Mitogenomics of the suborder Cottoidei (Teleostei: Perciformes): Improved assemblies, mitogenome features, phylogeny, and ecological implications

We determined the mitogenome of Cyclopterus lumpus using a hybrid sequencing approach, and another four closely related species in the Liparidae based on available next-generation sequence data. We found that the mitogenome of C. lumpus was 17,266 bp in length, where the length and organisation were comparable to those reported for cottoids. However, we found a GC-homopolymer region in the intergenic space between tRNALeu2 and ND1 in liparids and cyclopterids. Phylogenetic reconstruction confirmed the monophyly of infraorders and firmly supported a sister-group relationship between Cyclopteridae and Liparidae. Purifying selection was the predominant force in the evolution of cottoid mitogenomes. There was significant evidence of relaxed selective pressures along the lineage of deep-sea fish, while selection was intensified in the freshwater lineage. Overall, our analysis provides a necessary expansion in the availability of mitogenomic sequences and sheds light on mitogenomic adaptation in Cottoidei fish inhabiting different aquatic environments. •Complete mitogenome of Cyclopterus lumpus was determined to be 17,266 bp in length.•Inferred mitogenome assembly for Liparis tanakae (probably L. ochotensis;17,036 bp), Myoxocephalus scorpius (16,607 bp), Pseudoliparis swirei (20,607 bp) and P. yapensis (20,560 bp).•A GC-homopolymer region in the intergenic space between tRNALeu2 and ND1 was present in liparids and cyclopterids.•Phylogenetic reconstruction confirmed the monophyly of Cottoidei infraorders and recovered the family Stichaeidae and Cottidae as polyphyletic.•A sister-group relationship between Cyclopteridae and Liparidae was firmly supported by phylogenetic reconstruction.•Purifying selection was the predominant force in the evolution of cottoid mitogenomes.