Status

This draft was generated using a whole genome shotgun method. Genomic DNA was used to create six main libraries; four small insert (2 - 4 kb) pUC18 libraries, one medium insert (6 - 8 kb) pMCL200 library, and one large insert (35 - 40 kb) pCC1Fos library. A total of 611,025 end sequences were used in the assembly, corresponding to approximately 10.6X sequence depth.

The current draft release, version 2.0, includes a total of 10,048 gene models (BestModels v2.1). Genes have been predicted and functionally annotated using the JGI annotation pipeline.

Releases

v2.0 (February 2005): A total of 611,025 paired sequence fragments (10.6X coverage) were assembled with the JGI assembler, JAZZ. The assembly contains 35.1 million base pairs of non-redundant sequence in 232 scaffolds greater than 1 Kbp. 90% of the assembly was in 21 scaffolds, while 50% was found in 8 scaffolds longer than 1.9 Mbp.

v1.0 (February 2002): A total of 619,903 paired sequence fragments (10.5X coverage) were assembled with the JGI assembler, JAZZ. The assembly contains 29.6 million base pairs of non-repetitive sequence in 349 scaffolds greater than 3 kbp. 90% of the assembly was in 165 scaffolds. 50% was found in 45 scaffolds longer than 203 Kbp. Gene modeling and analysis were performed at the JGI and ORNL.

Collaborators

• Dan Cullen, PI, USDA, Forest Service, Forest Products Laboratory (Madison, WI, USA)
• Catholic University, Departmento de Genética Molecular y Microbiologíca, Facultad de Ciencias Biológicas, Pontifica Universidad Católica de Chile, Santiago, Chile and Millenium Institute for Fundamental and Applied (Santiago, Chile)
• Department of Physics, University of California, Berkeley (Berkeley, CA, USA)
• Novozyme Biotech, Inc. (Davis, CA, USA)
• Oak Ridge National Laboratory (Oak Ridge, TN, USA)
• Center National De La Recherche Scientifique (France)
• Department of Biological Sciences, Columbia University (New York, NA USA)

References

• Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins. Vanden Wymelenberg A, Minges P, Sabat G, Martinez D, Aerts A, Salamov A, Grigoriev I, Shapiro H, Putnam N, Belinky P, Dosoretz C, Gaskell J, Kersten P, Cullen D. Fungal Genetics and Biology - Volume 43, Issue 5, May 2006, Pages 343-356 [doi:10.1016/j.fgb.2006.01.003]

• The Phanerochaete chrysosporium secretome: database predictions and initial mass spectrometry peptide identifications in cellulose-grown medium. Wymelenberg AV, Sabat G, Martinez D, Rajangam AS, Teeri TT, Gaskell J, Kersten PJ, Cullen D. Journal of Biotechnology - Volume 118, Issue 1, 2 July 2005, Pages 17-34 [DOI:10.1016/j.jbiotec.2005.03.01]

• Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D. Nature Biotechnology 22, 695 - 700 (2004) [DOI: 10.1038/nbt967]

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.