Status
[Dec 2015] The Crucibulum laeve genome was sequenced
using the Illumina platform and assembled with AllPathsLG release
version R49403 (Gnerre et al.,
2011)
Mitochondrial genome was assembled separately and is available in
the downloads section.
Summary statistics for the Crucibulum laeve v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 44.73 |
| Sequencing read coverage depth | 106.6x |
| # of contigs | 1536 |
| # of scaffolds | 574 |
| # of scaffolds >= 2Kbp | 406 |
| Scaffold N50 | 19 |
| Scaffold L50 (Mbp) | 0.63 |
| # of gaps | 962 |
| % of scaffold length in gaps | 3.6% |
| Three largest Scaffolds (Mbp) | 3.28, 2.53, 1.85 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 36666 | 35584 | 97.0% |
| Ests | est.fasta | 112265152 | 108265107 | 96.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1732 | 1465 |
| transcript | 1402 | 1161 |
| exon | 232 | 142 |
| intron | 68 | 57 |
| description: | ||
| protein length (aa) | 402 | 322 |
| exons per gene | 6.03 | 5 |
| # of gene models | 14218 |
Collaborators
Laszlo Nagy at the Biological Research Centre, Szeged.
Joseph Spatafora, Oregon State University, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Varga T, Krizsán K, Földi C, Dima B, Sánchez-GarcÃa M, Sánchez-RamÃrez S, SzöllÅ‘si GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, AntonÃn V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Dämon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, KarasiÅ„ski D, Kautmanova I, Kiss B, Kocsubé S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukács Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Rácz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, TomÅ¡ovský M, Tulloss RE, Uehling J, Grigoriev IV, Vágvölgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG
Megaphylogeny resolves global patterns of mushroom evolution.
Nat Ecol Evol. 2019 Apr;3(4):668-678. doi: 10.1038/s41559-019-0834-1
Varga T, Krizsán K, Földi C, Dima B, Sánchez-GarcÃa M, Sánchez-RamÃrez S, SzöllÅ‘si GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, AntonÃn V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Dämon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, KarasiÅ„ski D, Kautmanova I, Kiss B, Kocsubé S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukács Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Rácz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, TomÅ¡ovský M, Tulloss RE, Uehling J, Grigoriev IV, Vágvölgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG
Megaphylogeny resolves global patterns of mushroom evolution.
Nat Ecol Evol. 2019 Apr;3(4):668-678. doi: 10.1038/s41559-019-0834-1
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.
