The Chlamydomonas reinhardtii Genome Project
The Chlamydomonas reinhardtii genome project (Grossman et al., 2003) involves 1) sequencing of cDNAs isolated from cells exposed to various environmental conditions, 2) construction of a high density DNA microarray, 3) construction of genomic contigs that nucleate around specific physical and genetic markers, 4) generation of a complete chloroplast genome sequence and analyses of chloroplast gene expression, and 5) placement of the genomic information on the network in a user friendly format. The aspects of the project emphasized by our group at Stanford has involved the generation of normalized cDNA libraries (Shrager et al., 2001; Shrager et al., 2003), sequencing of the cDNAs to generate both contigs and unigene families and to use this information to construct a high density cDNA microarray (Im et al., 2002; Zhang et al., 2003). Furthermore a draft genome sequence has been generated by the Joint Genome Institute and that sequence is being used to expedite the isolation of specific genes and to gain information on gene function (Elrad and Grossman, 2003). Many molecular tools are also being coupled with genomics to examine the function of specific genes in C. reinhardtii. Some of these tools include RNAi strains, insertional mutagenesis, reporter gene analyses, and TILLING. An image of one of our recent microarrays showing sulfur stress responses in both wild-type cells and the sac1 mutant, a strain unable to acclimate to sulfur deprivation conditions. This project is being performed in collaboration with Jeff Shrager, David Stern, Kris Niyogi, Charles Hauser, Elizabeth Harris and Olivier Vallon. Olivier, who works primarily in Paris, is shown below in Figure 2. You can learn more about C. reinhardtii genomics by visiting the websites http://www.biology.duke.edu/chlamy_genome/ and http://genome.jgi-psf.org/chlre1/chlre1.home.html
Figure 1. Microarray analysis of sulfur stress in wild-type cells of C. reinhardtii and the sac1 mutant. Genes showing various expression characteristics in the mutant and wild-type cells are marked by either numbers or arrows.
Figure 2. Olivier Vallon, glass in hand, is enjoying the warm Palo Alto climate over lunch on the grounds of the Carnegie Institution of Washington.
References
Elrad, D. and A. R. Grossman (2003) A genome’s-eye view of the Lhc polypeptides of Chlamydomonas reinhardtii. Curr Genet. In Press.
Grossman, A.R., O. Vallon, J. Shrager, Z. Zhang, C. Hauser, E. Harris, D. Martinez, D. Rokhsar. 2003. Chlamydomonas reinhardtii at the crossroads of genomics. Euk Cell. In Press.
Im, C.-S., Z. Zhang and A.R. Grossman (2003) Analysis of light and CO2 regulation in Chlamydomonas reinhardtii using genome-wide approaches. Photosyn Res 75: 111-125.
Shrager, J., C.-W. Chang, J. Davies, E. Harris, C. Hauser, R. Tamse, R. Surzycki, M. Gurjal, Z. Zhang, and A. R. Grossman. (2001) Chlamydomonas cDNAs; Assembly and potential role in understanding metabolic processes. Proceedings of the 12th International Congress on Photosynthesis
Shrager, J., C.-W. Chang, C. Hauser, E. Harris, R. Tamse, J. Davies, Z. Zhang, and A. R. Grossman. (2003) Chlamydomonas reinhardtii genome project: Sequence analysis, assembly and annotation. Plant Physiol. 131: 401-408.
Zhang, Z., J. Shrager, C.-W. Chang, O. Vallon, and A. R. Grossman (2003) Global analysis of sulfur deprivation of wild-type cells and the sac1 mutant of Chlamydomonas. In Preparation.