Chlamydomonas reinhardtii Assembly and Gene Annotation

About Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is a unicellular green alga from the phylum Chlorophyta, which diverged from land plants over a billion years ago. C. reinhardtii is a model species for studying a broad range of fundamental biological processes including the evolution of chloroplast-based photosynthesis and the structure of eukaryotic flagella.


Chlamydomonas reinhardtii is haploid, and has a nuclear genome comprising 17 chromosomes with a total size of ~120 Mbp, a 203 kbp chloroplast genome and a ~16 kbp mitochondrial genome.


The genome annotation for Chlamydomonas reinhardtii has been derived from annotation submitted to the ENA/Genbank/DDBJ databases; and enhanced by importing data from additional sources, principally UniProtKB and GOA. The archive records in turn reflect submissions from the JGI Chlamydomonas sequencing project.

The non-coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997) , RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.


  1. The Chlamydomonas genome reveals the evolution of key animal and plant functions.
    Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marchal-Drouard L et al. 2007. Science. 318:245-250.

Picture credit: Emmanuel Boutet

More information

General information about this species can be found in Wikipedia.



Assemblyv3.1, INSDC Assembly GCA_000002595.2, Nov 2007
Database version92.1
Base Pairs120,404,952
Golden Path Length120,404,952
Genebuild byJGI
Genebuild methodGenerated from ENA and UniProtKB annotation
Data sourceJGI

Gene counts

Coding genes14,416
Non coding genes253
Small non coding genes246
Long non coding genes7
Gene transcripts14,757

About this species