Status
Assembly v2.0 (March 2010): The assembly release version 2.0 of
whole genome shotgun reads was constructed with Arachne, using
paired end sequencing reads at an average coverage of ~8.50X. After
trimming for vector and quality, 372,996 reads assembled into 29
main genome scaffolds totaling 30.2 MB. Roughly half of the genome
is contained in 6 scaffolds all at least 2.3 MB in length. This is
an update to the v1.0 release that makes two additional breaks
based on map integration. v1.0 (Sept 2009): The assembly release
version 1.0 of whole genome shotgun reads was constructed with
Arachne, using paired end sequencing reads at an average coverage
of ~8.50X. After trimming for vector and quality, 372,996 reads
assembled into 27 main genome scaffolds totaling 30.3 MB. Roughly
half of the genome is contained in 5 scaffolds all at least 2.4 MB
in length.
| Nuclear Genome Assembly: | v1.0 | v2.0 |
| Scaffold count: | 27 | 29 |
| All Contig count: | 253 | 254 |
| Scaffold sequence bases total: | 30.0 Mb | 30.0 Mb |
| Scaffolded (Large) Contig sequence bases total: | 30.3 Mb | 30.2 Mb |
| Estimated % sequence bases in gaps: | 0.7% | 0.7% |
| Scaffold N50: | 5 | 6 |
| Contig N50: | 35 | 35 |
| Number of scaffolds > 50.0 Kb: | 17 | 19 |
| % in scaffolds > 50.0 Kb: | 99.7% | 99.7% |
Annotation v2.0 (March 2010): Annotation of the v2.0 assembly was
produced by the JGI Annotation Pipeline, using a variety of
homology-based and ab initio gene predictors. After filtering for
EST support, completeness and homology support, a total of 10,438
genes were structurally and functionally annotated. v1.0 (Sept
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 EST support, completeness and
homology support, a total of 10,387 genes were structurally and
functionally annotated.
| Nuclear Genome Annotation: | v1.0 | v2.0 |
| # gene models: | 10,387 | 10,438 |
| Gene density(genes/Mb scaffold): | 342.81 | 345.63 |
| Avg.gene length: | 1771.79 | 1764.23 |
| Avg. protein length: | 426.20 | 425.89 |
| Avg. exon frequency: | 6.10 exons/gene | 6.05 exons/gene |
| Avg. exon length: | 232.25 | 234.22 |
| Avg. intron length: | 71.72 | 70.96 |
| % complete gene models (with start and stop codons): | 90% | 90% |
| % genes with homology support: | 83% | 83% |
| % genes with Pfam domains: | 52% | 52% |
Collaborators
- Mike Challen,Warwick HRI, University of Warwick, Wellesbourne, UK.
- Rick Kerrigan, Sylvan Inc., USA
- Anton Sonnenberg, Plant Research International, The Netherlands
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hildén K, Kües U, Labutti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wösten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17501-6. doi: 10.1073/pnas.1206847109
Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hildén K, Kües U, Labutti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wösten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17501-6. doi: 10.1073/pnas.1206847109
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.
