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Welcome to the Chlamydomonas Center !
This site provides access to Chlamydomonas genomic, genetic and bibliographic information, the Chlamydomonas culture collection, and other resources for the Chlamydomonas community.
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News
 Cover Illustrations Needed for the New Chlamydomonas Sourcebook
[posted April 4, 2008]
As you're probably aware, a new edition of The Chlamydomonas Sourcebook is currently in production. We are looking for photographs or drawings suitable for the covers of each of the three volumes. These illustrations can be in full color.
The three volumes, with their working subtitles, are as follows:
Volume 1. Introduction to Chlamydomonas and Its Laboratory Use (by Elizabeth Harris)
Suitable illustrations might include light micrographs or EMs of individual cells or gametes pairing; we're open to all possibilities here
Volume 2. Organellar and Metabolic Processes (edited by David Stern)
For this one, perhaps something on the "green" side of Chlamy? Roughly half of this volume is concerned with various aspects of metabolism, and half with photosynthesis, respiration, and biogenesis of chloroplast and mitochondria.
Volume 3. Cell Motility and Behavior (edited by George Witman)
Here we'd like to see an immunofluorescence image of the cell, an EM of the flagellum/basal body, or perhaps a line drawing illustrating IFT or some other process or structure.
Our editors at Elsevier would like to have the final illustrations in hand by April 18th, so we need to work quickly. If you have images that you think might be suitable, please send low-resolution .jpg files for review to Elizabeth Harris, chlamy@duke.edu
- EMBO Workshop on the Cell and Molecular Biology of Chlamydomonas
[updated April 4, 2008]
The 13th International Chlamydomonas Conference will be held on the southern coast of France
May 27 to June 1, 2008
Presqu'île de Giens, Hyères-les-Palmiers, Var,
France
Abstracts for the meeting are now on line at http://www.chlamy.org/abstracts2008
May 27 to June 1, 2008
Presqu'île de Giens, Hyères-les-Palmiers, Var,
France
See the conference
web site for more information
Organizers: Michel Goldschmidt-Clermont, Carolyn Silflow and Francis-Andr é Wollman
Contact: michel.goldschmidt-clermont@molbio.unige.ch
- Chlamydomonas genome paper, published in Science, October 12, 2007
[posted October 11, 2007; revised October 15]
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions, by Sabeeha Merchant, Simon Prochnik, et al. appears in the October 12 issue of Science. Please see the press release at JGI for additional information.
More press releases:
National Science Foundation
UCLA, including a very nice photo of Sabeeha Merchant
Carnegie Institution
CNRS
- Volvox carteri genome at JGI
[posted June 6, 2007]
The Joint Genome Institute is pleased to announce the public release of
the Volvox carteri genome. Our annotation includes the 1265
scaffolds and 138 Mbp of the 8.1x assembly and we predicted 15,544
genes, with the following average properties:
Gene length 5269 nt
Transcript length 1833 nt
Protein length 558 aa
Exon frequency 7.78 exons per gene
Exon length 235.59 nt
Intron length 508.53 nt
Gene density 112.64 genes/Mbp scaffold
The genes were predicted by the following methods:
Known genes 143 (1%)
Homology-based 3,645 (23%)
ab initio 11,756 (76%)
Total models 15,544
The genes were validated by the following evidence:
ESTs 5,356 (34%)
Swissprot hit 9,944 (64%)
Pfam hit 2,733 (18%)
manually curated 844 (0.5%)
The annotation may be browsed, searched and downloaded at the /Volvox
carteri/ (database name Volca1) portal:
www.jgi.doe.gov/Volvox (Please use this url when referring to the portal
in publications)
To register to annotate/edit gene model structure
http://genome.jgi-psf.org:8080/annotator/servlet/jgi.annotation.Annotation?pDb=Volca1&pStateVar=Register
All comments, suggestions, and feedback are welcome.
