Status
Assembly
Agaricus bisporus bar burnettii (May 2010). The original draft assembly for this project was produced using Roche (454) and velveted short read assembly (Illumina) shreds. Newbler was the assembly software used. The assembly was then improved using gapResolution and manual scaffold joining based on synteny to Agaricus bisporus var bisporus v2.0.
Agaricus bisporus var bisporus v2.0 (Nov 2009): 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.
| Nuclear Genome Assembly: | A. bisporus var burnettii | A bisporus var bisporus v2.0 |
| Scaffold count: | 2016 | 29 |
| All Contig count: | 2487 | 254 |
| Scaffold sequence bases total: | 31.2 Mb | 30.0 Mb |
| Scaffolded (Large) Contig sequence bases total: | 32.6Mb | 30.2 Mb |
| Estimated % sequence bases in gaps: | 4.2% | 0.7% |
| Scaffold N50: | 8 | 6 |
| Contig N50: | 38 | 35 |
| Number of scaffolds > 50.0 Kb: | 52 | 19 |
| % in scaffolds > 50.0 Kb: | 87.9% | 99.7% |
Annotation
Agaricus bisporus var burnettii (May 2010): Annotation of the assembly was produced by the JGI annotation pipeline, using a variety of homlogy-based and ab initio gene predictors. ESTs from Agaricus bisporus var bisporus were used. After filtering for EST support, completeness and homology support, a total of 11,289 genes were structurally and functionally annotated.
Agaricus bisporus var bisporus v2.0 (Nov 2009): 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.
| Nuclear Genome Annotation: | Agaricus bisporus var burnettii | Agaraicus bisporus var bisporus v2.0 |
| # gene models: | 11,289 | 10,438 |
| Gene density(genes/Mb scaffold): | 374 | 346 |
| Avg.gene length: | 1669 | 1764 |
| Avg. protein length: | 410 | 426 |
| Avg. exon frequency: | 5.72 exons/gene | 6.05 exons/gene |
| Avg. exon length: | 236 | 234 |
| Avg. intron length: | 69.15 | 70.96 |
| % complete gene models (with start and stop codons): | 87% | 90% |
| % genes with homology support: | 79% | 83% |
| % genes with Pfam domains: | 62% | 52% |
Collaborators
- Francis Martin, Ph.D., Tree-Microbe Interactions Department, INRA-Nancy
- Rick Kerrigan, Sylvan Inc., USA
- Anton Sonnenberg, Plant Research International, The Netherlands
Genome Reference(s)
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
