Info • Hygrocybe coccinea JK88 v1.0


[August 2022] The Hygrocybe coccinea JK88 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The 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) 167.43
Sequencing read coverage depth 77.9x
# of contigs 1846
# of scaffolds 1846
# of scaffolds >= 2Kbp 1833
Scaffold N50 304
Scaffold L50 (Mbp) 0.17
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.72, 0.70, 0.67

Note: RNA data suffers from contamination. A small read percentage of reads contributed to the creation of unmatched contigs.

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 120728 83745 69.4%
Ests est.fasta 216431877 212261197 98.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1782 1436
transcript 1409 1110
exon 241 152
intron 79 58
protein length (aa) 432 330
exons per gene 5.84 5
# of gene models 23450



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.