Status

v 1.0 (June 13, 2008): The assembly release version 1.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 8.95x. After trimming for vector and quality, 551,740 reads assembled into 414 scaffolds totaling 46.2 Mbp. Roughly half of the genome is contained in 12 scaffolds all at least 1.5 Mbp in length.

The draft annotation release includes a total of 9791 gene models. This data set is composed of gene models built by homology to known proteins from other model organisms and ab initio gene predictions as well as from available Chlorella EST and cDNA data. Approximately 98% of the ESTs/cDNAs mapped to the v.1.0 assembly. Average gene length is 2.92 kb and average transcript length is 1.4 kb, with the average protein containing 456 amino acids. There are approximately 8.30 exons per gene averaging 170 bp each with intron spacing of 209 bp. 89% of the genes have homology support, 57% have Pfam support, and 42% have EST support.

Collaborators

• 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 Claverieicrono, Structural and Genomic Information Lab, CNRS, Marseille, France

References

Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J, Polle J, Salamov A, Terry A, Yamada T, Dunigan DD, Grigoriev IV, Claverie JM, Van Etten JL.The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant cell.2010 Sep;22(9):2943-55. Epub 2010 Sep 17.

Links

• http://www.igs.cnrs-mrs.fr/
• http://greengene.uml.edu/

Other JGI Algae Portals:

• Aureococcus anophagefferens
• Chlamydomonas reinhardtii
• Ostreococcus tauri
• Ostreococcus lucimarinus
• Volvox carteri
• Micromonas sp.RCC299
• Micromonas sp CCMP1545

Funding

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.