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
This article has been cited by other articles:
|
|
|
|
 
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]
|
|
|
|
|
|
|
J. Voigt, J. Woestemeyer, and R. Frank
The Chaotrope-soluble Glycoprotein GP2 Is a Precursor of the Insoluble Glycoprotein Framework of the Chlamydomonas Cell Wall
J. Biol. Chem.,
October 19, 2007;
282(42):
30381 - 30392.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. K. Ledford, B. L. Chin, and K. K. Niyogi
Acclimation to Singlet Oxygen Stress in Chlamydomonas reinhardtii
Eukaryot. Cell,
June 1, 2007;
6(6):
919 - 930.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
T. Zhao, G. Li, S. Mi, S. Li, G. J. Hannon, X.-J. Wang, and Y. Qi
A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii
Genes & Dev.,
May 15, 2007;
21(10):
1190 - 1203.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Jain, J. Shrager, E. H. Harris, R. Halbrook, A. R. Grossman, C. Hauser, and O. Vallon
EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome
Nucleic Acids Res.,
April 1, 2007;
(2007)
gkm081v2.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Hanawa, M. Watanabe, Y. Karatsu, H. Fukuzawa, and Y. Shiraiwa
Induction of a High-CO2-Inducible, Periplasmic Protein, H43, and its Application as a High-CO2-Responsive Marker for Study of the High-CO2-Sensing Mechanism in Chlamydomonas reinhardtii
Plant Cell Physiol.,
February 1, 2007;
48(2):
299 - 309.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Wang and M. H. Spalding
An inorganic carbon transport system responsible for acclimation specific to air levels of CO2 in Chlamydomonas reinhardtii
PNAS,
June 27, 2006;
103(26):
10110 - 10115.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
P. R. Gilson, V. Su, C. H. Slamovits, M. E. Reith, P. J. Keeling, and G. I. McFadden
From the Cover: Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus
PNAS,
June 20, 2006;
103(25):
9566 - 9571.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Sekimoto, Y. Tanabe, Y. Tsuchikane, H. Shirosaki, H. Fukuda, T. Demura, and M. Ito
Gene Expression Profiling Using cDNA Microarray Analysis of the Sexual Reproduction Stage of the Unicellular Charophycean Alga Closterium peracerosum-strigosum-littorale Complex
Plant Physiology,
May 1, 2006;
141(1):
271 - 279.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
P. Yang, D. R. Diener, C. Yang, T. Kohno, G. J. Pazour, J. M. Dienes, N. S. Agrin, S. M. King, W. S. Sale, R. Kamiya, et al.
Radial spoke proteins of Chlamydomonas flagella
J. Cell Sci.,
March 15, 2006;
119(6):
1165 - 1174.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Kajikawa, K. T. Yamato, Y. Kohzu, S.-i. Shoji, K. Matsui, Y. Tanaka, Y. Sakai, and H. Fukuzawa
A Front-end Desaturase from Chlamydomonas reinhardtii Produces Pinolenic and Coniferonic Acids by {omega}13 Desaturation in Methylotrophic Yeast and Tobacco
Plant Cell Physiol.,
January 1, 2006;
47(1):
64 - 73.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
F. Willmund and M. Schroda
HEAT SHOCK PROTEIN 90C Is a Bona Fide Hsp90 That Interacts with Plastidic HSP70B in Chlamydomonas reinhardtii
Plant Physiology,
August 1, 2005;
138(4):
2310 - 2322.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
B. Naumann, E. J. Stauber, A. Busch, F. Sommer, and M. Hippler
N-terminal Processing of Lhca3 Is a Key Step in Remodeling of the Photosystem I-Light-harvesting Complex Under Iron Deficiency in Chlamydomonas reinhardtii
J. Biol. Chem.,
May 27, 2005;
280(21):
20431 - 20441.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C.-W. Chang, J. L. Moseley, D. Wykoff, and A. R. Grossman
The LPB1 Gene Is Important for Acclimation of Chlamydomonas reinhardtii to Phosphorus and Sulfur Deprivation
Plant Physiology,
May 1, 2005;
138(1):
319 - 329.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Lohr, C.-S. Im, and A. R. Grossman
Genome-Based Examination of Chlorophyll and Carotenoid Biosynthesis in Chlamydomonas reinhardtii
Plant Physiology,
May 1, 2005;
138(1):
490 - 515.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. Liu, F. Willmund, J. P. Whitelegge, S. Hawat, B. Knapp, M. Lodha, and M. Schroda
J-Domain Protein CDJ2 and HSP70B Are a Plastidic Chaperone Pair That Interacts with Vesicle-Inducing Protein in Plastids 1
Mol. Biol. Cell,
March 1, 2005;
16(3):
1165 - 1177.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. R. Grossman
Paths toward Algal Genomics
Plant Physiology,
February 1, 2005;
137(2):
410 - 427.
