Status
Assembly v2 (27 Apr 2010) is a hybrid assembly of 454 and Sanger gDNA reads that has been polished with Solexa reads and improved with targeted Sanger reads. 8 scaffolds and 13.2 Mbp were assembled using Newbler v2:
| Nuclear Genome Assembly | v2.0 |
| Scaffold count: | 8 |
| All Contig count: | 26 |
| Scaffold sequence bases total: | 13.2Mb |
| Scaffolded (Large) Contig sequence bases total: | 13.1Mb |
| Estimated % sequence bases in gaps: | 0.8 |
| Scaffold N50 / L50: | 3 / 2.1 Mb |
| Contig N50 / L50: | 4 / 1.6 Mb |
| Number of scaffolds > 50.0 Kb: | 8 |
| % in scaffolds > 50.0 Kb: | 100% |
| Percent GC: | 42% |
Annotation v2 (27 Apr 2010) of the v2.0 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 5983 genes were structurally and functionally annotated.
| Nuclear Genome Annotation | v2.0 |
| # gene models: | 5983 |
| Gene density: | 454 genes per Mbp scaffold |
| Ave. gene length: | 1786 nt |
| Ave. protein length: | 451 aa |
| Ave. exon frequency : | 1.2 exons per gene |
| % genes with intron: | 17% |
| % complete gene models (with start and stop codons) | 92% |
| % genes with EST support: | 97% |
| % genes with homology support | 96% |
| % genes with Pfam domains: | 68% |
| % genes in multigene family: | 49% |
| % genes with transmembrane domain: | 19% |
Assembly v1 (27 Apr 2009) is a 'hybrid' assembly of 454 and Sanger gDNA reads. 47 scaffolds and 13.3 Mbp were assembled using Newbler v2:
| Nuclear Genome Assembly | v1.0 |
| Scaffold count: | 47 |
| All Contig count: | 1126 |
| Large (>500bp) Contig count: | 194 |
| Scaffold sequence bases total: | 13.3 Mb |
| Scaffolded (Large) Contig sequence bases total: | 13.0 Mb |
| Estimated % sequence bases in gaps: | 2.0% |
| Scaffold N50: | 1.7 Mb |
| Contig N50: | 0.2 Mb |
| Number of scaffolds > 50.0 Kb: | 9 |
| % in scaffolds > 50.0 Kb: | 98.6% |
| Percent GC: | 37% |
The draft annotation release version 1.0 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 homology support, a total of 5726 genes were structurally and functionally annotated. 98% of the genes have homology support and 71% have Pfam support.
| Nuclear Genome Annotation | v1.0 |
| # gene models: | 5726 |
| Gene density: | 431 genes per Mbp scaffold |
| Ave. gene length: | 1472 nt |
| Ave. protein length: | 1433 aa |
| Ave. exon frequency : | 1.3 exons per gene |
| Ave. exon length: | 1151 nt |
| Ave. intron length: | 161 nt |
| % complete gene models (with start and stop codons) | 97% |
| % genes with homology support | 98% |
| % genes with Pfam domains: | 71% |
Collaborators
Genome Reference(s)
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
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231
