Status
Assembly v1 (May 2011) is a draft assembly of 454 gDNA reads and shredded Velvet contigs. The latter were assembled from Solexa gDNA reads. A total of 100 scaffolds and 46.4 Mbp were assembled using Newbler.
Summary statistics for the Oidiodendron maius v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 46.43 |
| Sequencing read coverage depth | 28.70x |
| # of contigs | 387 |
| # of scaffolds | 100 |
| # of scaffolds >= 2Kbp | 100 |
| Scaffold N50 | 8 |
| Scaffold L50 (Mbp) | 1.95 |
| # of gaps | 287 |
| % of scaffold length in gaps | 0.4% |
| Three largest Scaffolds (Mbp) | 6.61, 3.15, 3.00 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | 454_ESTs | 559321 | 333121 | 59.6% |
| Ests | Sanger_ESTs | 218 | 206 | 94.5% |
| Other | Mira_contigs | 28007 | 25169 | 89.9% |
| Other | Newbler_contigs | 12616 | 12402 | 98.3% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1578 | 1342 |
| transcript | 1401 | 1187 |
| exon | 472 | 291 |
| intron | 91 | 58 |
| description: | ||
| protein length (aa) | 429 | 358 |
| exons per gene | 2.97 | 3 |
| # of gene models | 16703 |
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
Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S
Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.
New Phytol. 2018 Feb;217(3):1213-1229. doi: 10.1111/nph.14974
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
Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S
Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.
New Phytol. 2018 Feb;217(3):1213-1229. doi: 10.1111/nph.14974
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.
