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.

Keywords:

• Chondrichthyes
• Holocephali
• Chimaera
• mitogenome
• phylogenetics

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. 2019a, 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 (Fletán 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).

Mitogenome assembly was obtained using NOVOPlasty (v.3.7.1) (Dierckxsens et al. 2016) with 10% of the PE reads (SRR11071609) and annotated using MITOS2 (Bernt et al. 2013).

All available (614) mitogenomes of cartilaginous fishes were retrieved from GenBank (01 November 2019) and their 13 protein-coding genes (PCGs) aligned and concatenated using MAFFT (v.7.402) on XSEDE (Katoh and Standley 2013) and SequenceMatrix (v.1.7.8) (Vaidya et al. 2011), respectively (final length: 11,405 bp). The best partition-scheme for each gene was estimated using PartitionFinder2 (v.2.1.1) on XSEDE (Lanfear et al. 2016) and used for Bayesian phylogeny (GTR + I + G) in MrBayes (v.3.2.6), on XSEDE (Ronquist et al. 2012) with two independent runs (10⁷ generations, sampling frequency one tree for 1000 generations) and maximum likelihood (ML) estimations on RAxML (v.8.2.12) (Stamatakis 2014) HPC Black Box, with a ‘halt bootstrapping automatically’ and 20 ML searches. All analyses were implemented in CIPRES (Miller et al. 2010). Genetic sequence divergence (uncorrected p-distance) was calculated using MEGAX (Kumar et al. 2018).

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).

Figure 1. Bayesian inference phylogenetic tree based on 615 cartilaginous fishes mitogenomes sequences of 13 concatenated protein coding genes. GenBank accession numbers for Holocephalan taxa are behind species names. *Both posterior probabilities and bootstrap support values above 99%.

In Holocephali, three well-supported clades were identified, Callorhinchidae, Rhinochimaeridae, and Chimaeridae, supporting the most comprehensive Holocephalan phylogenetic reconstructions (Arnason et al. 2001; Inoue et al. 2010). Although Hydrolagus and Chimaera cluster within the Chimaeridae group (Figure 1), neither genus was recovered as monophyletic. The two Hydrolagus species show a sequence divergence of 14%. Hydrolagus affinis clusters together with C. monstrosa and C. fluva, showing between 10% and 9% p-distances. Conversely, H. lemures clusters with C. phantasma, showing only 5% p-distance. Together these results reinforce the need for multidisciplinary approaches to further clarify Holocephali systematics and taxonomy.

Acknowledgements

We thank all the participants and crew of the cruise Demersales19 performed on board the R/V Miguel Oliver.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This oceanographic campaign was funded by ERDEM [2015 00000003, Instituto Español de Oceanografía]. This work was financed by the Project The Sea and the Shore, Architecture and Marine Biology: The Impact of Sea Life on the Built Environment [PTDC/ART-DAQ/29537/2017] from FCT/MCTES through National Funds (PIDDAC) and co-financing from the European Regional Development Fund (FEDER) [POCI-01-0145-FEDER-029537], in the aim of the new partnership agreement PT2020 through COMPETE 2020 – Competitiveness and Internationalization Operational Program (POCI), and by FCT – Fundação para a Ciência e a Tecnologia; UIDB/04423/2020, UIDP/04423/2020 which also supported A.G.S. [SFRH/BD/137935/2018]. EU-Spain NAFO Groundfish survey has been co-funded by the European Union through the European Maritime and Fisheries Fund (EMFF) within the National Program of collection, management and use of data in the fisheries sector and support for scientific advice regarding the Common Fisheries Policy and IEO-BIOPESLE Project.