Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic Implications
The spotted catfish, <i>Arius maculatus</i> (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 insufficien...
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MDPI AG
2022-11-01
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| author | Min Yang Zimin Yang Cuiyu Liu Xuezhu Lee Kecheng Zhu |
| author_facet | Min Yang Zimin Yang Cuiyu Liu Xuezhu Lee Kecheng Zhu |
| author_sort | Min Yang |
| collection | DOAJ |
| description | The spotted catfish, <i>Arius maculatus</i> (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 <i>A. maculatus</i> mitochondrial genome (mtDNA). The <i>A. maculatus</i> 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 <i>A. maculatus</i> 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 <i>A. maculatus</i> and <i>Netuma thalassina</i> (Netuma), <i>Occidentarius platypogon</i> (Occidentarius), and <i>Bagre panamensis</i> (Bagre) were clustered as sister clade. The complete mtDNA of <i>A. maculatus</i> provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species. |
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| spelling | doaj.art-12d742a3a56b47af9a318e73e4b087f72023-11-24T08:26:44ZengMDPI AGGenes2073-44252022-11-011311212810.3390/genes13112128Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic ImplicationsMin Yang0Zimin Yang1Cuiyu Liu2Xuezhu Lee3Kecheng Zhu4Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaJoint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaJoint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaJoint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaKey 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, ChinaThe spotted catfish, <i>Arius maculatus</i> (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 <i>A. maculatus</i> mitochondrial genome (mtDNA). The <i>A. maculatus</i> 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 <i>A. maculatus</i> 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 <i>A. maculatus</i> and <i>Netuma thalassina</i> (Netuma), <i>Occidentarius platypogon</i> (Occidentarius), and <i>Bagre panamensis</i> (Bagre) were clustered as sister clade. The complete mtDNA of <i>A. maculatus</i> provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.https://www.mdpi.com/2073-4425/13/11/2128<i>Arius maculatus</i>mitochondrial genomeRSCUKa/Ksphylogenetic analysis |
| spellingShingle | Min Yang Zimin Yang Cuiyu Liu Xuezhu Lee Kecheng Zhu Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic Implications Genes <i>Arius maculatus</i> mitochondrial genome RSCU Ka/Ks phylogenetic analysis |
| title | Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic Implications |
| title_full | Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic Implications |
| title_fullStr | Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic Implications |
| title_full_unstemmed | Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic Implications |
| title_short | Characterization of the Complete Mitochondrial Genome of the Spotted Catfish <i>Arius maculatus</i> (Thunberg, 1792) and Its Phylogenetic Implications |
| title_sort | characterization of the complete mitochondrial genome of the spotted catfish i arius maculatus i thunberg 1792 and its phylogenetic implications |
| topic | <i>Arius maculatus</i> mitochondrial genome RSCU Ka/Ks phylogenetic analysis |
| url | https://www.mdpi.com/2073-4425/13/11/2128 |
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