Status
Assembly v1 (Feb 2013) is a standard draft assembly from Illumina gDNAs using AllPathsLG.
Annotation v1 (October 2014) is a standard draft annotation using the JGI Annotation Pipeline.
Summary statistics for the Rhizoscyphus ericae UAMH 7357
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 57.41 |
| Sequencing read coverage depth | 120.9x |
| # of contigs | 1025 |
| # of scaffolds | 267 |
| # of scaffolds >= 2Kbp | 195 |
| Scaffold N50 | 26 |
| Scaffold L50 (Mbp) | 0.70 |
| # of gaps | 758 |
| % of scaffold length in gaps | 1.1% |
| Three largest Scaffolds (Mbp) | 1.93, 1.61, 1.56 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_RNA_contigs | 33904 | 33592 | 99.1% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1650 | 1422 |
| transcript | 1479 | 1257 |
| exon | 490 | 307 |
| intron | 87 | 57 |
| description: | ||
| protein length (aa) | 423 | 342 |
| exons per gene | 3.02 | 3 |
| # of gene models | 16784 |
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:
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
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.
