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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
 New annotation tool and EST mapping
from Sabeeha Merchant and Matteo Pellegrini
posted August 12, 2010
We have developed a functional annotation tool for Chlamydomonas, which is a resource to visualize pathway maps, identify enriched biological terms or convert Chlamydomonas reinhardtii gene identifiers. Please visit http://pathways.mcdb.ucla.edu/chlamy/ to use this tool.
We have also mapped the ~ 5 million-plus EST reads from JGI-UCLA and Genoscope (see 23 June post below) to the version 3 browser because of some interest in using the previous version of the assembly. The alignment can be viewed by following appropriate links at http://genomes.mcdb.ucla.edu/.
The Algal Functional Annotation Tool
This is a web-based tool that uses
lists of protein identifiers (such as Chlamydomonas JGI protein IDs
and Augustus model IDs) and searches the entire list against a
comprehensive list of annotation databases to elucidate enriched (and
therefore interesting) biological functions/processes within the given
gene list.
This tool aims to eliminate the need to manually search these
individual databases on a gene-by-gene basis to reveal underlying
biological themes. These databases have been parsed and pre-processed
to optimize this process from the point of view of the end-user.
The databases currently included are:
- KEGG Pathways (Kyoto Encyclopedia of Genes and Genomes)
- Panther Pathways
- MetaCyc (Encyclopedia of Metabolic Pathways)
- Reactome Pathways
- Gene Ontology (GO)
- MapMan Ontology
- KOG (Eukaryotic Clusters of Orthologous Groups)
- Pfam (PfamA and Pfam Clans)
- Interpro
For some databases, such as GO and MapMan, in addition to searching
against the Chlamydomonas annotation, terms inferred from Arabidopsis
homology are also searched against. KEGG pathways may also be
dynamically visualized using the proteins in the given gene list.
Subsets of enrichment may be re-run through the tool and in most cases
the results data may be downloaded as a tab-delimited text file.
The tool may be accessed directly at http://pathways.mcdb.ucla.edu/chlamy/ .
Examples of use and a sample gene list are included to explore the tool.
Feedback about the tool (including requests for other
databases/features you'd like to see) may be directed at
davidlopez@ucla.edu
To all my friends in the Chlamy community:
from Elizabeth Harris
posted July 1, 2010
Last week I received a wonderful package, including an album containing photographs and messages from many of you, a framed copy of the cover of the Chlamydomonas montage that appeared on the cover of Genetics in 2008, a Chlamy pin, a very generous check that I'll use to buy something special for my retirement, and a video of the tribute you gave me in absentia at the recent meeting. (It's probably a good thing I wasn't there to hear the applause - I would have dissolved in tears!)
The preface to the album is a letter of thanks from our little friends, Chlamydomonas reinhardtii Dangeard, which I've learned is "as told to" Ursula Goodenough. It's much too good to keep to myself, and I have her permission to share it here: pdf file
Many, many thanks to all of you!
Lib Harris
Chlamydomonas Transcriptome
from Sabeeha Merchant
posted June 23, 2010
We are pleased to report the availability of 2 Gigabases of 454 reads from the JGI that describe the Chlamydomonas transcriptome under various conditions. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
RNAs were prepared from cells sampled under various nutrient deficiencies (S, P, Cu, Fe, Zn, Mn, O2, dark), various nutrient sources (CO2, acetate, nitrate), various stages of the cell cycle, after de-flagellation, during the mating pathway. RNAs were provided by Madeli Castruita, Ursula Goodenough, Arthur Grossman, Anja Hemschemeier, Janette Kropat, Karl Lechtreck, Jae-Hyeok Lee, Sabeeha Merchant, Aimee Terauchi, James Umen, Eugen Urzica, George Witman and Matt Zones.
The data have been submitted to the Short Read Archive under accession SRA020135 and may be viewed as alignments to the JGI version 4 genome (C. reinhardtii, October 2007 assembly) at http://genomes.mcdb.ucla.edu/Cre454/
0.5 Gb of Roche Titanium 454 reads from Genoscope are also aligned to the browser. The mRNA was isolated from strains S1D2 (mt-) and cw15 petC-D1 (a 137c mt+ derivative with mutations affecting cell wall synthesis and photosynthesis, abbreviated cw below). Cells were grown under various nutrient regimes (acetate, CO2, dark, low or high light, N-limitation) or stress (heat, chloramphenicol treatment). The Genoscope data are made available for the purpose of structural annotation of the Chlamydomonas genome, including delination of transcripts, analysis of splicing and polyadenylation. As two of the four libraries are made with cDNAs from the S1D2 strain, this data can also be used to mine for polymorphisms, but Genoscope at this stage reserves the right to publish first on this topic.
Please refer also to http://genomes.mcdb.ucla.edu/CreSulfur/ (click on browser) to view alignments from the sulfur-deficiency transcriptome.
