Status
Assembly v1 (Nov 2013) is an improved draft assembly, derived from Illumina gDNAs using AllPathsLG and improved with PacBio reads using PBJelly.
Annotation v1.1 (Dec 2014) is an improved draft annotation, generated by the JGI Annotation Pipeline using various gene modelers and supporting evidence, including RNA-Seq that was not available for Annotation v1.0.
Summary statistics for the Terfezia boudieri ATCC MYA-4762
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 63.23 |
| Sequencing read coverage depth | 104.4x |
| # of contigs | 2078 |
| # of scaffolds | 516 |
| # of scaffolds >= 2Kbp | 401 |
| Scaffold N50 | 24 |
| Scaffold L50 (Mbp) | 0.78 |
| # of gaps | 1562 |
| % of scaffold length in gaps | 5.7% |
| Three largest Scaffolds (Mbp) | 2.60, 2.35, 2.11 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | NCBI_ESTs | 125 | 76 | 60.8% |
| Other | JGI_RNA_contigs | 40993 | 38503 | 93.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1557 | 1275 |
| transcript | 1379 | 1092 |
| exon | 444 | 267 |
| intron | 87 | 65 |
| description: | ||
| protein length (aa) | 388 | 288 |
| exons per gene | 3.10 | 2 |
| # of gene models | 12114 |
Collaborators
- DOE Joint Genome Institute
- Francis Martin at MycorWeb
- Annegret Kohler at MycorWeb
- Claude Murat 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, Žifčáková 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, Žifčáková 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.
