Status
(Oct 2015) The Coprinellus micaceus FP101781 genome was sequenced using PacBio and assembled with Falcon version 20140820, improved with finisherSC, and polished with Quiver.
The JGI annotation pipeline identified 4,948 gene models as possible diploid alleles, and removed them from the filtered model set. The removed models are shown in the track "FM1_removed_alleles", and are available from the download page.
Summary statistics for the Coprinellus micaceus v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 77.39 |
| Sequencing read coverage depth | 74.8x |
| # of contigs | 704 |
| # of scaffolds | 704 |
| # of scaffolds >= 2Kbp | 703 |
| Scaffold N50 | 55 |
| Scaffold L50 (Mbp) | 0.32 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.25, 2.14, 2.07 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 49465 | 47831 | 96.7% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1619 | 1344 |
| transcript | 1330 | 1083 |
| exon | 274 | 167 |
| intron | 77 | 59 |
| description: | ||
| protein length (aa) | 384 | 303 |
| exons per gene | 4.85 | 4 |
| # of gene models | 23559 |
Collaborators
Joseph Spatafora, Oregon State University
Laszlo Nagy, 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-García M, Sánchez-Ramírez S, Szöllősi GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonín 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, Karasiński 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, Tomšovský 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-García M, Sánchez-Ramírez S, Szöllősi GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonín 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, Karasiński 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, Tomšovský 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
Links
Coprinopsis cinerea (Broad) portal on MycoCosm
Coprinopsis cinerea AmutBmut pab1-1 portal on MycoCosm
Agaricales home page on MycoCosm
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.
