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

Nucleic Acids Research

Volumn 35, Issue 6, 2007, Pages 2074-2083

  Jain, Monica ^a   Shrager, Jeff ^a   Harris, Elizabeth H ^b   Halbrook, Renee ^a   Grossman, Arthur R ^a   Hauser, Charles ^b,d   Vallon, Olivier ^a,c  

^a GEOPHYSICAL LABORATORY   (United States)

^b DUKE UNIVERSITY   (United States)

^c INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^d ST EDWARD'S UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; TRANSCRIPTOME; ALGAL PROTEIN;

ALTERNATIVE RNA SPLICING; ARTICLE; CHLAMYDOMONAS REINHARDTII; CONTROLLED STUDY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE SEQUENCE; GENETIC ALGORITHM; GREEN ALGA; NONHUMAN; PREDICTION; PRIORITY JOURNAL; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; CONTIG MAPPING; GENETIC TRANSCRIPTION; GENETICS; GENOMICS;

CHLAMYDOMONAS REINHARDTII; CHLOROPHYTA; EUKARYOTA;

ALGAL PROTEINS; ALGORITHMS; ANIMALS; CHLAMYDOMONAS REINHARDTII; CONTIG MAPPING; EXPRESSED SEQUENCE TAGS; GENOMICS; MODELS, GENETIC; TRANSCRIPTION, GENETIC;

EID: 34247874791     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm081     Document Type: Article

References (21)

1. Windsor,A.J. and Mitchell-Olds,T. (2006) Comparative genomics as a tool for gene discovery. Curr. Opin. Biotechnol., 17, 161-167.
2. Liolios,K., Tavernarakis,N., Hugenholtz,P. and Kyrpides,N.C. (2006) The Genomes On Line Database (GOLD) v.2: A monitor of genome projects worldwide. Nucleic Acids Res., 34, D332-D334.
3. Grossman,A.R., Harris,E.E., Hauser,C., Lefebvre,P.A., Martinez,D., Rokhsar,D., Shrager,J., Silflow,C.D., Stern,D. et al. (2003) Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryot. Cell, 2, 1137-1150.
4. Asamizu,E., Nakamura,Y., Sato,S., Fukuzawa,H. and Tabata,S. (1999) A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 non-redundant expressed sequence tags. DNA Res., 6, 369-373.
5. 2 adapted cells of Chlamydomonas reinhardtii. DNA Res., 7, 305-307.
6. Asamizu,E., Nakamura,Y., Miura,K., Fukuzawa,H., Fujiwara,S., Hirono,M., Iwamoto,K., Matsuda,Y., Minagawa,J. et al. (2004) Establishment of publicly available cDNA material and information resource of Chlamydomonas reinhardtii (Chlorophyta), to facilitate gene function analysis. Phycologia, 43, 722-726.
7. Shrager,J., Hauser,C., Chang,C.W., Harris,E.H., Davies,J., McDermott,J., Tamse,R., Zhang,Z. and Grossman,A.R. (2003) Chlamydomonas reinhardtii genome project. A guide to the generation and use of the cDNA information. Plant Physiol., 131, 401-408.
8. Gordon,D., Abajian,C. and Green,P. (1998) Consed: A graphical tool for sequence finishing. Genome Res., 8, 195-202.
9. Chou,H.H. and Holmes,M.H. (2001) DNA sequence quality trimming and vector removal. Bioinformatics, 17, 1093-1104.
10. Kent,W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
11. Zhang,L.D., Yuan,D.J., Zhang,J.W., Wang,S.P. and Zhang,Q.F. (2003) A new method for EST clustering. Yi Chuan Xue Bao, 30, 147-153.
12. Kalyanaraman,A., Aluru,S., Kothari,S. and Brendel,V. (2003) Efficient clustering of large EST data sets on parallel computers. Nucleic Acids Res., 31, 2963-2974.
13. Udall,J.A., Swanson,J.M., Haller,K., Rapp,R.A., Sparks,M.E., Hatfield,J., Yu,Y., Wu,Y., Dowd,C. et al. (2006) A global assembly of cotton ESTs. Genome Res., 16, 441-450.
14. Eberhard,S., Jain,M., Im,C.S., Pollock,S., Shrager,J., Lin,Y., Peek,A.S. and Grossman,A.R. (2006) Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii. Curr. Genet., 49, 106-124.
15. 2 availability. Proc. Natl. Acad. Sci. U.S.A., 98 5347-5352.
16. Falciatore,A., Merendino,L., Barneche,F., Ceol,M., Meskauskiene,R., Apel,K. and Rochaix,J.D. (2005) The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas. Genes Dev., 19, 176-187.
17. Beligni,M.V., Yamaguchi,K. and Mayfield,S.P. (2004) Chloroplast elongation factor ts pro-protein is an evolutionarily conserved fusion with the s1 domain-containing plastid-specific ribosomal protein-7. Plant Cell, 16, 3357-3369.
18. Li,J.B., Lin,S., Jia,H., Wu,H., Roe,B.A., Kulp,D., Stormo,G.D. and Dutcher,S.K. (2003) Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III. J. Eukaryot. Microbiol., 50, 145-155.
19. Schroda,M., Vallon,O., Whitelegge,J.P., Beck,C.F. and Wollman,F.A. (2001) The chloroplastic GrpE homolog of Chlamydomonas: Two isoforms generated by differential splicing. Plant Cell, 13, 2823-2839.
20. Shearwin,K.E., Callen,B.P. and Egan,J.B. (2005) Transcriptional interference - a crash course. Trends. Genet., 21, 339-345.
21. Jain,M., Holz,H., Shrager,J., Vallon,O., Hauser,C. and Grossman,A.R. 18th International Conference on Pattern Recognition. (ICPR'06). IEEE.