Abstract
We present the complete genome sequences of 18 species of Gadiformes from 9 genera. Illumina sequencing was performed on genetic material from single wild-caught individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.
Keywords: gadiformes, genomes
Introduction
Gadiformes have been characterized as a monophyletic group within the supra-ordinal taxon Paracanthopterygii (Greenwood et al. 1966). Within the order different authors recognize between 11 and 17 families, about 84 genera, and more than 613 species based on morphological (Endo 2002) and molecular (Roa-Varón and Ortí 2009; Roa-Varón et al. 2021) data. They are distributed from the Arctic to Antarctic oceans, and occupy deep-sea to shallow marine waters, with a single fully freshwater species (Roa-Varón et al. 2021). The gadiforms include some of the most important commercially harvested fishes in the world (e.g., Alaskan Pollock, Atlantic and Pacific cods, Blue Whiting, Hake), accounting for more than a fifth of the world’s catch of marine fishes (FAO 2016).
We present the assembled genome sequences from 18 species of Gadiformes. Tissue samples were obtained from museum specimens representing wild-caught individuals. More detailed information about the specimen used for each species can be found in the Biosample linked to each genome assembly in Genbank.
Methods
DNA extraction was performed using the Qiagen DNAeasy genomic extraction kit using the standard process. A paired-end sequencing library was constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150 bp format. The resulting fastq files were trimmed of adapter/primer sequence and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v2.5 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Funding
Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.
Results and Data Availability
All data, including raw reads and assembled genome sequence, is available via Genbank.
| Eleginus gracilis | SRR12199771 | JAOSLM000000000 |
| Enchelyopus cimbrius | SRR12200187 | JAOPJJ000000000 |
| Gadus macrocephalus | SRR12200186 | JAOSYZ000000000 |
| Gaidropsarus macrophthalmus | SRR12200220 | JAOTIX000000000 |
| Merluccius bilinearis | SRR12199800 | JAOEJO000000000 |
| Merluccius hubbsi | SRR16638530 | JAOEJN000000000 |
| Merluccius paradoxus | SRR12200188 | JAOSLR000000000 |
| Merluccius polylepis | SRR12200221 | JAOPJH000000000 |
| Merluccius productus | SRR12200189 | JAOPJI000000000 |
| Molva macrophthalma | SRR12200191 | JAOPJO000000000 |
| Phycis chesteri | SRR12200192 | JAOPJK000000000 |
| Trisopterus esmarkii | SRR12200185 | JAOPJL000000000 |
| Trisopterus luscus | SRR12199799 | JAOPUA000000000 |
| Trisopterus minutus | SRR16369795 | JAOPUD000000000 |
| Urophycis chuss | SRR12200190 | JAOYML000000000 |
| Urophycis cirrata | SRR12200217 | JAOPUH000000000 |
| Urophycis floridana | SRR12200218 | JAOPUI000000000 |
| Urophycis regia | SRR12200219 | JAOQGG000000000 |
REFERENCES
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
All data, including raw reads and assembled genome sequence, is available via Genbank.
| Eleginus gracilis | SRR12199771 | JAOSLM000000000 |
| Enchelyopus cimbrius | SRR12200187 | JAOPJJ000000000 |
| Gadus macrocephalus | SRR12200186 | JAOSYZ000000000 |
| Gaidropsarus macrophthalmus | SRR12200220 | JAOTIX000000000 |
| Merluccius bilinearis | SRR12199800 | JAOEJO000000000 |
| Merluccius hubbsi | SRR16638530 | JAOEJN000000000 |
| Merluccius paradoxus | SRR12200188 | JAOSLR000000000 |
| Merluccius polylepis | SRR12200221 | JAOPJH000000000 |
| Merluccius productus | SRR12200189 | JAOPJI000000000 |
| Molva macrophthalma | SRR12200191 | JAOPJO000000000 |
| Phycis chesteri | SRR12200192 | JAOPJK000000000 |
| Trisopterus esmarkii | SRR12200185 | JAOPJL000000000 |
| Trisopterus luscus | SRR12199799 | JAOPUA000000000 |
| Trisopterus minutus | SRR16369795 | JAOPUD000000000 |
| Urophycis chuss | SRR12200190 | JAOYML000000000 |
| Urophycis cirrata | SRR12200217 | JAOPUH000000000 |
| Urophycis floridana | SRR12200218 | JAOPUI000000000 |
| Urophycis regia | SRR12200219 | JAOQGG000000000 |