Arctic charr / Salvelinus alpinus

The Arctic charr (Salvelinus alpinus) is a cold-adapted salmonid fish with a circumpolar distribution across northern freshwater and coastal environments. It is well known for its extensive ecological and morphological diversity, often forming multiple sympatric morphs within the same lake that differ in body size, habitat use, feeding ecology, and life-history strategies. This phenotypic plasticity and genetic differentiation make Arctic charr a valuable model for studying adaptive divergence, speciation, and the genomic basis of ecological polymorphism.

The Arctic charr (Salvelinus alpinus) reference genome assembly fSalAlp1.1 (accession GCA_964197945.1) was produced as part of the European Reference Genome Atlas (ERGA) pilot project. The assembly is based on a single male large benthivorous morph sampled from Lake Thingvallavatn, Iceland, and was generated using PacBio HiFi long reads together with Illumina Hi-C scaffolding. The final assembly spans ~2.4 Gb across 40 chromosome-level scaffolds.

The accompanying annotation, Saalp_EIv1.0, was constructed using the REAT and Minos pipelines by integrating Illumina short read RNA-seq and PacBio Iso-Seq full-length transcripts, protein homology from related salmonids, and ab initio predictions. The resulting dataset provides a consolidated gene set organized by confidence level (high- and low-confidence), with functional annotation based on InterProScan and UniProt homology.

Details about the assembly and annotation are described in the article Whole genome sequencing reveals how plasticity and genetic differentiation underlie sympatric morphs of Arctic charr (Kurta et al., 2025, Molecular Ecology). The assembly and annotation was downloaded from the associated Zenodo repository. The underlying sequence read data are deposited in ENA project PRJEB76174.