Status
[December 2017] The Cercophora scortea SMH4131-1 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Cercophora scortea v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 40.17 |
| Sequencing read coverage depth | 103.21x |
| # of contigs | 9 |
| # of scaffolds | 9 |
| # of scaffolds >= 2Kbp | 9 |
| Scaffold N50 | 3 |
| Scaffold L50 (Mbp) | 5.95 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 9.50, 9.34, 5.95 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 35381 | 34093 | 96.4% |
| Ests | est.fasta | 116876517 | 116719087 | 99.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1928 | 1686 |
| transcript | 1743 | 1512 |
| exon | 621 | 384 |
| intron | 104 | 77 |
| description: | ||
| protein length (aa) | 489 | 403 |
| exons per gene | 2.81 | 2 |
| # of gene models | 11779 |
Collaborators
Pierre Gladieux, INRA, Montpellier
Francis M. Martin, INRA, France.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Hensen N, Bonometti L, Westerberg I, Brännström IO, Guillou S, Cros-Aarteil S, Calhoun S, Haridas S, Kuo A, Mondo S, Pangilinan J, Riley R, LaButti K, Andreopoulos B, Lipzen A, Chen C, Yan M, Daum C, Ng V, Clum A, Steindorff A, Ohm RA, Martin F, Silar P, Natvig DO, Lalanne C, Gautier V, Ament-Velásquez SL, Kruys Å, Hutchinson MI, Powell AJ, Barry K, Miller AN, Grigoriev IV, Debuchy R, Gladieux P, Hiltunen Thorén M, Johannesson H
Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.
Mol Phylogenet Evol. 2023 Oct 10;189():107938. doi: 10.1016/j.ympev.2023.107938
Hensen N, Bonometti L, Westerberg I, Brännström IO, Guillou S, Cros-Aarteil S, Calhoun S, Haridas S, Kuo A, Mondo S, Pangilinan J, Riley R, LaButti K, Andreopoulos B, Lipzen A, Chen C, Yan M, Daum C, Ng V, Clum A, Steindorff A, Ohm RA, Martin F, Silar P, Natvig DO, Lalanne C, Gautier V, Ament-Velásquez SL, Kruys Å, Hutchinson MI, Powell AJ, Barry K, Miller AN, Grigoriev IV, Debuchy R, Gladieux P, Hiltunen Thorén M, Johannesson H
Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.
Mol Phylogenet Evol. 2023 Oct 10;189():107938. doi: 10.1016/j.ympev.2023.107938
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.
