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Info • Phanerochaete chrysosporium RP-78 v2.2

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.

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.
Summary statistics for the Phanerochaete chrysosporium v3.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 35.15
Sequencing read coverage depth 10.6x
# of contigs 1253
# of scaffolds 232
# of scaffolds >= 2Kbp 204
Scaffold N50 8
Scaffold L50 (Mbp) 1.91
# of gaps 1021
% of scaffold length in gaps 7.5%
Three largest Scaffolds (Mbp) 3.27, 3.04, 2.44


ESTs Data set # sequences total # mapped to genome % mapped to genome
Other EST_contigs 68995 63043 91.4%


Gene Models FilteredModels1
length (bp) of: average median
gene 1684 1416
transcript 1401 1184
exon 259 157
intron 66 56
description:
protein length (aa) 408 332
exons per gene 5.41 4
# of gene models 13602


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)

Genome Reference(s)

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.