Status
This draft release was produced using shredded consensus from Velvet-assembled Illumina data, Roche (454) standard and Roche (454) paired end. Newbler was the assembler. Gap closure with gapResolution closed 793 gaps (26%) in initial assembly. The nuclear genome sequence from this finished assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses.
Summary statistics for the Gymnopus luxurians v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 66.28 |
| Sequencing read coverage depth | 29.73 |
| # of contigs | 1848 |
| # of scaffolds | 383 |
| # of scaffolds >= 2Kbp | 383 |
| Scaffold N50 | 30 |
| Scaffold L50 (Mbp) | 0.64 |
| # of gaps | 1465 |
| % of scaffold length in gaps | 1.6% |
| Three largest Scaffolds (Mbp) | 3.44, 2.08, 1.76 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | EstClusters | 60531 | 55342 | 91.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1566 | 1262 |
| transcript | 1233 | 1008 |
| exon | 234 | 143 |
| intron | 80 | 57 |
| description: | ||
| protein length (aa) | 364 | 291 |
| exons per gene | 5.26 | 4 |
| # of gene models | 22057 |
Collaborators
- PI: David Hibbett, Clark University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
Nat Genet. 2015 Apr;47(4):410-5. doi: 10.1038/ng.3223
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
Nat Genet. 2015 Apr;47(4):410-5. doi: 10.1038/ng.3223
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.
