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Chlamydomonas reinhardtii (Chlamydomonas_reinhardtii_v5.5)

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 Mb.


The 121 Mb 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 by JGI. Assembly into chromosomes was done on the basis of genetic mapping.


The set of gene predictions in version 5.5 incorporates JGI gene expression data from 1 million reads generated from nitrogen-starved cells on the 454 Titanium platform as well as 239 million 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).

Additional analysis was carried out in house: non coding RNA genes have been annotated using tRNAScan-SE, Rfam, and RNAmmer.


  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 (https://creativecommons.org/licenses/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 version112.3
Golden Path Length111,098,438
Genebuild byJGI
Genebuild methodImport
Data sourceJoint Genome Institute

Gene counts

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