A Gateway to Resources for Chlamydomonas Research
This site provides access to genomic, genetic and bibliographic information on Chlamydomonas and related algae, the Chlamydomonas Resource Center (which now has its own web site), and other resources for the Chlamydomonas community.
Batch conversion of Chlamydomonas gene identifiers
posted April 2, 2014
The tool for converting batches of Chlamydomonas gene identifiers between different annotation versions has been updated to include all versions from JGI v3 onwards.
The tool is available here: http://pathways.mcdb.ucla.edu/algal/id_conversion.html
The versions that can be converted are JGI v3, v4, v4.3 (Augustus u10.2), v5.3.1, v5.5 as well as Augustus u5 and u9 and GenBank accessions corresponding to the JGI v3 version that was deposited in GenBank.
Details of the algorithms used to complete the mapping between versions as well as example identifiers and a summary of the different annotations is available under the 'Details…' link at the conversion tool page.
Joint Genome Institute
16th International Conference on the Cell and Molecular Biology of Chlamydomonas
posted January 23, 2014
Registration and abstract submission are now open for the forthcoming Chlamydomonas meeting, to be held at the Asilomar Conference Center in Pacific Grove, California.
Web site for the meeting
Chlamy mutant library
posted December 8, 2013
Dear Chlamy community,
Thanks to letters of support from many of you, the Chlamy mutant library project is now well underway, and we currently have a pilot collection covering ~10% of all genes. While the paper is still a ways away, we have received many requests for collaborative distribution of individual mutants before we publish. Rather than sharing the mutants with a select few collaborators, we are trying to make it possible for any lab in the community to collaborate with us and receive a mutant. For logistical reasons, we can only distribute one mutant per lab, and we can only accept requests until December 31, 2013. We apologize for the somewhat impersonal and constraining nature of this approach, but we hope that it will nonetheless be helpful to everyone.
Please click on the link below for more information:
Please read the information on the website before contacting us. If you need to contact us regarding the mutants, please write to this address: firstname.lastname@example.org
BAC library is OK
posted January 26, 2013
From Olivier Vallon, IBPC, Paris:
Recently, concerns were raised about possible plate swaps in the BAC library distributed by Clemson University Genomics Institute and sequenced by JGI under the accessions PTQ....
While the copy #23 received by the Paris group indeed suffers from plate swaps, this seems to be due to a one-time error of the robotics, and NOT to a general mixup at Clemson or at the JGI. Several other labs have now confirmed that their copy of the library does NOT show the problems reported by the Paris group. Clemson also sequenced some of their BAC ends, and they find that all their copies of the library are OK and consistent with JGI's sequencing.
The Paris group wishes to apologize to Clemson, JGI and the Chlamy community for needlessly creating these concerns. And to thank their colleagues who took the time to check their records and investigate the question.
Please disregard the previous post and keep using the library with confidence. In case you experience difficulties in retrieving the expected clone, you may want to explore the possibility of a plate swap, but there is no need to worry a priori.
The BAC conversion Excel file has been changed accordingly, and the new and approved version can be downloaded here.
Signed: Olivier Vallon, Katia Wostrikoff
Carolyn Silflow, Pete Lefebvre, David Mitchell, Susan Dutcher, Andrea Plecenikova
BAC library debugged
posted September 28, 2012
From Katia Wostrikoff and Olivier Vallon, IBPC, Paris:
While trying to complement mutations in specific regions of the genome using the BAC library from the Silflow/Lefebvre labs, we have come to realize that for many plates, the sequences indicated by the JGI browser (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) were not correct.
We have systematically sequenced BAC ends from all plates of our copy of the library (obtained through the Clemson Genomics Institute, http://www.genome.clemson.edu/). We have found that for eleven of the forty 384-well plates, the sequence obtained from a particular well is actually that described by JGI and the old BAC converter (http://www.chlamy.org/bac_conv.html) as coming from the same well OF A DIFFERENT PLATE. We conclude that while rearraying the plates in 96-well format for sequencing, JGI probably mislabelled some of them, resulting in a mixup of accession numbers. For example, plate 21 would have been sequenced as if it were 20, 22 as 21 etc..