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Hanikenne, U. Kramer, V. Demoulin, and D. Baurain
A Comparative Inventory of Metal Transporters in the Green Alga Chlamydomonas reinhardtii and the Red Alga Cyanidioschizon merolae
Plant Physiology,
February 1, 2005;
137(2):
428 - 446.
[Full Text]
[PDF]
|
|
|
|
|
|
|
P. Cardol, D. Gonzalez-Halphen, A. Reyes-Prieto, D. Baurain, R. F. Matagne, and C. Remacle
The Mitochondrial Oxidative Phosphorylation Proteome of Chlamydomonas reinhardtii Deduced from the Genome Sequencing Project
Plant Physiology,
February 1, 2005;
137(2):
447 - 459.
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. M. Dent, C. M. Haglund, B. L. Chin, M. C. Kobayashi, and K. K. Niyogi
Functional Genomics of Eukaryotic Photosynthesis Using Insertional Mutagenesis of Chlamydomonas reinhardtii
Plant Physiology,
February 1, 2005;
137(2):
545 - 556.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Montsant, K. Jabbari, U. Maheswari, and C. Bowler
Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum
Plant Physiology,
February 1, 2005;
137(2):
500 - 513.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
D. Gonzalez-Ballester, A. de Montaigu, J. J. Higuera, A. Galvan, and E. Fernandez
Functional Genomics of the Regulation of the Nitrate Assimilation Pathway in Chlamydomonas
Plant Physiology,
February 1, 2005;
137(2):
522 - 533.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
I. Cohen, J. A. Knopf, V. Irihimovitch, and M. Shapira
A Proposed Mechanism for the Inhibitory Effects of Oxidative Stress on Rubisco Assembly and Its Subunit Expression
Plant Physiology,
February 1, 2005;
137(2):
738 - 746.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Z. Zhang, J. Shrager, M. Jain, C.-W. Chang, O. Vallon, and A. R. Grossman
Insights into the Survival of Chlamydomonas reinhardtii during Sulfur Starvation Based on Microarray Analysis of Gene Expression
Eukaryot. Cell,
October 1, 2004;
3(5):
1331 - 1348.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Miura, T. Yamano, S. Yoshioka, T. Kohinata, Y. Inoue, F. Taniguchi, E. Asamizu, Y. Nakamura, S. Tabata, K. T. Yamato, et al.
Expression Profiling-Based Identification of CO2-Responsive Genes Regulated by CCM1 Controlling a Carbon-Concentrating Mechanism in Chlamydomonas reinhardtii
Plant Physiology,
July 1, 2004;
135(3):
1595 - 1607.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Geimer and M. Melkonian
The ultrastructure of the Chlamydomonas reinhardtii basal apparatus: identification of an early marker of radial asymmetry inherent in the basal body
J. Cell Sci.,
June 1, 2004;
117(13):
2663 - 2674.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
D Jeganathan, R Chodhari, M Meeks, O Faeroe, D Smyth, K Nielsen, I Amirav, A S Luder, H Bisgaard, R M Gardiner, et al.
Loci for primary ciliary dyskinesia map to chromosome 16p12.1-12.2 and 15q13.1-15.1 in Faroe Islands and Israeli Druze genetic isolates
J. Med. Genet.,
March 1, 2004;
41(3):
233 - 240.
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. Tokutsu, H. Teramoto, Y. Takahashi, T.-a. Ono, and J. Minagawa
The Light-Harvesting Complex of Photosystem I in Chlamydomonas reinhardtii: Protein Composition, Gene Structures and Phylogenic Implications
Plant Cell Physiol.,
February 15, 2004;
45(2):
138 - 145.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. R. Grossman, E. E. Harris, C. Hauser, P. A. Lefebvre, D. Martinez, D. Rokhsar, J. Shrager, C. D. Silflow, D. Stern, O. Vallon, et al.
Chlamydomonas reinhardtii at the Crossroads of Genomics
Eukaryot. Cell,
December 1, 2003;
2(6):
1137 - 1150.
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. M. Quinn, J. Kropat, and S. Merchant
Copper Response Element and Crr1-Dependent Ni2+-Responsive Promoter for Induced, Reversible Gene Expression in Chlamydomonas reinhardtii
Eukaryot. Cell,
October 1, 2003;
2(5):
995 - 1002.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
