Status
This draft assembly was produced using Roche (454) and Illumina data, followed by a round of gapResolution automated gap closure where 19 gaps were closed. The assembler used was Newbler.
Annotation of the assembly was done with the JGI annotation pipeline, using a variety of homology-based and ab initio gene predictors. Some 2.2M ESTs were generated using the Roche (454) sequencing technology. Clustering ESTs with Newbler yielded 6,708 clusters. After filtering for EST support, completeness and homology support, a total of 5,284 genes were structurally and functionally annotated.
Summary statistics for the Wallemia mellicola v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 9.82 |
| Sequencing read coverage depth | 71 |
| # of contigs | 114 |
| # of scaffolds | 56 |
| # of scaffolds >= 2Kbp | 56 |
| Scaffold N50 | 9 |
| Scaffold L50 (Mbp) | 0.34 |
| # of gaps | 29 |
| % of scaffold length in gaps | 0.2% |
| Three largest Scaffolds (Mbp) | 0.90, 0.66, 0.63 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | EstClusters | 6708 | 6061 | 90.4% |
| Ests | Ests | 2239146 | 2083886 | 93.1% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1812 | 1501 |
| transcript | 1652 | 1366 |
| exon | 410 | 196 |
| intron | 55 | 48 |
| description: | ||
| protein length (aa) | 423 | 341 |
| exons per gene | 4.03 | 3 |
| # of gene models | 5284 |
Collaborators
- Igor Grigoriev - DOE Joint Genome Institute
- Joey Spatafora - Oregon State University, Department of Botany and Plant Pathology
- Mahajabeen Padamsee - Louisiana State University Agricultural Center, Plant Pathology and Crop Physiology Department
- Mary Aime - Louisiana State University Agricultural Center, Plant Pathology and Crop Physiology Department
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S, James TY, LaButti K, Lapidus A, Lindquist E, Lucas S, Miller K, Shantappa S, Grigoriev IV, Hibbett DS, McLaughlin DJ, Spatafora JW, Aime MC
The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction.
Fungal Genet Biol. 2012 Mar;49(3):217-26. doi: 10.1016/j.fgb.2012.01.007
Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S, James TY, LaButti K, Lapidus A, Lindquist E, Lucas S, Miller K, Shantappa S, Grigoriev IV, Hibbett DS, McLaughlin DJ, Spatafora JW, Aime MC
The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction.
Fungal Genet Biol. 2012 Mar;49(3):217-26. doi: 10.1016/j.fgb.2012.01.007
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.
