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. It is haploid, and has a nuclear genome comprising 17 chromosomes with a total size of ~120 Mbp.


The 121 Mbp draft sequence of the Chlamydomonas nuclear genome was generated at 13x coverage by whole-genome, shotgun sequencing of plasmid and fosmid libraries, followed by assembly into ~1500 contigs [1]. Assembly into chromosomes was done on the basis of genetic mapping.


The set of gene predictions in version 5.5 incorporates new JGI gene expression data from 1M reads generated from nitrogen-starved cells on the 454 Titatnium platform as well as 239M 2x150 stranded Illumina reads and other smaller RNA-Seq datasets. The underlying gene prediction was performed by Mario Stanke using Augustus (annotation version u11.6)

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).


  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: By Ninghui Shi [CC BY-SA 3.0 (], from Wikimedia Commons

More information

General information about this species can be found in Wikipedia.



AssemblyChlamydomonas_reinhardtii_v5.5, INSDC Assembly GCA_000002595.3, Jan 2018
Database version94.3
Base Pairs107,048,224
Golden Path Length111,098,438
Genebuild by29
Genebuild methodImported from ENA
Data sourceJoint Genome Institute

Gene counts

Coding genes17,743
Non coding genes200
Small non coding genes200
Gene transcripts19,728

About this species