Chondrichthyans comprise a diverse group of vertebrate species with extraordinary ecological relevance. Yet, multiple members of this evolutionary lineage are associated with significant extinction risk. The sailfin roughshark Oxynotus paradoxus is a deep-water benthic shark currently listed as vulnerable due to population declines in parts of its range. Here we provide the first complete mitochondrial genome of O. paradoxus, comprising also the first record for the genus and family Oxynotidae. These data can facilitate future monitoring of the genetic diversity in this and related species. Genomic DNA was extracted from O. paradoxus collected in the eastern North Atlantic off western Portugal (37.59°N, 9.51°W) and sent for Illumina Paired-End (2 × 150 bp) library construction and whole genome sequencing on a Novaseq6000 platform. Trimmomatic (version 0.38) was used to remove adapters and MitoZ (version 3.4) to assemble and annotate the mitogenome. This mitogenome with 17 100 bp has a total of 38 genes, 13 of which are protein-coding genes, 23 transfer RNA genes, and 2 ribosomal RNA genes. Eight transfer RNAs and 1 protein-coding gene (NADH dehydrogenase subunit 6, NAD6) are in the complementary strand. In the provided phylogenetic inference, with all available and verified Squalomorphii mitogenomes, the four orders are well separated, and as expected, O. paradoxus is placed in the Squaliformes order. This data reinforces the need for more genomic resources for the Oxynotidae family.
Deep-water sharks are among the most vulnerable deep-water taxa because of their extremely conservative life-history strategies (i.e., late maturation, slow growth, and reproductive rates), yet little is known about their biology and ecology. Thus, this study aimed at investigating the trophic ecology of five deep-water shark species, the birdbeak dogfish (Deania calcea), the arrowhead (D. profundorum), the smooth lanternshark (Etmopterus pusillus), the blackmouth catshark (Galeus melastomus) and the knifetooth dogfish (Scymnodon ringens) sampled onboard a crustacean bottom-trawler off the south-west coast of Portugal. We combined carbon and nitrogen stable isotopes with RNA and DNA (RD) ratios to investigate the main groups of prey assimilated by these species and their nutritional condition, respectively. Stable isotopes revealed overall small interspecific variability in the contribution of different taxonomic groups to sharks' tissues, as well as in the origin of their prey. S. ringens presented higher δ15 N and δ13 C values than the other species, suggesting reliance on bathyal cephalopods, crustaceans and teleosts; the remaining species likely assimilated bathy-mesopelagic prey. The RD ratios indicated that most of the individuals had an overall adequate nutritional condition and had recently eaten. This information, combined with the fact that stable isotopes indicate that sharks assimilated prey from the local or nearby food webs (including commercially important shrimps), suggests a potential overlap between this fishing area and their foraging grounds, which requires further attention.
Skates, Chondrichthyes fishes from order Rajiformes, are the most species-rich group of all Batoidea. However, their phylogenetic relationships and systematics is still a highly discussed and controversial subject. The use of complete mitogenome has shown to be a promising tool to fill this gap of knowledge. Here, the complete mitogenome of the Iberian pygmy skate Neoraja iberica (Stehmann, Séret, Costa & Baro 2008) was sequenced and assembled. The mitogenome is 16,723 bp long and its gene content (i.e. 13 protein-coding genes, 22 transfer RNA, and 2 ribosomal RNA genes) and arrangement are the expected for Batoidea. Phylogenetic reconstructions, including 89 Rajiformes and two outgroup Rhinopristiformes, recovered family Rajidae as monophyletic, and further divided in the monophyletic tribe Rajini, sister to tribes Amblyrajini and Rostrorajini. The newly sequenced N. iberica mitogenome is the first representative of the tribe Rostrorajini.
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