Status
The genome sequence and gene models of Chlamydomonas reinhardtii were downloaded from Phytozome, the Joint Genome Institute (JGI) Plant genomics portal. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm.
We applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, and 4) unsupported short models. This resulted in removal of 3,123 models from C. reinhardtii v5.6 and generation of the FilteredModels1 gene track. All published models are available in the ExternalModels track. JGI tools were used to automatically annotate predicted proteins.
Summary statistics for the Chlamydomonas reinhardtii v5.6
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 111.10 |
| Sequencing read coverage depth | 13x |
| # of contigs | 1495 |
| # of scaffolds | 54 |
| # of scaffolds >= 2Kbp | 54 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 7.78 |
| # of gaps | 1441 |
| % of scaffold length in gaps | 3.6% |
| Three largest Scaffolds (Mbp) | 9.73, 9.22, 9.22 |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 5482 | 4444 |
| transcript | 3318 | 2618 |
| exon | 367 | 155 |
| intron | 271 | 230 |
| description: | ||
| protein length (aa) | 762 | 522 |
| exons per gene | 9.05 | 7 |
| # of gene models | 16403 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-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, Fernández E, Fukuzawa H, González-Ballester D, González-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, Riaño-Pachón 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, Martínez 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. doi: 10.1126/science.1143609
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-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, Fernández E, Fukuzawa H, González-Ballester D, González-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, Riaño-Pachón 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, Martínez 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. doi: 10.1126/science.1143609
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Archaeplastida Viridiplantae Chlorophyta Chlorophyceae Chlamydomonadales
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.
