Status
[Feb 2015] The Phialocephala scopiformis 5WS22E1 genome was sequenced using the Illumina platform and assembled together with AllPathsLG version R49403, (Gnerre et al., 2010). Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Phialocephala scopiformis
5WS22E1 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 48.88 |
| Sequencing read coverage depth | 80.5x |
| # of contigs | 302 |
| # of scaffolds | 71 |
| # of scaffolds >= 2Kbp | 64 |
| Scaffold N50 | 15 |
| Scaffold L50 (Mbp) | 1.33 |
| # of gaps | 231 |
| % of scaffold length in gaps | 0.5% |
| Three largest Scaffolds (Mbp) | 2.76, 1.96, 1.91 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | RNNotator_assembled_Illumina_ESTs | 37002 | 36721 | 99.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1649 | 1429 |
| transcript | 1491 | 1287 |
| exon | 485 | 310 |
| intron | 78 | 55 |
| description: | ||
| protein length (aa) | 428 | 356 |
| exons per gene | 3.07 | 3 |
| # of gene models | 18573 |
Collaborators
Dr. Allison Walker, Acacia University, Canada
Dr. Joseph Spatafora, Oregon State University, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Walker AK, Frasz SL, Seifert KA, Miller JD, Mondo SJ, LaButti K, Lipzen A, Dockter RB, Kennedy MC, Grigoriev IV, Spatafora JW
Full Genome of Phialocephala scopiformis DAOMC 229536, a Fungal Endophyte of Spruce Producing the Potent Anti-Insectan Compound Rugulosin.
Genome Announc. 2016 Feb 25;4(1):. doi: 10.1128/genomeA.01768-15
Walker AK, Frasz SL, Seifert KA, Miller JD, Mondo SJ, LaButti K, Lipzen A, Dockter RB, Kennedy MC, Grigoriev IV, Spatafora JW
Full Genome of Phialocephala scopiformis DAOMC 229536, a Fungal Endophyte of Spruce Producing the Potent Anti-Insectan Compound Rugulosin.
Genome Announc. 2016 Feb 25;4(1):. doi: 10.1128/genomeA.01768-15
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.
