Info • Mycena vulgaris CBHHK164 v1.0


[June 2018] The Mycena vulgaris genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. Mitochondrial genome was assembled separately and is available in the downloads section.

M. vulgaris is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 1004 of the 1522 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 Mycena vulgaris CBHHK164 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 193.68
Sequencing read coverage depth 89.79x
# of contigs 1522
# of scaffolds 1522
# of scaffolds >= 2Kbp 1505
Scaffold N50 145
Scaffold L50 (Mbp) 0.34
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.88, 1.81, 1.80

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 80824 76218 94.3%
Ests est.fasta 87049398 86478433 99.3%

Gene Models FilteredModels1
length (bp) of: average median
gene 1601 1353
transcript 1241 1044
exon 215 138
intron 77 55
protein length (aa) 376 307
exons per gene 5.77 4
# of gene models 45257


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.