Due to a planned NERSC power outage, JGI portals will be unavailable 6:00am PDT July 10 - 11:59pm PDT July 14. System Status updates available here.
Info • Schizophyllum radiatum CBS 301.32 v1.0

Status

[February 2020] The Schizophyllum radiatum CBS 301.32 v1.0 genome was sequenced with Illumina, assembled with SPAdes, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

The genome is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Schizophyllum radiatum CBS 301.32 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 65.76
Sequencing read coverage depth 105.07x
# of contigs 4177
# of scaffolds 4038
# of scaffolds >= 2Kbp 3345
Scaffold N50 553
Scaffold L50 (Mbp) 0.03
# of gaps 139
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.24, 0.22, 0.20


Note: The following EST alignment statistics reflect alignment of Schizophyllum commune H4-8 RNAseq to the Schizophyllum radiatum assembly. Based on poor mapping, H4-8 EST contig assemblies were included only as fgenesh_kg training data when determining the final S. radiatum FilteredModels1 annotation.
ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 83121 27701 33.3%


Gene Models FilteredModels2
length (bp) of: average median
gene 1653 1402
transcript 1319 1110
exon 246 147
intron 79 55
description:
protein length (aa) 427 357
exons per gene 5.37 4
# of gene models 17979


Collaborators

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.