Status
v1.0 (July, 2012): The assembly release version 1.0 of Amanita thiersii Skay4041 was generated using the Roche 454 and Illumina sequencing platforms and the Newbler, Velvet and AllPathsLG (version R38445) assemblers.
Summary statistics for the Amanita thiersii Skay4041 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 33.69 |
| Sequencing read coverage depth | 135.9x |
| # of contigs | 2164 |
| # of scaffolds | 1446 |
| # of scaffolds >= 2Kbp | 1172 |
| Scaffold N50 | 95 |
| Scaffold L50 (Mbp) | 0.08 |
| # of gaps | 718 |
| % of scaffold length in gaps | 1.7% |
| Three largest Scaffolds (Mbp) | 1.04, 0.67, 0.60 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | ESTs (grown on grass medium, sequenced with 454 technology) | 1375222 | 1333143 | 96.9% |
| Ests | ESTs (grown on rich medium, sequenced with 454 technology) | 1231280 | 1192657 | 96.9% |
| Other | Clusters (assemblies of the ESTs) | 25107 | 24399 | 97.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1687 | 1399 |
| transcript | 1360 | 1107 |
| exon | 226 | 138 |
| intron | 67 | 57 |
| description: | ||
| protein length (aa) | 423 | 340 |
| exons per gene | 6.02 | 5 |
| # of gene models | 10354 |
Collaborators
- Anne Pringle, Harvard University
- Benjamin Wolfe, Harvard University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Hess J, Skrede I, Wolfe BE, LaButti K, Ohm RA, Grigoriev IV, Pringle A
Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.
Genome Biol Evol. 2014 Jun 12;6(7):1564-78. doi: 10.1093/gbe/evu121
Chaib De Mares M, Hess J, Floudas D, Lipzen A, Choi C, Kennedy M, Grigoriev IV, Pringle A
Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita.
New Phytol. 2015 Mar;205(4):1552-1564. doi: 10.1111/nph.13140
Hess J, Skrede I, Wolfe BE, LaButti K, Ohm RA, Grigoriev IV, Pringle A
Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.
Genome Biol Evol. 2014 Jun 12;6(7):1564-78. doi: 10.1093/gbe/evu121
Chaib De Mares M, Hess J, Floudas D, Lipzen A, Choi C, Kennedy M, Grigoriev IV, Pringle A
Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita.
New Phytol. 2015 Mar;205(4):1552-1564. doi: 10.1111/nph.13140
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.
