Status
Assembly v1.0 (December 2009): The assembly release version 1.0 of whole genome shotgun reads was constructed with Arachne, using paired end sequencing reads at an average coverage of ~8.01X. After trimming for vector and quality, 494,556 reads assembled into 46 main genome scaffolds totaling 42.8 MB. Roughly half of the genome is contained in 6 scaffolds all at least 2.9 MB in length.
| Nuclear Genome Assembly: | v1.0 |
| Scaffold count: | 46 |
| All Contig count: | 434 |
| Scaffold sequence bases total: | 42.8 Mb |
| Scaffolded (Large) Contig sequence bases total: | 42.4 Mb |
| Estimated % sequence bases in gaps: | 0.9% |
| Scaffold N50: | 6.0 Mb |
| Contig N50: | 0.6 Mb |
| Number of scaffolds > 50.0 Kb: | 24 |
| % in scaffolds > 50.0 Kb: | 99.6% |
Annotation v1.0 (December 2009) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. After filtering for EST support, completeness and homology support, a total of 12917 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | v1.0 |
| # gene models: | 12917 |
| Gene density: | 301.80 genes per Mbp scaffold |
| Ave.gene length: | 1599.71 nt |
| Ave. protein length: | 339.18 aa |
| Ave. exon frequency: | 5.63 exons/gene |
| Ave. exon length: | 222.22 nt |
| Ave. intron length: | 77.19 nt |
| % complete gene models (with start and stop codons): | 87% |
| % genes with homology support: | 69% |
| % genes with Pfam domains: | 42% |
Collaborators
- Daniel Eastwood,Warwick HRI, University of Warwick, Wellesbourne, UK.
- Nils Hogberg, Department of Forest Mycology & Pathology, Swedish University of Agricultural Sciences, UPPSALA, Sweden.
- Olaf Schmidt, Department of Wood Biology, University of Hamburg, Hamburg, Germany.
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.
