Status
(Mar 2016) The Pycnoporus puniceus CIRM-BRFM 1868 genome was sequenced using PacBio technology and assembled with Falcon, improved with finisherSC, polished with Quiver, and annotated using the JGI annotation pipeline.
Summary statistics for the Pycnoporus puniceus CIRM-BRFM
1868 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 30.26 |
| Sequencing read coverage depth | 97x |
| # of contigs | 105 |
| # of scaffolds | 105 |
| # of scaffolds >= 2Kbp | 105 |
| Scaffold N50 | 12 |
| Scaffold L50 (Mbp) | 0.79 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 3.00, 1.82, 1.52 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 51087 | 48914 | 95.7% |
| Ests | est.fasta | 43420270 | 43109843 | 99.3% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1924 | 1656 |
| transcript | 1571 | 1347 |
| exon | 253 | 153 |
| intron | 70 | 59 |
| description: | ||
| protein length (aa) | 446 | 365 |
| exons per gene | 6.21 | 5 |
| # of gene models | 10050 |
Collaborators
Marie-Noëlle Rosso, Biodiversité et Biotechnologie Fongique 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.
