Complete mitochondrial genome and the phylogenetic position of the Blotchy swell shark Cephaloscyllium umbratile

Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications

The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.

The Nursehound Scyliorhinus stellaris Mitochondrial Genome—Phylogeny, Relationships among Scyliorhinidae and Variability in Waters of the Balearic Islands

The complete mitochondrial DNA sequence of the Nursehound Scyliorhinus stellaris has been determined for the first time and compared with congeneric species. The mitogenome sequence was 16,684 bp in length. The mitogenome is composed of 13 PCGs, 2 rRNAs, 22 transfer RNA genes and non-coding regions. The gene order of the newly sequenced mitogenome is analogous to the organization described in other vertebrate genomes. The typical conservative blocks in the control region were indicated. The phylogenetic analysis revealed a monophyletic origin of the Scyliorhininae subfamily, and within it, two subclades were identified. A significant divergence of Scyliorhinus spp. together with Poroderna patherinum in relation to the group of Cephaloscyllium spp. was observed, except for Scyliorhinus torazame, more related to this last cited clade. A hypothesis of a divergent evolution consequent to a selective pressure in different geographic areas, which lead to a global latitudinal diversity gradient, has been suggested to explain this phylogenetic reconstruction. However, convergent evolution on mitochondrial genes could also involve different species in some areas of the world.

The complete mitogenome of the Critically Endangered smalltooth sand tiger shark, Odontaspis ferox (Lamniformes: Odontaspididae)

Here, we report the first complete mitochondrial genome for the smalltooth sand tiger shark, Odontaspis ferox (Risso, 1810). The circular mitochondrial genome was found to be 16,682 bp in length and contains 37 genes, a control region and the replication origin of the L-strand (O_L). The base composition of this mitogenome is 32.6% A, 23.3% C, 12.8% G, and 31.3% T. Phylogenetic analysis of Lamniformes indicates that O. ferox did not group with Carcharias taurus and so the taxonomic classification of Odontaspididae needs to be revised. This study promotes conservation genetics for this poorly studied shark species which is listed critically endangered in the Mediterranean Sea.

Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.

The phylogenomic position of the sabre squirrelfish Sargocentron spiniferum (beryciformes: holocentridae) inferred from the mitochondrial genome

In this study, the complete mitochondrial genome of the sabre squirrelfish Sargocentron spiniferum, one member of family Holocentridae, is determined. It is a circular molecule whose length reaches 16,548 bp, consisting of 37 genes with typical order to most Chinese vertebrates. The nucleotide composition is: 30.3% A, 29.0% C, 15.3% G and 25.5% T. Located in gene junctions, there are total 39 bp short intergenic spaces and 30 bp overlaps. Two initial codons (GTG and ATG) and three terminal codons (TAG, AGG and TAA/T) are used in the protein-coding genes. Twenty-two tRNAs range from 67 to 74 bp. The control region (865 bp) is located between the tRNA-Pro and tRNA-Phe genes. The phylogenetic results show that S. spiniferum is sister to S. rubrum.

Complete mitochondrial genome and the phylogenetic position of theTaiwan spurdog shark Squalus formosus (Squaliformes: Squalidae)

The complete mitogenome of the Taiwan spurdog shark Squalus formosus (Squaliformes: Squalidae) is determined in this study. It is a circle molecular (16,735 bp), containing 37 genes with typical order to that of most other vertebrates. The nucleotide composition is: A 30.9%; C 24.5%; G 14.2%; T 30.5%. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) are used in the protein-coding genes. 22 tRNA genes range from 66 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic result shows that S. formosus clusters to the (Squalus acanthias + Cirrhigaleus australis) clade.

The phylogenomic position of the Winghead Shark Eusphyra blochii (Carcharhiniformes, Sphyrnidae) inferred from the mitochondrial genome

The complete mitogenome of the Winghead Shark Eusphyra blochii (Carcharhiniformes: Sphyrnidae) is determined in this study, which is 16,727 bp with a nucleotide base composition: 31.6% A, 25.7% C, 13.0% G and 29.7% T, containing 37 genes with the typical gene arrangement pattern and translate orientation in vertebrates. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) are found in the protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic position showed that E. blochii clustered with the Sphyrna clade with strong posterior probability (100%).