The published snow crab (Chionoecetes opilio) genome assembly (GCA_016584305.1; ASM1658430v1) was downloaded from NCBI and screened for potential contamination using FCS-GX. Sequences identified as contaminants were removed from the assembly prior to annotation.

The cleaned genome assembly was annotated using the NCBI Eukaryotic Genome Annotation Pipeline (EGAPx) in offline mode. RNA-seq data from multiple snow crab life stages, tissues, and experimental conditions were included as transcriptomic evidence to support gene model prediction. RNA-seq libraries were selected across available experiments and treatment groups, generally prioritizing libraries with the greatest amount of sequence or mapped-read data within each group.

RNA-seq evidence included whole-body juvenile snow crab exposed to different ocean acidification treatments and exposure durations; gill, hepatopancreas, and muscle from adult snow crab; and additional RNA-seq datasets from closely related Tanner crab (Chionoecetes bairdi), including cuticle and gill, hepatopancreas, and muscle tissues. Publicly available RNA-seq datasets were also included to broaden the transcriptomic evidence available for annotation. In total, 60 paired-end RNA-seq libraries were supplied to EGAPx.

Predicted protein sequences from protein-coding gene models were also functionally annotated using eggNOG-mapper against the eggNOG orthology database (Hernández-Plaza et al. 2026) to generate Gene Ontology annotations. This was performed on Galaxy (Galaxy Community 2026).