Info • Schizophyllum commune v2.0
Please note that this organism is for archival use only. Please see the current Schizophyllum commune H4-8 v3.0 site for the latest data and information.

Status

Version 2, September 2011. This is an improved version of the Schizophyllum commune genome. The original assembly was sequenced using Sanger technology and assembled using Arachne. In this improved assembly one primer walk round reduced the contig count from 667 to 276. In addition to this, 18 telomer signatures were found by extending from the end of scaffolds.

The (Sanger sequenced) ESTs (assembled and unassembled) from version 1 were used to assist gene prediction. In addition to this, Illumina RNAseq data was used as input for both the Combest gene predictor and the RNNotator EST assembly algorithm. This Illumina data sample was previously published in Ohm et al 2011, Molecular Microbiology 81(6):1433-1445 (wild type sample).

 

Summary statistics for the Schizophyllum commune v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp} 38.62
Sequencing read coverage depth 8.29x
# of contigs 276
# of scaffolds 36
# of scaffolds >= 2Kbp 36
Scaffold N50 5
Scaffold L50 (Mbp) 2.55
# of gaps 240
% of scaffold length in gaps 1.5%
Three largest Scaffolds (Mbp) 6.26, 4.44, 3.49


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests ESTs 31336 30104 96.1%
Other EST_clusters 8932 8207 91.9%
Other Rnnotator 47007 33733 71.8%


Gene Models FilteredModels1
length (bp) of: average median
gene 1787 1501
transcript 1447 1216
exon 261 156
intron 77 55
description:
protein length (aa) 440 362
exons per gene 5.54 4
# of gene models 14652


Collaborators

  • Igor Grigoriev, DOE Joint Genome Institute
  • Han Wösten , Utrecht University, The Netherlands
  • Stephen Horton, Union College, NY
  • Erika Kothe, Friedrich-Schiller University Jena, Germany

Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wösten HA
Genome sequence of the model mushroom Schizophyllum commune.
Nat Biotechnol. 2010 Sep;28(9):957-63. doi: 10.1038/nbt.1643

Links

Schizophyllum commune strains sequenced at JGI:



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.