Info • Lyophyllum atratum CBS 144462 v1.0


[January 2019] The Lyophyllum atratum genome was sequenced using PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Lyophyllum atratum is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 119 of the 171 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 repertoire 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 Lyophyllum atratum DOB2229 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 64.90
Sequencing read coverage depth 30.2x
# of contigs 171
# of scaffolds 171
# of scaffolds >= 2Kbp 171
Scaffold N50 15
Scaffold L50 (Mbp) 1.21
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.67, 3.29, 2.63

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 69135 65412 94.6%
Ests est.fasta 227584787 225707481 99.2%

Gene Models FilteredModels1
length (bp) of: average median
gene 1847 1588
transcript 1505 1282
exon 237 145
intron 66 57
protein length (aa) 441 361
exons per gene 6.34 5
# of gene models 15046


  • Tom Bruns at University of California Berkeley

Genome Reference(s)



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.