving cDNA sequence quality with cQC Bioinformatics, December 15, 2005; 21(24): 4414 - 4415. [Abstract] [Full Text] [PDF]

				S. Zhang, C. Chen, L. Li, L. Meng, J. Singh, N. Jiang, X.-W. Deng, Z.-H. He, and P. G. Lemaux Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family Plant Physiology, November 1, 2005; 139(3): 1107 - 1124. [Abstract] [Full Text] [PDF]

				M. S. Katari, V. Balija, R. K. Wilson, R. A. Martienssen, and W. R. McCombie Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana Genome Res., April 1, 2005; 15(4): 496 - 504. [Abstract] [Full Text] [PDF]

				M. Lynch, D. G. Scofield, and X. Hong The Evolution of Transcription-Initiation Sites Mol. Biol. Evol., April 1, 2005; 22(4): 1137 - 1146. [Abstract] [Full Text] [PDF]

				S. Aubourg, V. Brunaud, C. Bruyere, M. Cock, R. Cooke, A. Cottet, A. Couloux, P. Dehais, G. Deleage, A. Duclert, et al. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts Nucleic Acids Res., January 1, 2005; 33(suppl_1): D641 - D646. [Abstract] [Full Text] [PDF]

				D. L. Cheo, S. A. Titus, D. R.N. Byrd, J. L. Hartley, G. F. Temple, and M. A. Brasch Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones Genome Res., October 1, 2004; 14(10b): 2111 - 2120. [Abstract] [Full Text] [PDF]

				P. Hilson, J. Allemeersch, T. Altmann, S. Aubourg, A. Avon, J. Beynon, R. P. Bhalerao, F. Bitton, M. Caboche, B. Cannoot, et al. Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications Genome Res., October 1, 2004; 14(10b): 2176 - 2189. [Abstract] [Full Text] [PDF]