Info • Cyathus pallidus NK-01 v1.0


[August 2022] The Cyathus pallidus NK-01 v1.0 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 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) 158.82
Sequencing read coverage depth 30.89x
# of contigs 235
# of scaffolds 235
# of scaffolds >= 2Kbp 235
Scaffold N50 23
Scaffold L50 (Mbp) 2.58
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 7.51, 6.30, 5.04

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 57448 56172 97.8%
Ests est.fasta 46264374 45401560 98.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1670 1377
transcript 1285 1053
exon 227 137
intron 84 56
protein length (aa) 397 320
exons per gene 5.67 4
# of gene models 32880


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.