Status
Serpula lacrymans S7.3 was sequenced using Roche 454 technology. v1.0 was assembled using Newbler. For v2.0, contigs from v1.0 were scaffolded using nucmer show-tiling against Serpula laccrymans S7.9
| Genome Assembly: | Serpula lacrymans S7.3 v2.0 | Serpula lacrymans S7.3 v1.0 | Serpula lacrymans S7.9 |
| Sequencing platform | 454 | 454 | Sanger |
| Scaffold count | 2128 | 6088 | 46 |
| Contig count | 6088 | 6088 | 434 |
| Scaffolds (Mb) | 47 Mb | 42.9 Mb | 42.4 Mb |
| Gaps (Mb) | 12.4 | 0.0 MB | 0.9 MB |
| Scaffold N/L50 | 7/2.7 Mb | 247/45.5 Kb | 6/2.9 Kb |
| Contig N/L50 | 143/86.6 Kb | 247/45.5 Kb | 62/228 Kb |
| Number of scaffolds > 50.0 Kb: | 49 | 219 | 24 |
| % in scaffolds > 50.0 Kb: | 95.1 % | 46.9 % | 99.6 % |
Annotation statistics table for three assemblies:
| Genome Annotation: | Serpula lacrymans S7.3 v2.0 | Serpula lacrymans S7.3 v1.0 | Serpula lacrymans S7.9 |
| # gene models: | 14495 | 16474 | 12917 |
| Gene density (genes/Mb): | 308 | 384 | 302 |
| Ave.gene length (nt): | 1501 | 1379 | 1600 |
| Ave. protein length (aa): | 322 | 295 | 339 |
| Ave. exon/gene: | 5.3 exons/gene | 4.8 exons/gene | 5.6 exons/gene |
| Ave. exon length (nt): | 226 | 230 | 222 |
| Ave. intron length (nt): | 75 | 74 | 77 |
| % complete gene models (with start and stop codons): | 82% | 79% | 87% |
| % genes with homology support: | 68% | 63% | 69% |
| % genes with Pfam domains: | 49% | 45% | 52% |
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.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC
The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi.
Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411
Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC
The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi.
Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411
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.
