Status
March 2014. The Aspergillus phoenicis (Corda) Thom genome was sequenced using the Illumina platform. The data were initially assembled with Velvet (Zerbino and Birney, 2008), filtered to remove mitochondrial contigs and finally assembled with AllPathsLG release version R47710, (Gnerre et al., 2010). The assembled genome was then annotated with the JGI annotation pipeline and custom analyses.
Summary statistics for the Aspergillus phoenicis (Corda)
Thom ATCC 13157 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 35.75 |
| Sequencing read coverage depth | 116 |
| # of contigs | 95 |
| # of scaffolds | 55 |
| # of scaffolds >= 2Kbp | 53 |
| Scaffold N50 | 10 |
| Scaffold L50 (Mbp) | 1.34 |
| # of gaps | 40 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.83, 2.13, 1.99 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_contigs | 20770 | 20691 | 99.6% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1896 | 1618 |
| transcript | 1686 | 1446 |
| exon | 501 | 293 |
| intron | 91 | 63 |
| description: | ||
| protein length (aa) | 490 | 413 |
| exons per gene | 3.37 | 3 |
| # of gene models | 11977 |
Collaborators
John Gladden, DOE Joint BioEnergy Institute
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR
Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.
Nat Genet. 2018 Dec;50(12):1688-1695. doi: 10.1038/s41588-018-0246-1
Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR
Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.
Nat Genet. 2018 Dec;50(12):1688-1695. doi: 10.1038/s41588-018-0246-1
Links
John Gladden, DOE Joint BioEnergy Institute (JBEI)
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.
