First published online January 23, 2003; 10.1104/pp.016899
Plant Physiol, February 2003, Vol. 131, pp. 401-408
Chlamydomonas reinhardtii Genome Project. A
Guide to the Generation and Use of the cDNA
Information1
Jeff
Shrager,*
Charles
Hauser,
Chiung-Wen
Chang,
Elizabeth H.
Harris,
John
Davies,2
Jeff
McDermott,
Raquel
Tamse,
Zhaodou
Zhang, and
Arthur R.
Grossman
Department of Plant Biology, The Carnegie Institution of
Washington, 260 Panama Street, Stanford, California 94305 (J.S.,
C.-W.C., Z.Z., A.R.G.); Biology Department, Duke University, DCMB Box
91000, Durham, North Carolina 27708 (C.H., E.H.H.); Department of
Botany, Iowa State University, 353 Bessey Hall, Ames, Iowa, 50011 (J.D., J.M.); and Stanford Genome Technology Center, 855 California
Avenue, Palo Alto, California 94304 (R.T.)
The National Science Foundation-funded Chlamydomonas
reinhardtii genome project involves (a) construction and
sequencing of cDNAs isolated from cells exposed to various
environmental conditions, (b) construction of a high-density cDNA
microarray, (c) generation of genomic contigs that are nucleated around
specific physical and genetic markers, (d) generation of a complete
chloroplast genome sequence and analyses of chloroplast gene
expression, and (e) the creation of a Web-based resource that allows
for easy access of the information in a format that can be readily
queried. Phases of the project performed by the groups at the Carnegie Institution and Duke University involve the generation of normalized cDNA libraries, sequencing of cDNAs, analysis and assembly of these
sequences to generate contigs and a set of predicted unique genes, and
the use of this information to construct a high-density DNA microarray.
In this paper, we discuss techniques involved in obtaining cDNA
end-sequence information and the ways in which this information is
assembled and analyzed. Descriptions of protocols for preparing cDNA
libraries, assembling cDNA sequences and annotating the sequence
information are provided (the reader is directed to Web sites for more
detailed descriptions of these methods). We also discuss preliminary
results in which the different cDNA libraries are used to identify
genes that are potentially differentially expressed.
1
This work was supported by the National Science
Foundation (Molecular and Cellular Biosciences grant no. 9975765). This
is a Carnegie Institution of Washington publication no. 1,554.
2
Present address: Exelixis Plant Sciences, 16160 SW Upper
Boones Ferry Road, Portland, OR 97224.
*
Corresponding author; e-mail
jshrager{at}andrew2.Stanford.edu; fax 650-325-1521 ext. 287.
© 2003 American Society of Plant Biologists
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