Agaricus bisporus var bisporus (H97) v2.0
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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

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.