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

Registration for Chlamy 2012

posted December 9, 2011

From Maria Mittag: The web site for the 2012 Chlamydomonas meeting is now on line, and registration is now open:

http://www.chlamy2012.uni-jena.de/

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

News items posted previously can be found on the Archive page