Regards,
Astrid Terry
Genome Analyst
DOE Joint Genome Institute
- Chlamydomonas reinhardtii adapted to grow in D2O
[posted March 8, 2007]
In the course of over one year, we managed to adapt Chlamy
wild type cells to grow in 100% D2O. Persons interested in
these cells should contact:
Christoph F. Beck
Institute of Biology III
University of Freiburg
Freiburg
Germany
- Ostreococcus draft genome sequence
[posted July 22, 2006]
JGI has released draft versions of the Ostreococcus tauri and lucimarinus genomes:
http://genome.jgi-psf.org/Ost9901_3/Ost9901_3.home.html
http://genome.jgi-psf.org/Ostta4/Ostta4.home.html
From the web site above: "Ostreococcus belongs to the Prasinophyceae, an early-diverging class within the green plant lineage, and is reported as a globally abundant, single-celled alga thriving in the upper (illuminated) water column of the oceans. The most striking feature of O. tauri and related species is their minimal cellular organization: a naked, nearly 1-micron cell, lacking flagella, with a single chloroplast and mitochondrion."
- Release of version 3.0 of the C. reinhardtii genome sequence
[posted December 23, 2005]
Dear Colleagues,
I am pleased to announce that JGI has completed automated annotation of Chlamydomonas reinhardtii v3.0.
15,256 gene models have been predicted and annotated; over 2,000 curated annotations have been transferred from the previous release.
Genome Portal is now publicly available from www.jgi.doe.gov/chlamy
Best regards,
Igor Grigoriev
Genome Annotation Group Leader
US DOE Joint Genome Institute,
2800 Mitchell Drive
Walnut Creek, CA 94598
tel: 925-296-5860
fax: 925-296-5752
email: IVGrigoriev@lbl.gov
- Chlamydomonas flagellar proteome database
[posted August 12, 2005, from George Witman]
The flagellar proteome database described by Pazour et al, J. Cell Biol. 170, 103-113 (2005) is now on line at http://labs.umassmed.edu/chlamyfp.
The website has a sortable list of all proteins identified in C. reinhardtii flagellar membrane, matrix and axonemal fractions by mass spectrometry. The list can be searched by Interpro descriptions or for transmembrane helices, etc. The site also has a list of previously known flagellar proteins, data on the induction of flagellar genes by deflagellation, BLAST comparisons and other data on homologues, and the ability to search for proteins found in a particular slice of a 1-D SDS gel.
- Molecular Markers for Map-Based Cloning
[posted August 12, 2005, from David Stern]
One of the goals of the current Chlamydomonas genome project is to saturate the genome with molecular markers, which can be use for map-based cloning or other genetic studies. Thanks to earlier work from the Mets, Dutcher and Silflow/Lefebvre laboratories, supplemented by our own, we compiled a list of 526 markers as recently published in Plant Physiology (http://www.plantphysiol.org/cgi/content/abstract/137/2/557)
We are now pleased to provide with the community with a large number of additional markers, giving an estimated total of 9,300. These are of several types, but all are based on PCR. Each marker is linked to a specific location on a genome scaffold, and primer sequences and annealing conditions are given. A representative number of each marker type has been tested, leading to the estimate of 9,300 markers which will perform correctly in mapping experiments using S1-D2 polymorphisms with laboratory strains.
Please see the web page for further information. We hope the community will take advantage of these resources to further our understanding of Chlamydomonas biology.
- Version 2 Microarray
[posted March 3, 2005]
The version 2 microarray is ready for shipping. This array consists of about 10,000 oligonucleotides, each approximately 70 nucleotides long. Each of the oligonucleotide should represent a unique gene. The set of 10,000 oligonucleotides was printed twice on the same slide (so each slide has duplicates). The oligonucleotides were prepared by Integrated DNA Technologies and their quality was checked by mass spectroscopy. The set of 'unigenes sequences' used for oligonucleotide generation was developed by Monica Jain and Stephan Eberhard in my laboratory. We will also provide information describing potentially empty and weak spots (there were very few of these in our initial examination). While the .gal file with a gene identifier and the sequence of the oligonucleotide used at each position on the array will be available, it may take a little more time to link whatever annotation is available to the individual spots (it will be a priority over the next month or two). We will also put a protocol onto the web site that we used for the hybridizations and will try to address any technical questions that you might have concerning the array. A manuscript describing how the unigene set was chosen and oligonucleotide design is in preparation, and we will make it available to people using the array as soon as possible.
The cost is $100 per slide. Please send orders to:
Arthur Grossman
Department of Plant Biology
Carnegie Institution of Washington
260 Panama Street
Stanford, CA 94305
Email: arthurg@stanford.edu
Telephone: 650 325-1521 X 212
If you have any questions contact me by Email or phone.
Cheers,
Arthur
See the microarray page for more information, including a downloadable Excel file listing the array sequences, and an MS Word file with the protocol for using the array.
draft site for 2008 abstracts
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