Status
Assembly
Ceriporiopsis subvermispora B. (May 2010) This draft assembly was produced using Roche (454) and Fosmid (Sanger) data and includes 147 gaps closed with gapResolution. Assembly was done with Newbler.
| Nuclear Genome Assembly: | v1.0 |
| Main genome scaffold total: | 740 |
| Main genome contig total: | 1154 |
| Main genome scaffold sequence total: | 39.0 Mb |
| Main genome contig sequence total total: | 37.9 Mb |
| Estimated % sequence bases in gaps: | 2.8 % |
| Scaffold N/L50: | 8 / 1.7 Mb |
| Contig N/L5050: | 45 / 238.9 KB |
| Number of scaffolds > 50.0 Kb: | 42 |
| % in scaffolds > 50.0 Kb: | 96.9% |
Annotation
Ceriporiopsis subvermispora B. (May 2010) Annotation of the assembly was JGI annotation pipeline, using a variety of homlogy-based and ab initio gene predictors. Some 2M ESTs from 454 sequencers were clustered with Newbler to yield 15,436 clusters. After filtering for EST support, completeness and homology support, a total of 12,125 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | v1.0 |
| # gene models: | 12,125 |
| Gene density(genes/Mb scaffold): | 311 |
| Avg.gene length: | 2006 |
| Avg. protein length: | 426 |
| Avg. exon frequency: | 6.7 exons/gene |
| Avg. exon length: | 241 |
| Avg. intron length: | 72.8 |
| % complete gene models (with start and stop codons): | 91% |
| % genes with homology support: | 76% |
| % genes with Pfam domains: | 49% |
| % genes with EST support: | 67% |
Collaborators
- Dan Cullen - USDA and University of Wisconsin
- Rafael Vicunã - Pontificia Universidad Catolica de Chile
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D
Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.
Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5458-63. doi: 10.1073/pnas.1119912109
Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D
Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.
Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5458-63. doi: 10.1073/pnas.1119912109
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.
