Overview

Chlamydomonas reinhardtii is a single celled chlorophyte. Highly adaptable, these green algae live in many different environments throughout the world. Normally deriving energy from photosynthesis, with an alternative carbon source, C. reinhardtii can also thrive in total darkness.

The relative adaptability and quick generation time has made Chlamydomonas an important model for biological research. Over the years, studies of Chlamydomonas have provided major research contributions in the areas of photosynthesis and molecular biology.(from JGI - The Joint Genome Institute).

Statistics

This release of Phytozome includes the Chlr3 genbank submission annotation freeze of Sept 13, 2007 from JGI - The Joint Genome Institute.

Genome

Approximately 120Mb arranged in 1557 scaffolds, with an L50 of 1.6Mb.

Loci

22273 loci containing protein-coding transcripts

Transcripts

22285 protein-coding transcripts

More information is available at JGI.

Exploring Chlamydomonas

Chlamydomonas in the context of Green Plant evolution

Chlamydomonas genes will be found in clusters defined at the Viridiplantae and Chlamydomonas (crown) nodes. If you know something about the chlamydomonas gene you're interested in (e.g., its JGI model name, a descriptive phrase), you can select "search" from the menu at the top of the page, enter your search terms, pick the Land Plants node (or All nodes), and search. The gene clusters you find can then be examined in detail, with summary pages that include descriptive and functional (domain) annotation, syntenic context, and links to each cluster's ancestors and descendants. If you don't have keyword information but do have a gene or gene product sequence, you can search for related gene clusters using BLAST (click on "search" and then select the BLAST tab).

The Chlamydomonas Genome

Use the Browse the Genome button at the top of this page to view Chlamydomonas gene models in their full genomic context. Alternatively, if you'd like to search the genome for regions homologous to a particular sequence, use the BLAST against the genome button. The browsing environment, Gbrowse, provides overview and detailed views of gene structure. Gbrowse provides a search interface allowing you to look up Chlamydomonas models by JGI model name or location. Once you've located a gene model of interest, click on it to go to its detail page (e.g, here). The detail page provides sequence information on the model and its translated peptide. From the detail page you can also jump to viewing Chlamydomonas genes in their evolutionary context. To see this gene's orthologs at the Viridiplantae node, click on the Cluster link on the detail page. If you'd like to see what other ancestral gene's share sequence similarity with this gene, click on the detail page's Phytozome BLAST link, which will pull up similar gene clusters.

Downloading Data

CDS and peptide sequence for individual genes is available from the details page of the Chlamydomonas Gbrowse environment. To get there from a Cluster Summary page, however, you'll need to click the "Display Options" tab and make sure that "Reference ID" column is selected. Then expand all the "Genes in the Cluster" rows (by clicking on the icon near the Org heading) and click on the "[PAC]" link, which will take you to the detail page for that model. You can also get gene sequences for all the members of one or more clusters from any Cluster Summary, Phytozome BLAST results, or Search Results page, by launching Jalview (by clicking links for Multiple Sequence Alignments"), which will provide access to CDS sequence or peptide sequence of the members of the gene clusters you selected. If you're are interested in bulk downloads of all data (gene models, proteomes, genomic sequence), this is available directly from JGI.