A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads

Abstract

Chondrichthyans (sharks, rays and chimeras) are a fascinating and highly vulnerable group of early branching gnathostomes. However, they remain comparatively poorly sampled from the point of view of molecular resources, with deep water taxa being particularly data deficient. The development of long-read sequencing technologies enables the analysis of phylogenetic relationships through a precise and reliable assembly of complete mtDNA genomes. The sequencing and characterization of the complete mitogenome of the opal chimera Chimera opalescens Luchetti, Iglésias et Sellos 2011, using the long-read technique PacBio HiFi is presented. The entire mitogenome was 23,411 bp long and shows the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes, as all other examined Chondrichthyan mitogenomes. Phylogenetic reconstructions using all available Chondrichthyan mitogenomes, including 11 Holocephali (chimeras and ratfishes), places C. opalescens within the Chimaeridae family. Furthermore, the results reinforce previous findings, showing the genus Chimera as paraphyletic and thus highlighting the need to expand molecular approaches in this group of cartilaginous fishes.

The Paleozoic assembly of the holocephalian body plan far preceded post-Cretaceous radiations into the ocean depths

“…Chimaeridae includes species traditionally placed in the genera Chimaera and Hydrolagus (Figure 2; Figure S3). However, as in previous studies we fail to resolve the reciprocal monophyly of these genera (Figure S3) [34,49,75,76]. Instead, we resolve four major clades in Chimaeridae, two of which necessitate the resurrection of available generic names.…”

“…Using this approach, we were able to sample 100% of all living holocephalian genera and species complexes, including all three species in Callorhinchus, seven of the nine recognized species in Rhinochimaeridae, and 35 of 47 described species of Chimaeridae [40], plus two specimens of Chimaera sp. with mitogenomes that appear to diverge considerably from other species [48,49]. We concatenated these data into a single set of aligned sequences for subsequent phylogenetic analyses.…”

Complete mitochondrial genome of Hydrolagus mitsukurii (Jordan & Snyder, 1904)

“… 2021 ; Vilas-Arrondo et al. 2022 ). Hydrolagus and Chimera were also resolved as paraphyletic by the mitochondrial genome tree in the present study, which indicated the affinity of the two genera and the necessity of a comprehensive phylogenetic review.…”

The complete mitogenome of the Atlantic longnose chimaera Rhinochimaera atlantica (Holt & Byrne, 1909)

“… 2001 ), OK638184 ( C. opalescens ) (Vilas-Arrondo et al. 2022 ), MT880605 ( Chimaera sp.) (unpublished), HM147138 ( C. fulva ) (Inoue et al.…”