Status
(May 2016) The Porodaedalea niemelaei PN71-100-IP13 genome was sequenced using PacBio technology, assembled with Falcon, improved with finisherSC, polished with Quiver, and annotated with the JGI annotation pipeline. The mitochondrial genome was assembled separately and is available in the downloads section.
The JGI annotation pipeline identified 4,576 gene models as possible diploid alleles, and excluded them from the filtered model/gene catalog set. These models are shown in the track "secondary_alleles", and are available from the download page.
Summary statistics for the Porodaedalea niemelaei
PN71-100-IP13 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 53.34 |
| Sequencing read coverage depth | |
| # of contigs | 951 |
| # of scaffolds | 951 |
| # of scaffolds >= 2Kbp | 945 |
| Scaffold N50 | 91 |
| Scaffold L50 (Mbp) | 0.14 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.90, 0.90, 0.83 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 69443 | 47613 | 68.6% |
| Ests | est.fasta | 71946140 | 68034492 | 94.6% |
| Gene Models | FilteredModels3 | |
| length (bp) of: | average | median |
| gene | 1713 | 1462 |
| transcript | 1378 | 1155 |
| exon | 237 | 147 |
| intron | 72 | 60 |
| description: | ||
| protein length (aa) | 400 | 324 |
| exons per gene | 5.82 | 5 |
| # of gene models | 14467 |
Collaborators
Konstantin V. Krutovsky, Büsgen-Institute Georg-August-University of Göttingen, Germany
Joseph W. Spatafora, Oregon State University
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.
