Status

v.1.0 (September 27, 2007): 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 6.98x. After trimming for vector and quality, 511,817 reads assembled into 1185 scaffolds totaling 56.7 Mbp. Roughly half of the genome is contained in 12 scaffolds all at least 1.4 Mbp in length.

The current draft release includes a total of 11,501 gene models predicted using the JGI annotation pipeline. 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 Aureococcus anophagefferens EST and cDNA data. Approximately 98% of the ESTs/cDNAs mapped to the v.1.0 assembly. Average gene length is 2.1 kb and average transcript length is 1.6 kb, with the average protein containing 523 amino acids. There are approximately 2.31 exons per gene averaging 693 bp each with intron spacing of 412 bp. Gene functions have been automatically assigned based on homology to known genes.

Collaborators

• Christopher J. Gobler, Ph.D., Associate Prof. of Marine Science
  Marine Sciences Research Center, Stony Brook University

• Steven Wilhelm, Ph.D., Associate Prof. of Microbiology and Ecology & Evolutionary Biology
  Department of Microbiology, The University of Tennesse

• Dianna L. Berry, Ph.D., Postdoctoral Research Associate
  Marine Sciences Research Center, Stony Brook University

References

Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL, Kustka AB, Dill BD, Shah M, Verberkmoes NC, Kuo A, Terry A, Pangilinan J, Lindquist EA, Lucas S, Paulsen IT, Hattenrath-Lehmann TK, Talmage SC, Walker EA, Koch F, Burson AM, Marcoval MA, Tang YZ, Lecleir GR, Coyne KJ, Berg GM, Bertrand EM, Saito MA, Gladyshev VN, Grigoriev IV. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.. Proc Natl Acad Sci U S A. 2011 Feb 23.

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.