1
|
Kundu S, Kang HE, Kim AR, Lee SR, Kim EB, Amin MHF, Andriyono S, Kim HW, Kang K. Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae). Int J Mol Sci 2024; 25:1822. [PMID: 38339100 PMCID: PMC10855530 DOI: 10.3390/ijms25031822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.
Collapse
Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Eun-Bi Kim
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea;
| | - Muhammad Hilman Fu’adil Amin
- Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia;
| | - Sapto Andriyono
- Department of Marine, Faculty of Fisheries and Marine, Airlangga University, Surabaya 60115, Indonesia
| | - Hyun-Woo Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Kyoungmi Kang
- International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
| |
Collapse
|
2
|
Zhang Q, Li F, Li G, Dong Y, Wang J, Chen D, Shen Z. The complete mitochondrial genome of a new geographical population of freshwater fish Macropodus hongkongensis (Freyhof & Herder, 2002). Mitochondrial DNA B Resour 2023; 8:1298-1300. [PMID: 38188427 PMCID: PMC10769546 DOI: 10.1080/23802359.2023.2278819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024] Open
Abstract
Macropodus hongkongensis (Freyhof & Herder, 2002), is sparsely distributed in Hong Kong and Guangdong provinces. Recently, a new geographical population of M. hongkongensis was discovered in the Wanquan River in the Hainan province. Therefore, this study focused on sequencing the complete mitochondrial genome of the new geographical population of Macropodus hongkongensis from the Wanquan River. The circular mtDNA molecule was 16,492 bp in size, and the overall base compositions were A (30.30%), C (24.90%), T (29.80%), and G (15.00%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis indicated that M. hongkongensis of the Hainan Wanquan River was most closely related to the M. hongkongensis of the Gongdong population. These results provide useful genetic information for species identification and phylogenetic studies of Macropodus species.
Collapse
Affiliation(s)
- Qingfeng Zhang
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Fangyuan Li
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Gaojun Li
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Yang Dong
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Ji Wang
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Dikai Chen
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Zhixin Shen
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| |
Collapse
|
3
|
Zhang R, Zhu T, Luo Q. The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis. Genes (Basel) 2023; 14:1227. [PMID: 37372406 DOI: 10.3390/genes14061227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Onychostoma ovale. The mitogenome of O. ovale was 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the O. ovale mitogenome was 31.47% A, 24.07% T, 15.92% G, and 28.54% C, with a higher A + T content (55.54%) than G + C content (44.46%). All PCGs began with the standard ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene and the NADH dehydrogenase 3 (ND3) gene with GTG, while six PCGs ended with incomplete termination codons (TA or T). The Ka/Ks ratios of 13 PCGs were all less than one, indicating that they were under purifying selection. All tRNA genes were folded into the typical cloverleaf secondary structures with the exception of tRNASer(AGY), whose dihydrouridine (DHU) arm was absent. The phylogenetic trees showed that Onychostoma and Acrossocheilus were classified into three clades. There was a mosaic relationship between Onychostoma and Acrossocheilus. Moreover, the phylogenetic tree analysis showed that O. rarum was the closest species to O. ovale. This study can provide a useful resource for further phylogeny and population genetic analyses of Onychostoma and Acrossocheilus.
Collapse
Affiliation(s)
- Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Tingting Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Qi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| |
Collapse
|
4
|
Comparative Mitogenomics of Two Sympatric Catfishes of Exostoma (Siluriformes: Sisoridae) from the Lower Yarlung Tsangpo River and Its Application for Phylogenetic Consideration. Genes (Basel) 2022; 13:genes13091615. [PMID: 36140782 PMCID: PMC9498720 DOI: 10.3390/genes13091615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Exostoma is a group of stenotopic and rheophilic glyptosternine catfishes distributed in South and Southeast Asia. So far, comprehensive studies on mitogenomics referring to this genus are very scarce. In this study, we first sequenced and annotated the complete mitochondrial genomes of Exostoma tibetanum and Exostoma tenuicaudatum—two sympatric congeners from the lower Yarlung Tsangpo River, Tibet, China. The mitogenomes of both species contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one light-strand origin of replication, and one control region, with lengths of 16,528 bp and 16,533 bp, respectively. The mitogenome architecture, nucleotide composition, and codon usage of protein-coding genes were almost identical between the two Exostoma species, although some estimated parameters varied. Phylogenetic analysis strongly supported the monophyly of Exostoma in the subfamily Glyptosternae, and Exostoma tibetanum had the closest relationship to Exostoma tenuicaudatum. The divergence time estimation demonstrated that these two species diverged approximately 1.51 Ma during the early Pleistocene, which was speculated to be triggered by the river system changes caused by the uplift of the southeastern Tibetan Plateau. Selection pressure analyses indicated that all protein-coding genes of Exostoma species underwent a strong purifying selection, while minority positive sites from NADH dehydrogenase complex genes were detected. These findings are expected to promote our understanding of the molecular phylogeny of the genus Exostoma and provide valuable mitogenomic resources for the subfamily Glyptosternae
Collapse
|