Status
[Aug 2015] The Heliocybe sulcata OMC1185 genome was sequenced using Illumina and assembled with AllPathsLG (Gnerre et al. 2010).
Summary statistics for the Heliocybe sulcata OMC1185 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 31.95 |
| Sequencing read coverage depth | 82.2x |
| # of contigs | 491 |
| # of scaffolds | 87 |
| # of scaffolds >= 2Kbp | 69 |
| Scaffold N50 | 9 |
| Scaffold L50 (Mbp) | 1.17 |
| # of gaps | 404 |
| % of scaffold length in gaps | 1.7% |
| Three largest Scaffolds (Mbp) | 3.42, 2.17, 1.91 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 52086 | 51449 | 98.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1778 | 1531 |
| transcript | 1469 | 1251 |
| exon | 247 | 150 |
| intron | 64 | 57 |
| description: | ||
| protein length (aa) | 416 | 343 |
| exons per gene | 5.95 | 5 |
| # of gene models | 12570 |
Collaborators
Joseph Spatafora, Oregon State University
Laszlo Nagy, Clark University
Otto Miettinen, Clark University
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.
