Status
v1.0 (June, 2011): The assembly release version 1.0 of Phanerochaete carnosa was generated using the Newbler assembler and Roche 454, Sanger Fosmids and shredded consensus from Velvet assembled Illumina Solexa input data.
Summary statistics for the Phanerochaete carnosa v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 46.29 |
| Sequencing read coverage depth | 58.10 |
| # of contigs | 2272 |
| # of scaffolds | 1137 |
| # of scaffolds >= 2Kbp | 1136 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 3.53 |
| # of gaps | 1135 |
| % of scaffold length in gaps | 6.8% |
| Three largest Scaffolds (Mbp) | 5.87, 4.58, 4.22 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EST clusters | EST clusters, 454 | 16234 | 13302 | 81.9% |
| EST clusters | EST clusters, Illumina | 98072 | 89338 | 91.1% |
| ESTs | 454 ESTs, hardwood | 19501 | 9456 | 48.5% |
| ESTs | 454 ESTs, softwood | 1,139,862 | 1,033,150 | 90.6% |
| Gene Models | FilteredModels4 | |
| length (bp) of: | average | median |
| gene | 1765 | 1448 |
| transcript | 1446 | 1190 |
| exon | 269 | 159 |
| intron | 75 | 57 |
| description: | ||
| protein length (aa) | 384 | 313 |
| exons per gene | 5.36 | 4 |
| # of gene models | 13937 |
Collaborators
- Emma Master, Ph.D.,University of Toronto, ON
- Radhakrishnan Mahadevan, Ph.D., University of Toronto, ON
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, VanKuyk PA, Barry K, Lindquist E, LaButti K, Lapidus A, Lucas S, Coutinho P, Gong Y, Samejima M, Mahadevan R, Abou-Zaid M, de Vries RP, Igarashi K, Yadav JS, Grigoriev IV, Master ER
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.
BMC Genomics. 2012 Sep 2;13():444. doi: 10.1186/1471-2164-13-444
Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, VanKuyk PA, Barry K, Lindquist E, LaButti K, Lapidus A, Lucas S, Coutinho P, Gong Y, Samejima M, Mahadevan R, Abou-Zaid M, de Vries RP, Igarashi K, Yadav JS, Grigoriev IV, Master ER
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.
BMC Genomics. 2012 Sep 2;13():444. doi: 10.1186/1471-2164-13-444
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.
