Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and Diversification
The mitogenome of an endemic catfish <i>Clarias camerunensis</i> was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accom...
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MDPI AG
2023-02-01
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| author | Piyumi S. De Alwis Shantanu Kundu Fantong Zealous Gietbong Muhammad Hilman Fu’adil Amin Soo-Rin Lee Hyun-Woo Kim Ah Ran Kim |
| author_facet | Piyumi S. De Alwis Shantanu Kundu Fantong Zealous Gietbong Muhammad Hilman Fu’adil Amin Soo-Rin Lee Hyun-Woo Kim Ah Ran Kim |
| author_sort | Piyumi S. De Alwis |
| collection | DOAJ |
| description | The mitogenome of an endemic catfish <i>Clarias camerunensis</i> was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accommodates 28 genes, whereas the light strand is constituted by <i>ND6</i> and eight transfer RNA (tRNA) genes. The <i>C. camerunensis</i> mitochondrial genome is AT biased (56.89%), as showcased in other <i>Clarias</i> species. The comparative analyses revealed that most of the <i>Clarias</i> species have 6 overlapping and 11 intergenic spacer regions. Most of the PCGs were initiated and terminated with the ATG start codon and TAA stop codon, respectively. The tRNAs of <i>C. camerunensis</i> folded into the distinctive cloverleaf secondary structure, except <i>trnS1</i>. The placement of the conserved domains in the control region was similar in all the <i>Clarias</i> species with highly variable nucleotides in CSB-I. Both maximum likelihood and Bayesian-based matrilineal phylogenies distinctly separated all <i>Clarias</i> species into five clades on the basis of their known distributions (South China, Sundaland, Indochina, India, and Africa). The TimeTree analysis revealed that the two major clades (Indo-Africa and Asia) of <i>Clarias</i> species might have diverged during the Paleogene (≈28.66 MYA). Our findings revealed the separation of Indian species (<i>C. dussumieri</i>) and African species (<i>C. camerunensis</i> and <i>Clarias gariepinus</i>) took place during the Paleogene, as well as the South Chinese species (<i>Clarias fuscus</i>) and Sundaland species (<i>Clarias batrachus</i>) splits from the Indochinese species (<i>Clarias macrocephalus</i>) during the Neogene through independent colonization. This pattern of biotic relationships highlights the influence of topography and geological events in determining the evolutionary history of <i>Clarias</i> species. The enrichment of mitogenomic data and multiple nuclear loci from their native range or type locality will confirm the true diversification of <i>Clarias</i> species in African and Asian countries. |
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| spelling | doaj.art-d3e4a69d62ba4727902c20b33466488f2023-11-16T21:41:52ZengMDPI AGLife2075-17292023-02-0113248210.3390/life13020482Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and DiversificationPiyumi S. De Alwis0Shantanu Kundu1Fantong Zealous Gietbong2Muhammad Hilman Fu’adil Amin3Soo-Rin Lee4Hyun-Woo Kim5Ah Ran Kim6Department of Marine Biology, Pukyong National University, Busan 48513, Republic of KoreaDepartment of Marine Biology, Pukyong National University, Busan 48513, Republic of KoreaThe Ministry of Livestock, Fisheries and Animal Industries (MINEPIA), Yaoundé 00237, CameroonAdvance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, IndonesiaResearch Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of KoreaDepartment of Marine Biology, Pukyong National University, Busan 48513, Republic of KoreaResearch Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of KoreaThe mitogenome of an endemic catfish <i>Clarias camerunensis</i> was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accommodates 28 genes, whereas the light strand is constituted by <i>ND6</i> and eight transfer RNA (tRNA) genes. The <i>C. camerunensis</i> mitochondrial genome is AT biased (56.89%), as showcased in other <i>Clarias</i> species. The comparative analyses revealed that most of the <i>Clarias</i> species have 6 overlapping and 11 intergenic spacer regions. Most of the PCGs were initiated and terminated with the ATG start codon and TAA stop codon, respectively. The tRNAs of <i>C. camerunensis</i> folded into the distinctive cloverleaf secondary structure, except <i>trnS1</i>. The placement of the conserved domains in the control region was similar in all the <i>Clarias</i> species with highly variable nucleotides in CSB-I. Both maximum likelihood and Bayesian-based matrilineal phylogenies distinctly separated all <i>Clarias</i> species into five clades on the basis of their known distributions (South China, Sundaland, Indochina, India, and Africa). The TimeTree analysis revealed that the two major clades (Indo-Africa and Asia) of <i>Clarias</i> species might have diverged during the Paleogene (≈28.66 MYA). Our findings revealed the separation of Indian species (<i>C. dussumieri</i>) and African species (<i>C. camerunensis</i> and <i>Clarias gariepinus</i>) took place during the Paleogene, as well as the South Chinese species (<i>Clarias fuscus</i>) and Sundaland species (<i>Clarias batrachus</i>) splits from the Indochinese species (<i>Clarias macrocephalus</i>) during the Neogene through independent colonization. This pattern of biotic relationships highlights the influence of topography and geological events in determining the evolutionary history of <i>Clarias</i> species. The enrichment of mitogenomic data and multiple nuclear loci from their native range or type locality will confirm the true diversification of <i>Clarias</i> species in African and Asian countries.https://www.mdpi.com/2075-1729/13/2/482catfishprimer walkingmitogenomephylogeneticsevolutiondiversification |
| spellingShingle | Piyumi S. De Alwis Shantanu Kundu Fantong Zealous Gietbong Muhammad Hilman Fu’adil Amin Soo-Rin Lee Hyun-Woo Kim Ah Ran Kim Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and Diversification Life catfish primer walking mitogenome phylogenetics evolution diversification |
| title | Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and Diversification |
| title_full | Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and Diversification |
| title_fullStr | Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and Diversification |
| title_full_unstemmed | Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and Diversification |
| title_short | Mitochondriomics of <i>Clarias</i> Fishes (Siluriformes: Clariidae) with a New Assembly of <i>Clarias camerunensis</i>: Insights into the Genetic Characterization and Diversification |
| title_sort | mitochondriomics of i clarias i fishes siluriformes clariidae with a new assembly of i clarias camerunensis i insights into the genetic characterization and diversification |
| topic | catfish primer walking mitogenome phylogenetics evolution diversification |
| url | https://www.mdpi.com/2075-1729/13/2/482 |
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