Status
Oct 2013. The Calocera viscosa genome was sequenced using Illumina technology, assembled with AllPathsLG version R44849, (Gnerre et al., 2010), and annotated using the JGI annotation pipeline and custom analyses.
Summary statistics for the Calocera viscosa TUFC12733 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 29.10 |
| Sequencing read coverage depth | 81.7 |
| # of contigs | 487 |
| # of scaffolds | 214 |
| # of scaffolds >= 2Kbp | 173 |
| Scaffold N50 | 23 |
| Scaffold L50 (Mbp) | 0.47 |
| # of gaps | 273 |
| % of scaffold length in gaps | 1.0% |
| Three largest Scaffolds (Mbp) | 1.24, 0.90, 0.88 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_contigs | 32218 | 31511 | 97.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1658 | 1409 |
| transcript | 1433 | 1220 |
| exon | 312 | 193 |
| intron | 65 | 54 |
| description: | ||
| protein length (aa) | 413 | 339 |
| exons per gene | 4.59 | 4 |
| # of gene models | 12378 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J, Larsson KH, Matsuura K, Barry K, Labutti K, Kuo R, Ohm RA, Bhattacharya SS, Shirouzu T, Yoshinaga Y, Martin FM, Grigoriev IV, Hibbett DS
Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.
Mol Biol Evol. 2016 Apr;33(4):959-70. doi: 10.1093/molbev/msv337
Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J, Larsson KH, Matsuura K, Barry K, Labutti K, Kuo R, Ohm RA, Bhattacharya SS, Shirouzu T, Yoshinaga Y, Martin FM, Grigoriev IV, Hibbett DS
Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.
Mol Biol Evol. 2016 Apr;33(4):959-70. doi: 10.1093/molbev/msv337
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.
