Status
June 2013. The Sodiomyces alkalinus genome was sequenced using Illumina technology and assembled using AllPathsLG version R44849. Subsequently it was annotated using the JGI annotation pipeline and custom analyses.
Summary statistics for the Sodiomyces alkalinus v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 43.45 |
| Sequencing read coverage depth | 113.5x |
| # of contigs | 290 |
| # of scaffolds | 29 |
| # of scaffolds >= 2Kbp | 25 |
| Scaffold N50 | 4 |
| Scaffold L50 (Mbp) | 3.52 |
| # of gaps | 261 |
| % of scaffold length in gaps | 0.7% |
| Three largest Scaffolds (Mbp) | 7.53, 6.54, 4.74 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_contigs | 24777 | 24123 | 97.4% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1929 | 1654 |
| transcript | 1649 | 1400 |
| exon | 497 | 241 |
| intron | 123 | 90 |
| description: | ||
| protein length (aa) | 467 | 374 |
| exons per gene | 3.32 | 3 |
| # of gene models | 9411 |
Collaborators
Alexey Grum Grzhimaylo, Wageningen University ([email protected])
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Grum-Grzhimaylo AA, Falkoski DL, van den Heuvel J, Valero-Jiménez CA, Min B, Choi IG, Lipzen A, Daum CG, Aanen DK, Tsang A, Henrissat B, Bilanenko EN, de Vries RP, van Kan JAL, Grigoriev IV, Debets AJM
The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.
Mol Ecol. 2018 Dec;27(23):4808-4819. doi: 10.1111/mec.14912
Grum-Grzhimaylo AA, Falkoski DL, van den Heuvel J, Valero-Jiménez CA, Min B, Choi IG, Lipzen A, Daum CG, Aanen DK, Tsang A, Henrissat B, Bilanenko EN, de Vries RP, van Kan JAL, Grigoriev IV, Debets AJM
The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.
Mol Ecol. 2018 Dec;27(23):4808-4819. doi: 10.1111/mec.14912
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.
