Status
[Feb 2016] The Absidia repens NRRL 1336 genome was sequenced using the PacBio platform and assembled together with Falcon version 0.3.0 (https://github.com/PacificBiosciences/FALCON). Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Absidia repens NRRL 1336
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 47.42 |
| Sequencing read coverage depth | 52.92x |
| # of contigs | 94 |
| # of scaffolds | 94 |
| # of scaffolds >= 2Kbp | 88 |
| Scaffold N50 | 11 |
| Scaffold L50 (Mbp) | 1.30 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 3.90, 2.51, 2.34 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 35484 | 33681 | 94.9% |
| Ests | est.fasta | 159653626 | 157653236 | 98.7% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1795 | 1522 |
| transcript | 1454 | 1208 |
| exon | 308 | 183 |
| intron | 94 | 83 |
| description: | ||
| protein length (aa) | 420 | 339 |
| exons per gene | 4.72 | 4 |
| # of gene models | 14919 |
Collaborators
Jason Stajich, UC Riverside, California
Joey Spatafora, Oregon State, Oregon
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV
Widespread adenine N6-methylation of active genes in fungi.
Nat Genet. 2017 Jun;49(6):964-968. doi: 10.1038/ng.3859
Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV
Widespread adenine N6-methylation of active genes in fungi.
Nat Genet. 2017 Jun;49(6):964-968. doi: 10.1038/ng.3859
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.
