Status
v1.0 (September,2009):The Pleurotus ostreatus PC9 genome sequence assembly v1.0 was built with Arachne assembler from whole genome shotgun and paired end sequencing reads. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses.
Summary statistics for the Pleurotus ostreatus PC15 v1.0 release:
| Nuclear Genome Assembly | PC15 v1.0 | PC9 v1.0 |
| Nuclear genome size(Mbp) | 34.3 | 35.6 |
| Sequencing read coverage depth | 8.67x | 21.14x |
| Reported # of contigs | 249 | 3272 |
| # of nuclear scaffolds | 19 | 572 |
| # of nuclear scaffolds >2 | 18 | 572 |
| Nuclear scaffold N/L50 | 5/3.3 Mbp | 6/2.1 Mbp |
| Three largest Scaffolds (Mbp) |
4.8 4.6 3.6 |
4.4 3.6 3.3 |
| Sequencing method | Sanger | Mixed: 454 + Sanger |
| Gene Models | PC15 v1.01 | PC9 v1.02 |
| length (bp) of: | average | average |
| gene | 1,772 | 1,692 |
| transcript | 1,377 | 1,310 |
| exon | 217 | 215 |
| intron | 76 | 77 |
| description: | ||
| protein length (aa) | 445 | 413 |
| exons per gene | 6.4 | 6.1 |
| # of gene models | 11.603 | 12.206 |
| Density (Genes/Mbp) | 338 | 343 |
1PleosPC15_1 track FilteredModels5
2PleosPC9_1 track FilteredModels2
| PC15 | PC9 | |||||||
| ESTs | Data set | # sequences total | # mapped to genome | # not mapped to genome | % mapped to genome | # mapped to genome | # not mapped to genome | % mapped to genome |
| EST clusters | PleosPC15_EstClusters_Fruit_bodies_20080420213521_cluster_consensus | 4,796 | 4,632 | 164 | 97% | 4,605 | 191 | 96% |
| PleosPC9_EstClusters_20080420213541_cluster_consensus | 4,338 | 4,182 | 156 | 96% | 4,184 | 154 | 96% | |
| Pleos_EstClusters_20081001000000_cluster_consensus | 9132 | 8,651 | 481 | 95% | 8,644 | 488 | 95% | |
| EST | PleosPC15_Ests_Fruit_bodies_20080420213521_good_ESTs | 13,184 | 12,869 | 315 | 98% | 12,845 | 339 | 97% |
| PleosPC9_Ests_20080420213541_good_ESTs | 13,931 | 13,541 | 390 | 97% | 13,624 | 307 | 98% | |
| Pleos_Ests_20081001000000_good_ESTs | 29,116 | 29,168 | 948 | 97% | 28,222 | 894 | 97% | |
| Other | GenBank_Pleurotus_CompleteCds | 64 | 42 | 22 | 66% | 44 | 20 | 69% |
Collaborators:
- Antonio Pisabarro (Public Univ. of Navarre)
- Lucia Ramirez (Public Univ. of Navarre)
- Allan C. Gathman (Southeast Missouri State Univ.)
- Francis Martin (INRA, France), Ursel Kues (Univ. of Gottingen)
- Yitzhak Hadar (Hebrew Univ. of Jerusalem)
- Christian Kubicek (Tech. Univ. of Vienna)
- Dan Cullen (Univ. of Wisconsin-Madison)
- Bernard Henrissat (Univ. Aix-Marseille)
- Rytas Vlgalys (Duke Univ.)
- Juan Francisco Martin (Instituto de Biotecnologia de Leon)
Links:
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.
