Archived News

  • 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: https://www.chlamylibrary.org/

    Please read the information on the website before contacting us. If you need to contact us regarding the mutants, please write to this address: chlamymutants@gmail.com

    Sincerely,
    Martin Jonikas

     

  • 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.

    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 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 (ovallon@ibpc.fr) 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)

    http://www.hagsc.org/restricted_access/chlamy_wga/C_reinhardtii.110311.tar.gz

    l: chlamy_wga
    p: 9413chlam

    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.

    Best wishes,
    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

    posted September 9, 2011

    We are pleased to alert you to new functionalities at the http://pathways.mcdb.ucla.edu/chlamy/ site. The site is designed to help you analyze gene lists and expression profiles. The site is being updated on a regular basis.

    paper by Lopez et al., describing this site

     

    • 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

International Volvox meeting, from Stephen Miller

posted September 29, 2011

Please join us for the 1st International Volvox Conference (focused on the green alga Volvox and its close relatives) to be held December 1-4, 2011 at the Biosphere 2, in Arizona, USA (http://www.b2science.org/).

This is the first of what we hope to be a long series of Volvox meetings to be held every other year, alternating with the Chlamydomonas meetings. The idea of a meeting on everything about Volvox and its relatives (aka Volvocales or volvocine algae) reflects both an increase in the size of the Volvox community and the realization that many researchers from fields traditionally not associated with Volvox research (e.g., physics, theoretical biology) are interested in various aspects of the system.

Volvocine algae have become an important model system for the evolution of multicellularity, development and cellular differentiation, and lately have yielded important results in fields as diverse as genomics, hydrodynamics, and social evolution. We hope that such a meeting will foster exchange of ideas and expertise, and will initiate new collaborations. With these meeting we also wish to attract new people and to build a stronger Volvox community.

In addition to sessions (contributed papers and posters) on various aspects of the biology, taxonomy, ecology, development and evolution of Volvox and its relatives, we are organizing a workshop on Volvox genetics and genomics that will provide a forum to discuss emerging tools and methods (or ways of adapting those that have been developed in other systems) to enhance our understanding of genetically-controlled processes in this group of algae.

 

 

  • Workshop Announcement
    from Maria Mittagposted January 6, 2011

Chlamydomonas and Phaeodactylum Workshop within the frame of DFG Research Group

“Specific Light Driven Reactions in Unicellular Model Algae”

Jena (Germany), March 27-28, 2011

We invite PhD students and postdocs to apply for participation in a workshop on selected methods established for C. reinhardtii and P. tricornutum (program, seehttp://www.uni-jena.de/en/DFG_Research__Group_1261.html under Workshop March 2011). The workshop will be held directly after a meeting (March 25-27, 2011; program, see site above under Meeting March 2011) organized within the frame of Research-Group “Specific light-driven reactions in unicellular model algae” that is financed by the German Research Foundation. The PhD students and postdocs who will be invited for the workshop can also participate in the meeting and present their work within a poster session. There will be no charge for the meeting and workshop, except for the supporting program for which a contribution of 25 EUR is required. Travel and hotel costs have to be covered by the PhD students/postdocs themselves. Due to space restrictions, we have to limit the number of PhD students/postdocs. E-mail your application including your CV and the title and co-authors of your poster (if you wish to present one) till February 21, 2011 latest to Maria Mittag (M.Mittag@uni-jena.de).

Maria Mittag (Coordinator of the Research Group)
Claudia Büchel, Peter Hegemann, Tilman Kottke, Peter Kroth, Georg Nagel and Christian Wilhelm (Members of the Research Group)

 

  • New annotation tool and EST mapping
    from Sabeeha Merchant and Matteo Pellegriniposted 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 Harrisposted 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 Merchantposted 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 updatesposted June 4, 2010Dear 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. 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 athttp://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 ProchnikAnnotation: Mario Stanke, Erik Hom, Lukas Mueller, Simon Prochnik, Olivier Vallon, Elizabeth HarrisTranscriptomics: Matteo Pellegrini, Sabeeha Merchant, Chun Liang, Simon Prochnik

 

 

  • 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 athttp://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