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 |
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% |
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
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)
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Alfaro M, Castanera R, LavÃn JL, Grigoriev IV, Oguiza JA, RamÃrez L, Pisabarro AG
Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus.
Environ Microbiol. 2016 Dec;18(12):4710-4726. doi: 10.1111/1462-2920.13360
Alfaro M, Castanera R, LavÃn JL, Grigoriev IV, Oguiza JA, RamÃrez L, Pisabarro AG
Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus.
Environ Microbiol. 2016 Dec;18(12):4710-4726. doi: 10.1111/1462-2920.13360
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.