Status
Assembly v1 (Nov 2013) is an improved draft assembly. A total of 1176 scaffolds and 126.0 Mbp were assembled from Illumina gDNAs using AllPathsLG and improved with PacBio reads using PBJelly.
Summary statistics for the Choiromyces venosus 120613-1
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 126.04 |
| Sequencing read coverage depth | 89.5x |
| # of contigs | 3183 |
| # of scaffolds | 1176 |
| # of scaffolds >= 2Kbp | 802 |
| Scaffold N50 | 62 |
| Scaffold L50 (Mbp) | 0.62 |
| # of gaps | 2007 |
| % of scaffold length in gaps | 2.4% |
| Three largest Scaffolds (Mbp) | 2.21, 2.10, 1.89 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_RNA_contigs | 128365 | 100576 | 78.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1310 | 960 |
| transcript | 1109 | 830 |
| exon | 391 | 263 |
| intron | 111 | 65 |
| description: | ||
| protein length (aa) | 302 | 195 |
| exons per gene | 2.84 | 2 |
| # of gene models | 17986 |
Collaborators
- DOE Joint Genome Institute
- Francis Martin at MycorWeb
- Annegret Kohler at MycorWeb
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsán K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, ŽifÄáková L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P, Martin FM
Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle.
Nat Ecol Evol. 2018 Dec;2(12):1956-1965. doi: 10.1038/s41559-018-0710-4
Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsán K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, ŽifÄáková L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P, Martin FM
Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle.
Nat Ecol Evol. 2018 Dec;2(12):1956-1965. doi: 10.1038/s41559-018-0710-4
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.
