Skip Navigation



Nucleic Acids Research Advance Access published online on March 13, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm081
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (158K) Freely available
Right arrow Screen PDF (178K) Freely available
Right arrow Supplementary Material
Right arrowOA All Versions of this Article:
35/6/2074    most recent
gkm081v2
gkm081v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Jain, M.
Right arrow Articles by Vallon, O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jain, M.
Right arrow Articles by Vallon, O.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome

Monica Jain1, Jeff Shrager1, Elizabeth E. Harris2, Renee Halbrook1, Arthur R. Grossman1, Charles Hauser2,4 and Olivier Vallon1,3,*

1The Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA, 2Biology Department, Duke University, Durham, NC 27708, USA, 3Institut de Biologie Physico-Chimique, UMR7141 CNRS/Université Pierre et Marie Curie-Paris6, 13 Rue Pierre et Marie Curie, 75005 Paris, France and 4St. Edwards University, Department of Biology, Austin, TX 78704, USA

*To whom correspondence should be addressed. Tel: +33 1 5841 5058; Fax: +33 1 5841 5022; Email: ovallon{at}ibpc.fr

Received December 21, 2006. Accepted January 26, 2007.

Clustering and assembly of expressed sequence tags (ESTs) constitute the basis for most genomewide descriptions of a transcriptome. This approach is limited by the decline in sequence quality toward the end of each EST, impacting both sequence clustering and assembly. Here, we exploit the available draft genome sequence of the unicellular green alga Chlamydomonas reinhardtii to guide clustering and to correct errors in the ESTs. We have grouped all available EST and cDNA sequences into 12 063 ACEGs (assembly of contiguous ESTs based on genome) and generated 15 857 contigs of average length 934 nt. We predict that roughly 3000 of our contigs represent full-length transcripts. Compared to previous assemblies, ACEGs show extended contig length, increased accuracy and a reduction in redundancy. Because our assembly protocol also uses ESTs with no corresponding genomic sequences, it provides sequence information for genes interrupted by sequence gaps. Detailed analysis of randomly sampled ACEGs reveals several hundred putative cases of alternative splicing, many overlapping transcription units and new genes not identified by gene prediction algorithms. Our protocol, although developed for and tailored to the C. reinhardtii dataset, can be exploited by any eukaryotic genome project for which both a draft genome sequence and ESTs are available.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 GeneticsHome page
C. Liang, Y. Liu, L. Liu, A. C. Davis, Y. Shen, and Q. Q. Li
Expressed Sequence Tags With cDNA Termini: Previously Overlooked Resources for Gene Annotation and Transcriptome Exploration in Chlamydomonas reinhardtii
Genetics, May 1, 2008; 179(1): 83 - 93.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
S. S. Merchant, S. E. Prochnik, O. Vallon, E. H. Harris, S. J. Karpowicz, G. B. Witman, A. Terry, A. Salamov, L. K. Fritz-Laylin, L. Marechal-Drouard, et al.
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
Science, October 12, 2007; 318(5848): 245 - 250.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.