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.

Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis

“…Previous studies have documented the occurrence of atypical initiation codons in Characiformes, such as Astyanax paranae and Hemigrammus armstrongi [ 13 , 40 ]. Most of the gene overlap regions appeared between PCGs and PCGs, with the largest overlaps all located between ATP8 and ATP6 , consistent with other fish mitogenomes [ 41 , 42 , 43 , 44 ]. Apart from ND3 , the Ka/Ks ratios of other PCGs were lower than 1.…”

Comparison genetic diversity and population structure of four Pseudaspius leptocephalus populations in Heilongjiang River Basin based on mitochondrial COI gene

“…(Javonillo et al, 2010;Lei et al, 2010;Zhang et al, 2015). Therefore, mtDNA is widely used in various research fields, such as DNA structure and gene expression (Yang et al, 2022), taxonomic resolution and species identification (Krzywinski et al, 2011;Zhu et al, 2017), species evolution and phylogenetic distribution (Sharma et al, 2020;Sun CH et al, 2021;Staden et al, 2022;Yang et al, 2022), and population genetics (Gissi et al, 2008;Fang et al, 2021;Zhang et al, 2022). To date, the classification about P. leptocephalus is still disputed.…”