[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.