Status
[June 2019] The Plectosphaerella cucumerina MPI-SDFR-AT-0117 v1.0 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 Plectosphaerella cucumerina
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 35.93 |
| Sequencing read coverage depth | 248.39x |
| # of contigs | 97 |
| # of scaffolds | 97 |
| # of scaffolds >= 2Kbp | 92 |
| Scaffold N50 | 12 |
| Scaffold L50 (Mbp) | 1.04 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.56, 2.36, 2.29 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 60051 | 28176 | 46.9% |
| Ests | est.fasta | 12898259 | 12700869 | 98.5% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1782 | 1572 |
| transcript | 1635 | 1443 |
| exon | 569 | 340 |
| intron | 80 | 58 |
| description: | ||
| protein length (aa) | 481 | 415 |
| exons per gene | 2.87 | 2 |
| # of gene models | 12460 |
Collaborators
Francis M. Martin, INRA, France.
Joseph Spatafora, Oregon State University, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S
Genetic determinants of endophytism in the Arabidopsis root mycobiome.
Nat Commun. 2021 Dec 10;12(1):7227. doi: 10.1038/s41467-021-27479-y
Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S
Genetic determinants of endophytism in the Arabidopsis root mycobiome.
Nat Commun. 2021 Dec 10;12(1):7227. doi: 10.1038/s41467-021-27479-y
Links
- 1000 Fungal Genomes Project
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Sordariomycetes
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.