Our conclusions seem to be in line with the difficulties encountered by Jane Grimwood when trying to use specific BACs for genome finishing (personal communication), but they require independent confirmation. Please let us know (email@example.com) if you have experienced similar problems. Also inform us immediately if in contrast you have used the incriminated plates without problems. This might indicate that we were mistaken, or that the BAC library distributed to different labs by Clemson are not identical...
In any event, this should not cast doubt on the quality of the work JGI has done in sequencing the genome. Mixups at sequencing do happen everywhere (for example, the first EST assembly at Stanford was affected by similar errors, see Jain et al (2007) Nucleic Acids Res. 35:2074). This does not affect the sequence assembly. It also does not affect the mapping data obtained with this library [Eukaryot Cell. 2003 Apr;2(2):362-79].
We are pleased to provide the community with a corrected Excel file that we believe now gives the exact correspondence between PTQ numbers and library well. We added a sheet allowing the reverse calculation (well to read), and a sheet listing the correspondence between the real and erroneous plate numbers. We also corrected small errors in the calculation, that led the old sheet to give the same well number for different PTQ accessions. Until the community confirms our conclusions, the old BAC converter will still be downloadable, but a cautionary note will be added.
Paris photosynthesis mutants collection
posted July 12, 2012
From Olivier Vallon:
The collection of photosynthesis mutants of the Institut de Biologie Physico-Chimique in Paris is made available to the Chlamydomonas research community. This collection includes about 500 strains generated in our laboratory, mostly single mutants but also double or triple mutants, all with rigorously verified phenotypes.
The stocks are stored in liquid nitrogen and available free of charge to academic researchers.
Please visit our ChlamyStation website at http://chlamystation.free.fr/
Version 5 genome assembly
posted December 26, 2011
Dear Chlamy Community,
The JGI is pleased to announce the release of Chlamydomonas assembly version 5.
This assembly represents a substantial improvement over version 4 and is the result of an effort led by Jane Grimwood and Jeremy Schmutz at HudsonAlpha with help from several members of the Community.
Highlights of this assembly include: contig count halved from 2739 to 1495 with 98.1% of the sequence mapped to 17 chromosomes in a much improved genetic map.
The genome sequence is available here (with release notes)
Repeat finding and masking is underway and a masked genome will be released soon.
Annotation efforts are underway and incorporate expression information from 1.1M new 454 ESTs from a nitrogen-free culture and Illumina-based mRNA end-capture sequences, both generated by the JGI.
Careful mapping of gene names (gene symbols), deflines and descriptions from v4 to v5 will be undertaken as soon as gene model annotations are completed.
Phytozome release of full Chlamy v5 browser due by March 2012.
Simon Prochnik and the JGI team
Chloroplast genome site
posted December 9, 2011
Back by popular demand: The chloroplast genome site created at Cornell University has been restored. We are aware that some features aren't working, notably the utility to retrieve sequences. We'll let you know when those have been fixed.
Welcome to the Chlamydomonas Connection!
posted November 2, 2011
If you're a regular visitor to www.chlamy.org, you'll see that we have a new look. This change coincides with the debut of the Chlamydomonas Resource Center web site, featuring on-line "shopping cart" ordering with credit card payments, and extensive revisions to the descriptions of individual strains.
Another new feature is ChlamyBiblio, a comprehensive database for literature pertaining to Chlamydomonas and its near relatives. This is freely accessible (you don't need to register to use it). A comprehensive genome database is currently under construction at the same site. Wiki editing will eventually be available to registered users.
Collectively, these new resources replace ChlamyDB, which was out of date, and running on obsolete software on an aging server. It served us well, beginning in 1994, but now it's ready for retirement.
We welcome suggestions of additional resource links - databases, web sites, methods, and anything else that will help the Chlamydomonas research community.
Annotation tool and EST mapping, from Sabeeha Merchant; update to a previous announcement
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
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)
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
News items posted previously can be found on the Archive page