Status
[May 2013] The Coprinopsis cinerea AmutBmut pab1-1 genome was sequenced using the Illumina platform and assembled with AllPathsLG release version R42328 (Gnerre et al., 2010).
Summary statistics for the Coprinopsis cinerea AmutBmut
pab1-1 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 34.12 |
| Sequencing read coverage depth | 141.2x |
| # of contigs | 1053 |
| # of scaffolds | 944 |
| # of scaffolds >= 2Kbp | 759 |
| Scaffold N50 | 89 |
| Scaffold L50 (Mbp) | 0.10 |
| # of gaps | 109 |
| % of scaffold length in gaps | 0.1% |
| Three largest Scaffolds (Mbp) | 0.62, 0.61, 0.57 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | RNASeq assemblies | 55884 | 51455 | 92.1% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1748 | 1482 |
| transcript | 1435 | 1194 |
| exon | 265 | 157 |
| intron | 73 | 58 |
| description: | ||
| protein length (aa) | 433 | 351 |
| exons per gene | 5.41 | 4 |
| # of gene models | 14245 |
Collaborators
Patricia Pukkila, UNC Department of Biology, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Muraguchi H, Umezawa K, Niikura M, Yoshida M, Kozaki T, Ishii K, Sakai K, Shimizu M, Nakahori K, Sakamoto Y, Choi C, Ngan CY, Lindquist E, Lipzen A, Tritt A, Haridas S, Barry K, Grigoriev IV, Pukkila PJ
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea.
PLoS One. 2015;10(10):e0141586. doi: 10.1371/journal.pone.0141586
Muraguchi H, Umezawa K, Niikura M, Yoshida M, Kozaki T, Ishii K, Sakai K, Shimizu M, Nakahori K, Sakamoto Y, Choi C, Ngan CY, Lindquist E, Lipzen A, Tritt A, Haridas S, Barry K, Grigoriev IV, Pukkila PJ
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea.
PLoS One. 2015;10(10):e0141586. doi: 10.1371/journal.pone.0141586
Links
Agaricomycotina at 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.
