Info • Clitocybe sp. CONT 1119283 v1.0


[August 2019] The Clitocybe sp. CONT 1119283 genome was sequenced with PacBio, assembled with Falcon, 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.

This project was originally conceived around a Lyophyllum montanum OKM 7240 sample but extracted ITS from reassembled ribosomal content suggested otherwise. Lyophyllum montanum is considered a synonym of Clitocybe glaciales. However, both ITS and UNITE barcoding identification was inconclusive. The most significant match to ITS vs UNITE was 97.8% to Clitocybe sp. 4 PA-2015 voucher AH42906.

Summary statistics for the Clitocybe sp. CONT 1119283 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 71.34
Sequencing read coverage depth 282.39x
# of contigs 1410
# of scaffolds 1410
# of scaffolds >= 2Kbp 1385
Scaffold N50 153
Scaffold L50 (Mbp) 0.13
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.95, 0.67, 0.64

Gene Models FilteredModels1
length (bp) of: average median
gene 1644 1386
transcript 1268 1044
exon 200 125
intron 72 57
protein length (aa) 423 348
exons per gene 6.34 5
# of gene models 15344


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.