Info • Coccomyxa subellipsoidea C-169 v2.0
Please note that this organism is for archival use only. Please see the current Coccomyxa subellipsoidea C-169 v3.0 site for the latest data and information.

Status

Assembly v2.0 (25 Sep 2009) is an improved assembly produced by the JGI Finishing Pipeline. The 49.0 Mbp assembly has 45 scaffolds, of which 12 represent whole chromosomes and 15 represent half chromosomes.
Nuclear Genome Assembly v2.0
# scaffolds: 45
# configs: 45
Scaffold sequence total: 49.0 Mb
Contig sequence total: 49.0Mb
% sequence in gaps: 0.0 %
Scaffold N50 / L50: 9 / 2.0 Mbp
Contig N50 / L50: 9 / 2.0 Mbp
# scaffolds > 50 kb: 9 / 29
% genome in scaffolds > 50 kb:: 99.7%
% ESTs aligned to scaffolds: 95%
Annotation v2.0 (25 Sep 2009) of the v2.0 assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA-based, protein-based, and ab initio gene predictors. After filtering for homology and EST support, a total of 9627 genes were structurally and functionally annotated. 84% of the genes have homology support, 71% have Pfam support, and 51% have EST support.
Nuclear Genome Annotation v2.0
# gene models: 9629
Gene density: 197 genes / Mbp scaffold
Ave. gene length: 3250 nt
Ave. protein length: 427 aa
Ave.exon frequency: 8,18 exons / gene
% genes with introns: 96 %
% models with start+stop codons: 92 %
% models with NR hits: 84 %
% models with Pfam domains: 60 %
% models with ESTs: 51 %

Assembly v1.0 (15 October 2007): the draft assembly release version 1.0 of whole genome shotgun reads was constructed with Arachne, using paired end sequencing reads at an average coverage of 8.16X. After trimming for vector and quality, the sequencing reads assembled into 51 main genome scaffolds totaling 49.1 MB. Roughly half of the genome is contained in 9 scaffolds all at least 2 Mbp in length.

Annotation v1.0 (30 April 2008): the draft annotation release version 1.0 of the v1.0 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, a total of 9607 genes were structurally and functionally annotated. 80% of the genes have homology support, 52% have Pfam support, and 49% have EST support.

Collaborators

  • DOE Joint Genome Institute,
  • James Van Etten, University of Nebraska, Lincoln, Department of Plant Pathology
  • Michael V. Graves, University of Massachusetts-Lowell
  • Takashi Yamada, Hiroshima University
  • Tae-Jin Choi, Pukyong National University, Korea
  • Rosevelt L. Pardy, University of Nebraska
  • Jean-Michel Claverie, Structural and Genomic Information Lab, CNRS, Marseille, France

Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Pröschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Lomsadze A, Borodovsky M, Claverie JM, Grigoriev IV, Van Etten JL
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.
Genome Biol. 2012 May 25;13(5):R39. doi: 10.1186/gb-2012-13-5-r39

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.