DOI: 10.5281/zenodo.17475568
title: Genome assemblies and annotations for various codfishes

description: Here we provide the gene annotations for Arctogadus glacialis, Boreogadus saida, Gadus morhua (coastal), Gadus morhua (NEAC; GCF_902167405.1), Lota lota, Melanogrammus aeglefinus and Merluccius merluccius and genome assemblies for Arctogadus glacialis, Boreogadus saida, Gadus morhua (coastal), Lota lota, Melanogrammus aeglefinus and Merluccius merluccius. We also provide draft assemblies of Arctogadus glacialis and Boreogadus saida based on Oxford Nanopore Technologies sequencing data. These have been assembled with hifiasm using --ont and approximately 45x coverage in Oxford Nanopore reads and the Hi-C mode. They were then scaffolded with YaHS and the Hi-C reads, before manually curated (assembled using a pre-release version of the EBP-Nor genome assembly pipeline (https://github.com/ebp-nor/GenomeAssembly)). We provide these for both convenience and because some of the functional annotations of genes/proteins are removed when we prepare these for uploading to ENA. We also provide the FASTA files for the assemblies we have made.

We annotated the genome assemblies using a pre-release version of the EBP-Nor genome annotation pipeline (https://github.com/ebp-nor/GenomeAnnotation). AGAT v1.4 agat_sp_keep_longest_isoform.pl and agat_sp_extract_sequences.pl were used on the zebrafish assembly and annotation to generate one protein (the longest isoform) per gene and miniprot (Li 2023) was used to align the proteins to the assemblies. UniProtKB/Swiss-Prot (UniProt Consortium 2023) release 2025_03 in addition to the actinopterygii part of OrthoDB v12 (Kuznetsov et al. 2023) were also aligned separately to the assemblies. Red (Girgis 2015) was run via redmask (https://github.com/nextgenusfs/redmask) on the assemblies to mask repetitive areas. GALBA (Brůna et al. 2023; Buchfink, Xie, and Huson 2015; Hoff and Stanke 2019; Li 2023; Stanke et al. 2006) was run with the B. stolonifera proteins using the miniprot mode on the masked assemblies. The funannotate-runEVM.py script from Funannotate was used to run EvidenceModeler (Haas et al. 2008) on the alignments of GRCh38 proteins, UniProtKB/Swiss-Prot proteins, vertebrata proteins and the predicted genes from GALBA. The resulting predicted proteins were compared to the protein repeats that Funannotate distributes using DIAMOND blastp and the predicted genes were filtered based on this comparison using AGAT. The filtered proteins were compared to the UniProtKB/Swiss-Prot release 2023_03 using DIAMOND (Buchfink, Xie, and Huson 2015) blastp to find gene names and InterProScan (Jones et al. 2014) was used to discover functional domains. AGATs agat_sp_manage_functional_annotation.pl was used to attach the gene names and functional annotations to the predicted genes. 

All raw sequences, as well as genome assemblies have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under the bioproject PRJEB77069.

List of files provided here and their description:

Arctogadus_glacialis.fa.gz - genome assembly of Arctogadus glacialis

Boreogadus_saida.fa.gz - genome assembly of  Boreogadus saida

Gadus_morhua_coastal.fa.gz - genome assembly of  Gadus morhua (coastal)

Lota_lota.fa.gz - genome assembly of  Lota lota

Melanogrammus_aeglefinus.fa.gz - genome assembly of  Melanogrammus aeglefinus

Merluccius_merluccius.fa.gz - genome assembly of Merluccius merluccius

Arctogadus_glacialis.gff.gz - genome annotation of Arctogadus glacialis

Boreogadus_saida.gff.gz - genome annotation of Boreogadus saida

Gadus_morhua_coastal.gff.gz - genome annotation of Gadus morhua (coastal)

Gadus_morhua_neac.gff.gz - genome annotation of Gadus morhua (NEAC; GCF_902167405.1)

Lota_lota.gff.gz - genome annotation of  Lota lota

Melanogrammus_aeglefinus.gff.gz - genome annotation of Melanogrammus aeglefinus

Merluccius_merluccius.gff.gz - genome annotation of  Merluccius merluccius

Arctogadus_glacialis.proteins.fa.gz - predicted proteins of Arctogadus glacialis

Boreogadus_saida.proteins.fa.gz - predicted proteins of Boreogadus saida

Gadus_morhua_coastal.proteins.fa.gz - predicted proteins of Gadus morhua (coastal)

Gadus_morhua_neac.proteins.fa.gz - predicted proteins of Gadus morhua (NEAC; GCF_902167405.1)

Lota_lota.proteins.fa.gz - predicted proteins of Lota lota

Melanogrammus_aeglefinus.proteins.fa.gz - predicted proteins of Melanogrammus aeglefinus

Merluccius_merluccius.proteins.fa.gz - predicted proteins of Merluccius merluccius

fArcGla1.1.hap1.draft.fa.gz - draft assembly of Arctogadus glacialis

fArcGla1.1.hap2.draft.fa.gz - draft assembly of Arctogadus glacialis 

fBorSai1.1.hap1.draft.fa.gz - draft assembly of Boreogadus saida

fBorSai1.1.hap2.draft.fa.gz - draft assembly of Boreogadus saida