Status
Assembly v1 (February 2012) is a draft assembly of Solexa, 454, and Sanger gDNA reads. A total of 1064 scaffolds and 53.0 Mbp were assembled using AllPathsLG.
Summary statistics for the Pisolithus microcarpus v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 53.03 |
| Sequencing read coverage depth | 87.1x |
| # of contigs | 5476 |
| # of scaffolds | 1064 |
| # of scaffolds >= 2Kbp | 877 |
| Scaffold N50 | 89 |
| Scaffold L50 (Mbp) | 0.15 |
| # of gaps | 4412 |
| % of scaffold length in gaps | 10.5% |
| Three largest Scaffolds (Mbp) | 0.95, 0.88, 0.79 |
| RNAs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | INRA_454_ESTs | 195303 | 153702 | 78.7% |
| Ests | NCBI_Sanger_ESTs | 995 | 535 | 53.8% |
| EST contigs | INRA_Mira_contigs | 59500 | 37321 | 62.7% |
| RNA contigs | JGI_Combest_contigs | 141897 | 116852 | 82.3% |
| RNA contigs | JGI_Rnnotator_contigs | 49874 | 40428 | 81.1% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1220 | 840 |
| transcript | 982 | 701 |
| exon | 243 | 162 |
| intron | 80 | 56 |
| description: | ||
| protein length (aa) | 282 | 181 |
| exons per gene | 4.04 | 3 |
| # of gene models | 21064 |
Collaborators
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.
