Status
The Pycnoporus coccineus genome was sequenced using the Illumina platform and assembled with AllPathsLG version R46652, (Gnerre et al., 2010). The nuclear genome was annotated with the JGI annotation pipeline and custom analyses.
Summary statistics for the Pycnoporus coccineus BRFM 310
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 32.76 |
| Sequencing read coverage depth | 99.4 |
| # of contigs | 469 |
| # of scaffolds | 222 |
| # of scaffolds >= 2Kbp | 182 |
| Scaffold N50 | 20 |
| Scaffold L50 (Mbp) | 0.47 |
| # of gaps | 247 |
| % of scaffold length in gaps | 1.3% |
| Three largest Scaffolds (Mbp) | 1.55, 1.42, 1.31 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_contigs | 32150 | 30279 | 94.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1852 | 1564 |
| transcript | 1509 | 1264 |
| exon | 256 | 154 |
| intron | 72 | 60 |
| description: | ||
| protein length (aa) | 430 | 350 |
| exons per gene | 5.88 | 5 |
| # of gene models | 12690 |
Collaborators
Eric Record (PI) and Marie-Noëlle Rosso, Biodiversity and Biotechnology of Fungi, INRA - Aix Marseille Université
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN
Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.
DNA Res. 2020 Apr 1;27(2):. doi: 10.1093/dnares/dsaa011
Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN
Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.
DNA Res. 2020 Apr 1;27(2):. doi: 10.1093/dnares/dsaa011
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.
