Status
[March 2019] The Amylocarpus encephaloides TRa018bII genome was sequenced with Illumina, assembled with SPAdes, and annotated with the JGI Annotation Pipeline.
The mitochondrial genome was assembled separately and is available on the Download page.
Summary statistics for the Amylocarpus encephaloides
TRa018bII v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 46.29 |
| Sequencing read coverage depth | 127.83x |
| # of contigs | 2449 |
| # of scaffolds | 2381 |
| # of scaffolds >= 2Kbp | 1600 |
| Scaffold N50 | 168 |
| Scaffold L50 (Mbp) | 0.07 |
| # of gaps | 68 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.42, 0.39, 0.37 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 37966 | 35934 | 94.6% |
| Ests | est.fasta | 98404598 | 97412939 | 99.0% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1770 | 1523 |
| transcript | 1602 | 1365 |
| exon | 534 | 329 |
| intron | 86 | 57 |
| description: | ||
| protein length (aa) | 454 | 368 |
| exons per gene | 3.00 | 3 |
| # of gene models | 11869 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Hagestad OC, Hou L, Andersen JH, Hansen EH, Altermark B, Li C, Kuhnert E, Cox RJ, Crous PW, Spatafora JW, Lail K, Amirebrahimi M, Lipzen A, Pangilinan J, Andreopoulos W, Hayes RD, Ng V, Grigoriev IV, Jackson SA, Sutton TDS, Dobson ADW, Rämä T
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation.
IMA Fungus. 2021 Aug 9;12(1):21. doi: 10.1186/s43008-021-00072-0
Hagestad OC, Hou L, Andersen JH, Hansen EH, Altermark B, Li C, Kuhnert E, Cox RJ, Crous PW, Spatafora JW, Lail K, Amirebrahimi M, Lipzen A, Pangilinan J, Andreopoulos W, Hayes RD, Ng V, Grigoriev IV, Jackson SA, Sutton TDS, Dobson ADW, Rämä T
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation.
IMA Fungus. 2021 Aug 9;12(1):21. doi: 10.1186/s43008-021-00072-0
Links
- 1000 Fungal Genomes Project
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Leotiomycetes Helotiales
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.
