Status
[November 2022] The Hyaloscypha variabilis MD1 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was assembled separately and is available in the Download tab.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 59.43 |
| Sequencing read coverage depth | 42.31x |
| # of contigs | 21 |
| # of scaffolds | 21 |
| # of scaffolds >= 2Kbp | 21 |
| Scaffold N50 | 9 |
| Scaffold L50 (Mbp) | 3.03 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 4.08, 3.85, 3.78 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 46131 | 45059 | 97.7% |
| Ests | est.fasta | 139522479 | 137048512 | 98.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1839 | 1615 |
| transcript | 1666 | 1453 |
| exon | 516 | 324 |
| intron | 79 | 56 |
| description: | ||
| protein length (aa) | 479 | 402 |
| exons per gene | 3.23 | 3 |
| # of gene models | 20037 |
Collaborators
- Petr Baldrian, Institute of Microbiology of the Czech Academy of Sciences, Czech Republic
- Petr Kohout, Institute of Microbiology of the Czech Academy of Sciences, Czech Republic
Links
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Leotiomycetes Helotiales Hyaloscyphaceae
- JGI EcoGroup Portals: Mycorrhizal Fungi Ericoid Mycorrhizal Fungi
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.
