Status
Dec 2013. The Schizopora paradoxa KUC8140 genome was sequenced using the Illumina platform and subsequently assembled with AllPathsLG release version R44008 (Gnerre et al., 2010) to produce an assembly that was used as input to PBJelly for PacBio patching. The genome was annotated with the JGI annotation pipeline and custom analyses.
Summary statistics for the Schizopora paradoxa KUC8140
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 44.41 |
| Sequencing read coverage depth | 133.3x |
| # of contigs | 1374 |
| # of scaffolds | 1291 |
| # of scaffolds >= 2Kbp | 988 |
| Scaffold N50 | 103 |
| Scaffold L50 (Mbp) | 0.12 |
| # of gaps | 51 |
| % of scaffold length in gaps | 0.1% |
| Three largest Scaffolds (Mbp) | 1.18, 0.79, 0.55 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_contigs | 37696 | 36437 | 96.7% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1735 | 1497 |
| transcript | 1419 | 1200 |
| exon | 246 | 145 |
| intron | 68 | 58 |
| description: | ||
| protein length (aa) | 413 | 339 |
| exons per gene | 5.78 | 4 |
| # of gene models | 17098 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Min B, Park H, Jang Y, Kim JJ, Kim KH, Pangilinan J, Lipzen A, Riley R, Grigoriev IV, Spatafora JW, Choi IG
Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremediation.
J Biotechnol. 2015 Oct 10;211():42-3. doi: 10.1016/j.jbiotec.2015.06.426
Min B, Park H, Jang Y, Kim JJ, Kim KH, Pangilinan J, Lipzen A, Riley R, Grigoriev IV, Spatafora JW, Choi IG
Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremediation.
J Biotechnol. 2015 Oct 10;211():42-3. doi: 10.1016/j.jbiotec.2015.06.426
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.
