Info • Pholiota sp. NL-8118 v1.0


[July 2022] The Pholiota sp. NL-8118 v1.0 genome was sequenced with PacBio, assembled with Flye (v2.9-b1768), and annotated with the JGI Fungal Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the Download 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 repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Genome Assembly
Genome Assembly size (Mbp) 86.48
Sequencing read coverage depth 47.3x
# of contigs 897
# of scaffolds 897
# of scaffolds >= 2Kbp 884
Scaffold N50 119
Scaffold L50 (Mbp) 0.21
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.93, 0.77, 0.75

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 78318 75856 96.9%
Ests est.fasta 92619167 91646475 98.9%

Gene Models FilteredModels1
length (bp) of: average median
gene 1921 1618
transcript 1560 1314
exon 261 153
intron 74 59
protein length (aa) 453 363
exons per gene 5.99 5
# of gene models 18143



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.