Status
Assembly
v2.0 (June 2010) The assembly release version 2.0 is an Arachne assembly that was improved with finishing reads and gap closure. The v2.0 assembly is now in 15 scaffolds at least 10 of which represent nearly complete chromosomes. Roughly half of the genome is contained in 6 scaffolds all at least 2.6 Mb in length.
v1.0 (June 2009) The assembly release version 1.0 of whole shotgun reads was constructed with the Arachne assembler using paired end sequencing reads at a coverage of 8.23x.
| Nuclear Genome Assembly | v1.0 | v2.0 |
| Scaffold count | 39 | 15 |
| All Contig count | 630 | 18 |
| Scaffold sequence bases total | 33.7 Mb | 33.1 Mb |
| Scaffolded (Large) Contig sequence bases total | 33.1 Mb | 33.6 Mb |
| Estimated % sequence bases in gaps | 1.9% | 0.0% |
| Scaffold N50/L50 | 6/2.2 Mb | 6/2.6 Mb |
| Contig N50/L50 | 82/127.0 Kb | 6/2.3 Mb |
| Number of scaffolds > 50.0 Kb | 18 | 14 |
| % in scaffolds > 50.0 Kb | 99.7% | 100.0% |
Annotation
v2.0 (June 2010) of the v2.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. The v1.0 gene catalog along with its manual curations was mapped to the v2.0 assembly and included in filtering. After filtering for EST support, completeness and homology support, a total of 13,405 genes were structurally and functionally annotated.
v1.0 (June 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 homology support, a total of 12,270 genes were structurally and functionally annotated.
| Nuclear Genome Annotation | v1.0 | v2.0 |
| # gene models | 12,270 | 13,405 |
| Gene density | 364.09 | 399.02 |
| Avg.gene length | 1618 nt | 1601 nt |
| Avg. protein length | 382 aa | 379 aa |
| Avg. exon frequency | 5.54 exons/gene | 5.39 exons/gene |
| Avg. exon length | 529 nt | 561 nt |
| Avg. intron length | 83 nt | 82 nt |
| % complete gene models (with start and stop codons) | 88% | 86% |
| % genes with homology support | 54% | 70% |
| % genes with Pfam domains | 34% | 44% |
Collaborators
Jan Stenlid Swedish University of Agricultural Sciences, Uppsala, Sweden
Genome Reference(s)
Olson Å, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canbäck B, Coutinho PM, Cullen D, Dalman K, Deflorio G, van Diepen LTA, Dunand C, Duplessis S, Durling M, Gonthier P, Grimwood J, Fossdal CG, Hansson D, Henrissat B, Hietala A, Himmelstrand K, Hoffmeister D, Högberg N, James TY, Karlsson M, Kohler A, Kües U, Lee YH, Lin YC, Lind M, Lindquist E, Lombard V, Lucas S, Lundén K, Morin E, Murat C, Park J, Raffaello T, Rouzé P, Salamov A, Schmutz J, Solheim H, Ståhlberg J, Vélëz H, de Vries RP, Wiebenga A, Woodward S, Yakovlev I, Garbelotto M, Martin F, Grigoriev IV, Stenlid J
Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.
New Phytol. 2012 Jun;194(4):1001-1013. doi: 10.1111/j.1469-8137.2012.04128.x