Sabeeha Merchant and Matteo Pellegrini, UCLA
Genomics updates
posted June 4, 2010
Dear Chlamydomnas Researcher,
In order to make effective use of the growing amount of Chlamydomonas sequence data, stronger ties are needed between the genomics groups and the experimental researchers. The genomics groups propose regular updates on our progress and how data is being made available (you are currently reading the first such update). Secondly, there will be new releases of gene sets about every six months.
The new gene models with stable identifiers from release to release are being generated by the Augustus gene predictor (Mario Stanke, Erik Hom, Chun Liang http://augustus.gobics.de/predictions/chlamydomonas/) which takes available evidence into account when making gene models. Other browsers are already available for ESTs (http://www.conifergdb.org/chlamyest/) and proteomics (links will be posted soon). We will be working to integrate resources as much as possible.
The current JGI browser (http://genome.jgi-psf.org/chlamy) will no longer be developed and the home for browsing and analysing Chlamydomonas genome data will be the Phytozome comparative genomics portal, where there is already a Chlamydomonas homepage (http://www.phytozome.net/chlamy) and gbrowser (Browse Genome link), with data from the old JGI browser being added over the next few weeks. Importantly, there is a tutorial for the new browser is available at http://www.phytozome.net/help.php.
More soon.
Best wishes,
The self-appointed Chlamydomonas genomics commitee with the following areas of expertise:-
Advisory: Elizabeth Harris, David Stern, George Witman, Sabeeha Merchant, Arthur Grossman, Olivier Vallon, Simon Prochnik
Annotation: Mario Stanke, Erik Hom, Lukas Mueller, Simon Prochnik, Olivier Vallon, Elizabeth Harris
Transcriptomics: Matteo Pellegrini, Sabeeha Merchant, Chun Liang, Simon Prochnik
- Chlamy2010
[updated June 18, 2010]
browse the abstracts for the recent Chlamydomonas meeting.
- Genome acknowledgement
[posted May 18, 2010]
If you find the Chlamydomonas genome useful in your work, please consider acknowledging the Department of Energy Joint Genome Institute by including this statement in your manuscripts and posters:
"The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231."
- Bill Ebersold
[posted August 6, 2009]
We have learned from Paul Levine that Bill Ebersold, one of the pioneers of genetics in C. reinhardtii, died on July 25. The following notice was posted on the UCLA web site:
07/28/2009 - PROFESSOR WILBUR T. EBERSOLD PASSES AWAY
Former friend and colleague "Bill" Wilbur T. Ebersold passed away Saturday 25 July after an extended illness. Bill was the second chair of Biology, following the merger of Zoology and Botany. Soon after Bill stepped down as Chair in the late 1970s, he suffered a major stroke, but returned to UCLA, retiring in 1991. He received his Ph. D. from Stanford University and did post doctoral studies at Dartmouth and Harvard before coming to UCLA. His research focused on Chlamydomonas genetics. Although Bill has been away from UCLA for a long time he will be missed.
There will be a memorial service for Bill on 14 August at Forest Lawn Hollywood Hills at the "Old North Church" at 2:30 PM. The family requests that in lieu of flowers contributions be made to the Department of Ecology and Evolutionary Biology at UCLA for the support of graduate students. Information may be found at http://www.eeb.ucla.edu/giving/. regarding a memorial contribution in memory of Bill.
- GreenGenie2
[posted June 12, 2009]
From Susan Dutcher:
The Chlamydomonas gene-finder, GreenGenie2, is now online. It was trained on Chlamydomonas EST sequences and shows excellent short-sequence prediction accuracy. Input sequences are limited to 150Kb. It has several new user-friendly features. (Kwan, Kulp, Dutcher, and Stormo, (2009) BMC Genomics 10: 210).
-Exon highlighting and underlining (for black and white printing)
-Translated amino acid sequence in output
-Optional automated generation of JGI custom track code
-Output sequences are searchable across line breaks in-browser
It is available at http://bifrost.wustl.edu/GreenGenie2
- Companion web site for The Chlamydomonas Sourcebook, Second Edition
[updated April 24, 2009]
Those of you who have the new Chlamydomonas Sourcebook, second edition, are probably aware that the "companion web site" for this volume at Elsevier is still a garbled mess. We've been trying since early December to get this fixed, without success. George Witman and I have therefore created an alternative site at http://www.chlamy.org/companion.html that provides descriptions and links for two methods files for volume 2, and the many terrific videos that accompany volume 3.
Please let me know if you have problems viewing or downloading these files: chlamy@duke.edu
Elizabeth Harris
- Updates to the Chlamydomonas Resource Center
[posted January 15, 2009]
A new on-line ordering form and secure on-line payment site are now working. A shopping cart-based order system is under construction and should be up soon.
Among the new acquisitions are the artificial miRNA plasmids recently described by Molnar et al. [PMID: 19054357]. See the plasmid list for additional information.
- Chlamydomonas Sourcebook
[posted December 8, 2008]
The Chlamydomonas Sourcebook, Second Edition, is now available for purchase from Elsevier Science and Technology. From the home page, a search for "Chlamydomonas" will retrieve the information on how to order. The three volumes can be purchased individually, or as a set.
- 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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