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

Abstract

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.

Figure 1

Map of the Cephalloscyllium umbratile mitochondrial genome. The genes outside the circle are transcribed clockwise, while the genes inside are transcribed counterclockwise. Gene blocks are filled with different colors as the cutline shows. The inner ring shadow indicates the GC content of the genome.

Figure 2

Comparison of codon usage within the mitochondrial genome of members of the Carcharhiniformes. Species (Sphyrna tiburo, Proscyllium habereri, Lamiopsis tephrodes, Pseudotriakis microdon, Cephalloscyllium umbratile, Carcharhinus acronotus, Triaenodon obesus, Loxodon macrorhinus) represent the superfamily to which the species belongs (Sphyrna, Proscyllium, Lamiopsis, Pseudotriakis, Cephaloscyllium, Carcharhinus, Triaenodon, Loxodon).

Figure 3

Codon distribution in members of eight superfamilies in the Carcharhiniformes. CDspT = codons per thousand codons.

Figure 4

Relative Synonymous Codon Usage (RSCU) of the mitochondrial genome of eight superfamilies in the Carcharhiniformes. Codon families are plotted on the x-axis. Codons indicated above the bar are not present in the mitogenome.

Figure 5

Putative secondary structures for 22 tRNA genes in mitochondrial genome of Cephalloscyllium umbratile. Watson-Crick and GT bonds are illustrated by “−” and “+”, respectively.

Figure 6

Ka/Ks ratios for the 13 mitochondrial protein-coding genes among the reference Cephalloscyllium umbratile (CU), Scyliorhinus canicula (SC), Proscyllium habereri (PH).

Figure 7

Phylogenetic trees of Cephalloscyllium umbratile relationships from the nucleotide (A) and amino acid datasets (B). Sequences alignment of mtDNA were analyzed using the MEGA 6.0 and Phylobayes 3.3 f software with Maximum likelihood (ML), Maximum parsimony (MP) and Bayesian inference (BI) method, respectively. The accession numbers of the sequences used in the phylogenetic analysis are listed in Supplementary Table 1.