Status
Assembly v1 (27 Apr 2009) is a 'hybrid' assembly of 454 and Sanger gDNA reads. 25 scaffolds and 10.7 Mbp were assembled using Newbler v2:
| Nuclear Genome Assembly | v1.0 |
| Scaffold count: | 25 |
| All Contig count: | 668 |
| Large (>500bp) Contig count: | 139 |
| Scaffold sequence bases total: | 10.7 Mb |
| Scaffolded (Large) Contig sequence bases total: | 10.6 Mb |
| Estimated % sequence bases in gaps: | 0.9% |
| Scaffold N50: | 1.2 Mb |
| Contig N50: | 0.4 Mb |
| Number of scaffolds > 50.0 Kb: | 8 |
| % in scaffolds > 50.0 Kb: | 99.3% |
| Percent GC: | 42% |
Annotation v1.1 (22 Dec 2009) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA-based, protein-based, and ab initio gene predictors. After filtering for EST and protein homology support, a total of 5533 genes were structurally and functionally annotated.
| Nuclear Genome Annotation | v1.1 |
| # gene models: | 5533 |
| Gene density: | 515 genes per Mbp scaffold |
| Ave. gene length: | 1614 nt |
| Ave. protein length: | 447 aa |
| Ave. exon frequency : | 1.2 exons per gene |
| % genes with intron: | 18 % |
| % complete models (with start and stop codons): | 97 % |
| % genes with EST support | 99 % |
| % genes with homology support | 95 % |
| % genes with Pfam domains: | 71 % |
| % genes with transmembrane domain: | 19 % |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP
Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.
Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13212-7. doi: 10.1073/pnas.1103039108
Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP
Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.
Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13212-7. doi: 10.1073/pnas.1103039108
Funding
This work was performed under the auspices of the US Department of
Energy's Office of Science, Biological and Environmental Research
Program, and by the University of California, Lawrence Berkeley
National Laboratory under contract No. DE-AC02-05CH11231, Lawrence
Livermore National Laboratory under Contract No. DE-AC52-07NA27344,
and Los Alamos National Laboratory under contract No.
DE-AC02-06NA25396.
