Chlamydomonas reinhardtii v4.0
To view archival data, please see Chlamydomonas reinhardtii v4.0. Please note that the latest data is available at Phytozome.

Assembly versions

Version 4.0 (Chlre4, March 4, 2009)

Improved Assembly v4 is the v3 draft assembly improved by finishing reads. It was constructed at JGI with the following stats:

Main genome chromosome/scaffold total: 88
Main genome contig total: 2739
Main genome scaffold sequence total: 112.3 MB
Main genome contig sequence total: 103.8 MB (-> 7.5% gap)
Main genome scaffold N/L50: 7/6.6 MB
Main genome contig N/L50: 322/90.6 KB
Number of scaffolds > 50 KB: 55 Mbp
% main genome in scaffolds >50 KB: 99.2%

232208 ESTs were processed from various public sources by Chlamy EST-Terminus.

Draft Annotation v4 of the v4 Assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA/EST-based, homology-based, and ab initio gene predictors. After filtering for EST and homology support and manual curation, a total of 16709 genes were structurally and functionally annotated, with the following stats:

Average gene properties:
Gene density: 149 genes/Mbp assembly
Gene length: 3895 nt
Transcript length: 1768 nt
Protein length: 497 aa
Exon length: 240 nt
Inton length: 336 nt
Exon frequency: 7.4 exons/gene

Version 3.0 (Chlre3)

Version 3.0 of the Chlamydomonas reinhardtii genome was generated using the whole genome shotgun strategy, using only data generated here at the JGI. This assembly was constructed with JAZZ, the JGI assembler, from WGS reads including small insert plasmids, fosmids and BACs. After trimming for vector and quality, 2.1 Million paired end sequencing reads assembled into 1557 scaffolds totaling 120 Mbp. Roughly half of the genome is contained in 24 scaffolds all at least 1.6 Mb in length. The depth of sequence coverage for the main genome scaffolds is estimated at approximately 12.8x.

The massive manual curation effort began during the Chlamydomonas Jamboree held at the JGI in the week of Dec 8th, 2003, on release version 2.0. Those annotations have been transferred forward onto version 3.0 Chlre3. Gene models for this release are available for manual curation by members of the Chlamydomonas Community

This release includes a total of 15,256 predicted gene models produced at the JGI and is composed of known Chlamydomonas reinhardtii genes mapped to the genomic sequence, gene models built by homology to known proteins from other model organisms and ab initio gene predictions, manually curated gene models from the version 2 and genes derived from EST assemblies (ACEGs). The models were consolidated and annotated using the JGI annotation pipeline.


The DNA used for the genomic sequence was CC-503 cw92 mt+, a cell-wall deficient strain, which was used in order to get high-quality DNA. In addition the BAC library was also prepared from strain CC-503 cw92 mt+. Most of the EST libraries sequenced at Stanford were prepared in the wild-type strain CC-1690 21 gr mt+. Both CC-503 and CC-1690 derive from the same original field isolate, made in Massachusetts in 1945, but they have been separate since at least the mid-1950s. S1 D2, a strain used for some ESTs and comparative sequencing, is a field isolate from Minnesota, dating from the 1980s.

For more complete information on libraries or to obtain clones please use the following

Web Links



Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007 Oct 12;318(5848):245-50.


This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.