The complete mitochondrial genome of the deep-water cartilaginous fish Hydrolagus affinis (de Brito Capello, 1868) (Holocephali: Chimaeridae)

Abstract Cartilaginous fishes are a highly vulnerable vertebrate group but remain poorly studied, especially those occupying deep-water ecological niches. Here, we describe the complete mitogenome of the deep-water chimaeriform Hydrolagus affinis (de Brito Capello, 1868) (Holocephali: Chimaeridae). The mitogenome has 19,437 nucleotides and the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA genes, as available for all cartilaginous fishes mitogenomes. Phylogenetic reconstructions including 615 cartilaginous fishes mitogenomes place the H. affinis within the family Chimaeridae but suggest that Hydrolagus and Chimera are not reciprocally monophyletic, highlighting the need for additional molecular data to improve phylogenetic reconstruction.

Research into Chondrichthyes Huxley, 1880 (cartilaginous fishes) biology is critical to understand the evolution of vertebrates. Their ecology, physiology, and evolutionary placement are decisive to understand the origin and evolution of gnathostomes (Inoue et al. 2010;Renz et al. 2013;Boisvert et al. 2019). The subclass Holocephali (chimaeras, ratfishes, and rabbitfishes) is composed of three families (Callorhinchidae Garman, 1901, Rhinochimaeridae Garman, 1901, and Chimaeridae Bonaparte, 1831 widely distributed in the oceans, usually found below 200 m and up to 2000 m (Didier et al. 2012). Their deep-water habitat poses many challenges, resulting in a generalized lack of taxonomic, biological, ecological, and evolutionary knowledge (Venkatesh et al. 2014;Boisvert et al. 2019). Chimaeridae includes nearly 70% of known Holocephalan and comprises two genera, Chimaera Linnaeus, 1758 and Hydrolagus Gill, 1862.
Application of molecular approaches, e.g. mitochondrial genomes (mtDNA), allowed a more comprehensive and detailed biodiversity assessment of cartilaginous fishes (Arnason et al. 2001;Inoue et al. 2010;Johri et al. 2019aJohri et al. , 2019b). Yet, and especially for holocephalans, most studies are still based on morphology or single mitochondrial markers (e.g. Didier et al. 2012;Walovich et al. 2017). Only 10 complete mtDNA have been sequenced for Holocephali; therefore, increasing taxonomic representation is essential to improve our understanding of their evolutionary relationships.
A male Hydrolagus affinis (de Brito Capello, 1868) specimen was captured in the Canadian North-Atlantic (47.3685 N; 46.6540 W) during the EU Groundfish Survey (Flet an Negro 3L-2018). Morphological identification was performed on board and later confirmed by COI mtDNA. Genomic DNA was extracted and used for whole-genome sequencing of 150 bp paired-end (PE) reads on Hiseq X Ten (BioProject PRJNA606208).
The new mitogenome was deposited in GenBank with accession number MT090368 (BioProject PRJNA606208), with a length of 19,437 bp, within the expected range for Holocephalan (16,758-24,889 bp). Gene content and orientation are expected for vertebrate mtDNA: 13 PCGs, 22 transfer RNA, and 2 ribosomal RNA genes. Only one PCG (NAD6) and eight tRNAs are encoded on the complementary strand.
Congruent BI and ML phylogenetic trees, rooted at the split between Holocephali and the remaining cartilaginous fishes (Figure 1), recovered the two subclasses as reciprocally monophyletic, i.e. Holocephali and Elasmobranchii (Boisvert et al. 2019).