Status
[February 2019] The Geranomyces variabilis JEL559 v1.0 genome was sequenced with Illumina, assembled with AllPathsLG, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Geranomyces variabilis JEL559
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 23.70 |
| Sequencing read coverage depth | 130.6x |
| # of contigs | 290 |
| # of scaffolds | 231 |
| # of scaffolds >= 2Kbp | 205 |
| Scaffold N50 | 30 |
| Scaffold L50 (Mbp) | 0.23 |
| # of gaps | 59 |
| % of scaffold length in gaps | 0.2% |
| Three largest Scaffolds (Mbp) | 0.91, 0.77, 0.72 |
Low rate of EST mapping is due to 1 of the 2 RNA libraries being
poor quality.
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 36064 | 35355 | 98.0% |
| Ests | est.fasta | 175423560 | 90455958 | 51.6% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1956 | 1623 |
| transcript | 1669 | 1374 |
| exon | 387 | 217 |
| intron | 89 | 77 |
| description: | ||
| protein length (aa) | 483 | 379 |
| exons per gene | 4.31 | 3 |
| # of gene models | 9411 |
Collaborators
- Mary Berbee, University of British Columbia, Canada
- Joey Spatafora, Oregon State University, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Amses KR, Simmons DR, Longcore JE, Mondo SJ, Seto K, Jerônimo GH, Bonds AE, Quandt CA, Davis WJ, Chang Y, Federici BA, Kuo A, LaButti K, Pangilinan J, Andreopoulos W, Tritt A, Riley R, Hundley H, Johnson J, Lipzen A, Barry K, Lang BF, Cuomo CA, Buchler NE, Grigoriev IV, Spatafora JW, Stajich JE, James TY
Diploid-dominant life cycles characterize the early evolution of Fungi.
Proc Natl Acad Sci U S A. 2022 Sep 6;119(36):e2116841119. doi: 10.1073/pnas.2116841119
Amses KR, Simmons DR, Longcore JE, Mondo SJ, Seto K, Jerônimo GH, Bonds AE, Quandt CA, Davis WJ, Chang Y, Federici BA, Kuo A, LaButti K, Pangilinan J, Andreopoulos W, Tritt A, Riley R, Hundley H, Johnson J, Lipzen A, Barry K, Lang BF, Cuomo CA, Buchler NE, Grigoriev IV, Spatafora JW, Stajich JE, James TY
Diploid-dominant life cycles characterize the early evolution of Fungi.
Proc Natl Acad Sci U S A. 2022 Sep 6;119(36):e2116841119. doi: 10.1073/pnas.2116841119
Links
- 1000 Fungal Genomes Project
- JGI PhyloGroup Portals: Fungi Chytridiomycota
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.
