Friday, October 12, 2007

The Genome of Chlamydomonas reinhardtii

This week's issue of Science (Oct. 12, 2007) contains a summary of the draft genome sequence of the green alga, Chlamydomonas reinhardtii (Merchant et al. 2007) [The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions].

Chlamydomonas is a single-cell green alga with a prominent chloroplast and cilia. It normally lives in the soil or in lakes and streams. Green algae are members of the division Chlorophyta, which includes all green algae. The complete genome sequencs of two other green alga, Ostreococcus tauri and Ostreococcus lucimarinus, have been published. Chlamydomonas is distantly related to Ostreococcus.

Interest in Chlamydomonas stems from the fact that it has long been a model organism and has a well-established genetic background. Furthermore, the relationship between the green algae and plants (mosses, liverworts, ferns, angiosperms etc.) is well established. The green algae share a common ancestor with all plants and this relationship is more recent than the relationship between plants and any other protists. (Red algae are the next closest group.)

The nuclear genome is 121 Mb (121,000,000 base pairs) in size and it's divided into 17 linkage groups (chromosomes). This is a draft genome sequence representing about 95% of the complete sequence with 13x coverage of the sequenced regions. The remaining 5% consists mostly of repeat regions and it's unlikely that they will ever be sequenced.

The preliminary analysis predicts 15,143 protein-encoding genes; three ribosomal RNA clusters; and 259 transfer RNA genes (tRNA). This is about the same number of genes as Drosophila melanogaster (fruit fly) but fewer than the number in mammals (~22,000). In most cases, the original estimates of gene number are inflated so we can expect this number to drop to about 12,000 as annotation continues. So far, 8631 genes have been confirmed.

There are 61 classes of simple repeat sequences; about 100 families of transposable elements; and 64 families of short interspersed elements (SINEs) that appear to be derived from tRNA genes. Most of the protein-encoding genes have introns (avg. 8 introns/gene). There are more introns and longer introns than in most unicelllar species.

Assuming 2Kb of coding region per gene, it looks like genes and their associated regulatory sequences make up about 30% of the genome. The remaining DNA (mostly junk) is evenly distributed between introns and intergenic regions.

The authors identified about 350 genes that are associated with chloroplast function. Most of these are genes that originally resided in the chloroplast DNA. Over time they have been transferred to the nucleus. These genes are easily recognized because they are related to genes from cyanobacteria, from which chloroplasts are derived, and they are only found in species that have chloroplasts.

The known genes in this group encode the proteins of the photosynthetic apparatus [A Simple Version of Photosynthesis] and the metabolic pathways found in the chloroplast (e.g., Rubisco, The Calvin Cycle). Surprisingly, over 200 of these genes have unknown functions and only half of those genes (100) belong to larger gene families from which putative functions can be surmised. This suggests that there may be some unknown pathways or functions in chloroplasts.

There are about 125 genes involved in assembly and function of the cilia (flagella) and most of these have been previously identified. Note that many different species of eukaryote contain cilia but they have been lost in plants. The only other sequenced genome from green algae is that from Ostreococcus and it's interesting to note that although Ostrecoccus does not have cilia its genome still retains half of the genes required for cilia assembly and function.

There are several other interesting features of Chlamydomonas that can now be studied with the aid of the genome sequence. For example, Chlamydomonas has a small eyespot that can detect light and trigger a phototactic response. The eyespot is related to plastids (chloroplast) except that the thylakoid membrane is packed with red pigment molecules. The specific genes involved in eyespot assembly are similar to genes found in mammalian retina and they probably interact with heme groups. The availability of a genome sequence should help to decipher the molecular architecture of this eyespot.

(The authors are from 63 different departments and institutes in the following countries: USA, France, China, Belgium, United Kingdom, Spain, Japan, Mexico, Germany, Australia, Canada, Turkey, Czech Republic, and Italy.)

Merchant, S.S. et al. (117 authors) (2007) The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions. Science 318:245-250.

[Photo Credits: The phylogenetic tree is part of Figure 2 in Merchant et al. 2007. The diagram of Chlamydomonas is from this website. It is probably taken from a textbook. The photograph of living Chlamydomonas is from this website.]


  1. many different species of eukaryote contain cilia but they have been lost in plants.

    ?? Bryophytes, ferns, cycads, and ginkgo have flagellated sperm. They are lacking in conifers and angiosperms, though.

  2. Are flagellated sperm the same as cilia?

  3. "The remaining DNA (mostly junk) is evenly distributed" -- A dangerous comment! Haven't we learnt anything since introns?