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

Abstract

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.

Keywords: Arius maculatus; Ka/Ks; RSCU; mitochondrial genome; phylogenetic analysis.

Figure 1

Map of the Arius maculatus mtDNA. Image of the A. maculatus was shown in the middle. The genes inside are transcribed counterclockwise, whereas the genes outside the circle are transcribed clockwise. Gene blocks are filled with different colors, as shown in the cutline. The inner ring shadow indicates the GC content of the mtDNA.

Figure 2

Comparison of codon usage within the mtDNA of members of the Siluriformes. Species (A. maculatus, Pangasius, Horabagrus brachysoma, Synodontis schoutedeni, Clarias gariepinus, Ictalurus furcatus, Ompok bimaculatus, and Glaridoglanis andersonii) represent the superfamily to which the species belongs (Ariidae, Pangasiidae, Bagridae, Mochokinae, Clariidae, Ictaluridae, Siluridae, and Sisoridae).

Figure 3

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

Figure 4

Relative synonymous codon usage (RSCU) of the mtDNA of 8 superfamilies in the Siluriformes. Codon families are plotted on the x-axis. Codons indicated above the bar are not present in the mtDNA.

Figure 5

Putative secondary structures for 22 tRNA genes in mtDNA of A. maculatus. Watson–Crick and GT bonds are expounded by “-” and “+”, respectively.

Figure 6

Ka/Ks ratios for the 13 PCGs among the reference A. maculatus (AM), A. arius (AA), N. thalassina (NT), and O. platypogon (OP).

Figure 7

Phylogenetic trees of A. maculatus relationships from the (A) nucleotide and (B) amino acid datasets. Sequences alignments of mtDNA were analyzed using the RAxML and MrBayes software with the ML and BI method, respectively. Numbers at the nodes are bootstrap values (right) and Bayesian posterior probabilities (left). The accession numbers of the sequences used in the phylogenetic analysis are listed in Table S1.