Status
v.1.0 (September 2006): Postia placenta genome assembly v1.0. The assembly release of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.23X. After trimming for vector and quality, 574,631 reads assembled into 1243 scaffolds totaling 90.9 Mbp.
Since Postia placenta is known to be highly polymorphic with a polymorphism rate in the neighborhood of 3-4%, this particular assembly uses extra stringent parameters that should only assemble sections of the genome that are more than 99% identical.
The current draft release, version 1.0, includes a total of 17,173 gene models predicted and functionally annotated using the JGI annotation pipeline.
Collaborators
- DOE Joint Genome Institute
- Dr. Daniel Cullen, Forest Products Laboratory, USDA Forest Service
- Catholic University of Chile
- Charles University, Czech Republic
- Dartmouth University
- Forest Products Laboratory
- Novozymes Biotech
- Pacific Northwest National Laboratory
- Technical University of Lisbon
- University of Toronto
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, LavÃn JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kües U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D
Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion.
Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1954-9. doi: 10.1073/pnas.0809575106
Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, LavÃn JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kües U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D
Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion.
Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1954-9. doi: 10.1073/pnas.0809575106
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.
