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Review
. 2003 Dec;2(6):1137-50.
doi: 10.1128/EC.2.6.1137-1150.2003.

Chlamydomonas reinhardtii at the crossroads of genomics

Arthur R Grossman  1 , Elizabeth E Harris, Charles Hauser, Paul A Lefebvre, Diego Martinez, Dan Rokhsar, Jeff Shrager, Carolyn D Silflow, David Stern, Olivier Vallon, Zhaoduo Zhang
Affiliations
Review

Chlamydomonas reinhardtii at the crossroads of genomics

Arthur R Grossman et al. Eukaryot Cell. 2003 Dec.
No abstract available

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Figures

FIG.1.
FIG.1.
(A) Schematic of JGI genome portal. The diagram shows the internal connections of the JGI Genome Portal. Information on BLAST results, EST alignments, and gene models can be accessed through the Search page. From the gene model information page, or protein page, InterPro domains and Smith-Waterman alignments to protein databases are displayed with a graphical interface. With the version 2.0 release GO and KEGG will be available, as well as the ability to annotate gene models. The Chlamydomonas Genome Portal is accessible at www.jgi.doe.gov/chlamy. (B) Browse view. Screen shot of the browse view for several gene models displayed on the genome. Displayed simultaneously are overlapping EST alignments and Blastx results. (C) Protein page. The protein page displays information about a gene model. InterPro results, Smith-Waterman alignments, and the protein and transcript sequence for this model can be retrieved from this page.
FIG. 2.
FIG. 2.
Chamydomonas microarrays. Shown are microarray images generated after 24 h of sulfur starvation of the parental strain (CC-425, left panel) and the sac1 mutant in the same genetic background (CC-3794, right panel). Red fluorescence indicates an increase in the level of the transcript during sulfur deprivation, while green fluorescence indicates a decrease in transcription. Spot 1 represents the Ecp76 gene (963017H04), and spot 6 represents an LI818 gene (894097E05), which encodes a polypeptide that is part of the light-harvesting protein family. The functions of the genes represented by spots 2 to 5 and 7 are not known (all of these spots are circled). The orange arrow marks a gene [encoding a putative poly(A) binding protein; 894006E07] for which the transcript increases in both CC-425 and the sac1 mutant, while the white arrow marks a gene whose transcript increases in sac1 but not CC-425 cells.
FIG. 3.
FIG. 3.
Chloroplast genome. The C. reinhardtii chloroplast genome and its genes are shown. Those that have been disrupted are highlighted.
FIG. 4.
FIG. 4.
SDR sequences on the chloroplast chromosome. The first 100 kb of the chloroplast chromosome were analyzed for SDRs using a genome self-comparison with the program Pipmaker (bio.cse.psu.edu/cgi-bin/pipmaker?basic). The approximate locations of genes are shown on the top row only; the “Wendy” transposon and its disabled duplicate copy are shown on the top row at around position 75,000. The thin gray line represents one copy of the large inverted repeat. Each dot represents a repeat of the sequence along the top line; e.g., Wendy is duplicated, so a second line appears underneath it. The SDRs are represented by the large numbers of dots, whose sequence identity to the particular place on the genome ranges from 50 to 100% as shown in the scale on the right.
FIG. 5.
FIG. 5.
Integration of databases. Data for an integrated C. reinhardtii database are gathered from ChlamyDB, ChlamyEST, the Chlamy database at JGI, and a variety of outside sources before being integrated in the relational database chado and served to users on the Internet. Links connecting ChlamyDB and JGI will be established to provide robust data retrieval.
See this image and copyright information in PMC

References

    1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. - PMC - PubMed
    1. Asamizu, E., K. Miura, K. Kucho, Y. Inoue, H. Fukuzawa, K. Ohyama, Y. Nakamura, and S. Tabata. 2000. Generation of expressed sequence tags from low-CO2 and high-CO2 adapted cells of Chlamydomonas reinhardtii. DNA Res. 7:305-307. - PubMed
    1. Aselson, C. M., and P. A. Lefebvre. 1998. Genetic analysis of flagellar length control in Chlamydomonas reinhardtii: a new long-flagella locus and extragenic suppressor mutations. Genetics 148:693-702. - PMC - PubMed
    1. Auchincloss, A. H., A. I. Loroch, and J. D. Rochaix. 1999. The arginosuccinate lyase gene of Chlamydomonas reinhardtii: cloning of the cDNA and its characterization as a selectable shuttle marker. Mol. Gen. Genet. 261:21-30. - PubMed
    1. Bateman, J. M., and S. Purton. 2000. Tools for chloroplast transformation in Chlamydomonas: expression vectors and a new dominant selectable marker. Mol. Gen. Genet. 263:404-410. - PubMed

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