Status
[June 2022] The Penicillium biforme ITEM 15300 v1.0 genome was sequenced with Illumina, assembled with SPAdes, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 35.45 |
| Sequencing read coverage depth | 178.91x |
| # of contigs | 532 |
| # of scaffolds | 473 |
| # of scaffolds >= 2Kbp | 377 |
| Scaffold N50 | 24 |
| Scaffold L50 (Mbp) | 0.47 |
| # of gaps | 59 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.46, 1.23, 1.14 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 48964 | 46828 | 95.6% |
| Ests | est.fasta | 161854028 | 160065887 | 98.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1942 | 1670 |
| transcript | 1764 | 1513 |
| exon | 552 | 330 |
| intron | 83 | 61 |
| description: | ||
| protein length (aa) | 480 | 395 |
| exons per gene | 3.19 | 3 |
| # of gene models | 12781 |
Collaborators
- Scott Baker at DOE Environmental Molecular Sciences Laboratory, Richland, WA, USA
- Giancarlo Perrone at Institute of Sciences of Food Production, National Research Council, Bari, Italy
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Visagie CM, Magistà D, Ferrara M, Balocchi F, Duong TA, Eichmeier A, Gramaje D, Aylward J, Baker SE, Barnes I, Calhoun S, De Angelis M, Frisvad JC, Hakalova E, Hayes RD, Houbraken J, Grigoriev IV, LaButti K, Leal C, Lipzen A, Ng V, Pangilinan J, Pecenka J, Perrone G, Piso A, Savage E, Spetik M, Wingfield MJ, Zhang Y, Wingfield BD
IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1.
IMA Fungus. 2023 Oct 6;14(1):21. doi: 10.1186/s43008-023-00121-w
Visagie CM, Magistà D, Ferrara M, Balocchi F, Duong TA, Eichmeier A, Gramaje D, Aylward J, Baker SE, Barnes I, Calhoun S, De Angelis M, Frisvad JC, Hakalova E, Hayes RD, Houbraken J, Grigoriev IV, LaButti K, Leal C, Lipzen A, Ng V, Pangilinan J, Pecenka J, Perrone G, Piso A, Savage E, Spetik M, Wingfield MJ, Zhang Y, Wingfield BD
IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1.
IMA Fungus. 2023 Oct 6;14(1):21. doi: 10.1186/s43008-023-00121-w
Links
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Eurotiomycetes Eurotiales Penicillium
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.
