Status
This draft release was produced using shredded consensus from Velvet-assembled Illumina data, Roche (454) standard and Roche (454) paired end. Newbler was the assembler. Gap closure with gapResolution closed 597 gaps (32%) in initial assembly. The nuclear genome sequence from this finished assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses.
Summary statistics for the Jaapia argillacea v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 45.05 |
| Sequencing read coverage depth | 20.58 |
| # of contigs | 1182 |
| # of scaffolds | 295 |
| # of scaffolds >= 2Kbp | 295 |
| Scaffold N50 | 13 |
| Scaffold L50 (Mbp) | 1.09 |
| # of gaps | 887 |
| % of scaffold length in gaps | 3.9% |
| Three largest Scaffolds (Mbp) | 3.43, 2.56, 2.07 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | EstClusters | 43770 | 41468 | 94.7% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1668 | 1402 |
| transcript | 1355 | 1142 |
| exon | 245 | 152 |
| intron | 71 | 59 |
| description: | ||
| protein length (aa) | 394 | 322 |
| exons per gene | 5.53 | 4 |
| # of gene models | 16419 |
Collaborators
- PI: David Hibbett, Clark University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.
Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9923-8. doi: 10.1073/pnas.1400592111
Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.
Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9923-8. doi: 10.1073/pnas.1400592111
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.
