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

Min Yang; Zimin Yang; Cuiyu Liu; Xuezhu Lee; Kecheng Zhu

doi:10.3390/genes13112128

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

Genes (Basel). 2022 Nov 16;13(11):2128. doi: 10.3390/genes13112128.

Authors

Min Yang¹, Zimin Yang¹, Cuiyu Liu¹, Xuezhu Lee¹, Kecheng Zhu²

Affiliations

¹ Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
² Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Catfishes* / genetics
DNA, Mitochondrial / genetics
Genome, Mitochondrial* / genetics
Phylogeny
RNA, Transfer / genetics

Substances

DNA, Mitochondrial
RNA, Transfer

Grants and funding

This research was supported by the Laboratory of Lingnan Modern Agriculture Project (NT2021008); Financial Fund of Ministry of Agriculture and Rural afairs of China (NHYYSWZZZYKZX2020).