Status
Jul 2014. Trametes ljubarskyi CIRM1659 v1.0 is a standard draft assembly produced with Illumina reads and and assembled with AllpathsLG.
Summary statistics for the Trametes ljubarskyi CIRM1659
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 34.00 |
| Sequencing read coverage depth | 86.3 |
| # of contigs | 761 |
| # of scaffolds | 311 |
| # of scaffolds >= 2Kbp | 257 |
| Scaffold N50 | 29 |
| Scaffold L50 (Mbp) | 0.33 |
| # of gaps | 450 |
| % of scaffold length in gaps | 2.1% |
| Three largest Scaffolds (Mbp) | 1.20, 1.11, 1.10 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_RNA_contigs | 45479 | 43320 | 95.3% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1785 | 1526 |
| transcript | 1455 | 1231 |
| exon | 254 | 155 |
| intron | 72 | 59 |
| description: | ||
| protein length (aa) | 414 | 339 |
| exons per gene | 5.72 | 4 |
| # of gene models | 13180 |
Collaborators
Eric Record (PI) and Marie-Noëlle Rosso, Biodiversity and Biotechnology of Fungi, INRA - Aix Marseille Université
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Hage H, Miyauchi S, Virágh M, Drula E, Min B, Chaduli D, Navarro D, Favel A, Norest M, Lesage-Meessen L, Bálint B, Merényi Z, de Eugenio L, Morin E, Martínez AT, Baldrian P, Štursová M, Martínez MJ, Novotny C, Magnuson JK, Spatafora JW, Maurice S, Pangilinan J, Andreopoulos W, LaButti K, Hundley H, Na H, Kuo A, Barry K, Lipzen A, Henrissat B, Riley R, Ahrendt S, Nagy LG, Grigoriev IV, Martin F, Rosso MN
Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.
Environ Microbiol. 2021 Oct;23(10):5716-5732. doi: 10.1111/1462-2920.15423
Hage H, Miyauchi S, Virágh M, Drula E, Min B, Chaduli D, Navarro D, Favel A, Norest M, Lesage-Meessen L, Bálint B, Merényi Z, de Eugenio L, Morin E, Martínez AT, Baldrian P, Štursová M, Martínez MJ, Novotny C, Magnuson JK, Spatafora JW, Maurice S, Pangilinan J, Andreopoulos W, LaButti K, Hundley H, Na H, Kuo A, Barry K, Lipzen A, Henrissat B, Riley R, Ahrendt S, Nagy LG, Grigoriev IV, Martin F, Rosso MN
Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.
Environ Microbiol. 2021 Oct;23(10):5716-5732. doi: 10.1111/1462-2920.15423
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.
