Status
Version 1.0 (December 2011) This draft assembly was produced using Illumina sequencing data. This assembly is believed to originate from a diploid organism. In the browser, FilteredModels1 represents the (partially) diploid gene set. Scaffolds that were present in duplicate were identified using the results of a self-self whole genome VISTA analysis, displayed in the synteny browser. Gene models present on the smallest of a duplicated scaffold pair were removed from FilteredModels1, resulting in the putatively haploid gene set FilteredModels3.
Summary statistics for the Gonapodya prolifera JEL478 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 48.79 |
| Sequencing read coverage depth | ? |
| # of contigs | 1154 |
| # of scaffolds | 352 |
| # of scaffolds >= 2Kbp | 294 |
| Scaffold N50 | 42 |
| Scaffold L50 (Mbp) | 0.35 |
| # of gaps | 401 |
| % of scaffold length in gaps | 1.0% |
| Three largest Scaffolds (Mbp) | 1.57, 1.49, 1.04 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_contigs | 39496 | 37454 | 94.8% |
| Gene Models | FilteredModels3 | |
| length (bp) of: | average | median |
| gene | 1818 | 1541 |
| transcript | 1388 | 1147 |
| exon | 249 | 157 |
| intron | 96 | 70 |
| description: | ||
| protein length (aa) | 414 | 334 |
| exons per gene | 5.58 | 5 |
| # of gene models | 13902 |
Collaborators
- Mary Berbee, University of British Columbia, Canada
- Joey Spatafora, Oregon State University, USA
- Igor Grigoriev, DOE Joint Genome Institute
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML
Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.
Genome Biol Evol. 2015 May 14;7(6):1590-601. doi: 10.1093/gbe/evv090
Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML
Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.
Genome Biol Evol. 2015 May 14;7(6):1590-601. doi: 10.1093/gbe/evv090
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.
