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Das SP, Krishnan R, Sunil M, Majhi A, Yakshita, Nan FH, Srivastava A. Low depth sequencing reveals the critically endangered Batagur kachuga (Red-crowned roofed turtle) mitochondrial genome and its evolutionary implications. Gene 2024; 927:148671. [PMID: 38866260 DOI: 10.1016/j.gene.2024.148671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/24/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024]
Abstract
The Batagur kachuga (B. kachuga), commonly known as the Red-crowned roofed turtle, is a critically endangered species native to India and its neighboring countries like Bangladesh, and Nepal. The present study is the first report of the complete mitochondrial genome of B. kachuga (16,517 bp) construed via the next-generation sequencing (NGS) approach from eggshell DNA. There are 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs), and one putative control region (CR/D-loop) in the mitogenome. The CR region from the current study reveals conserved TAS, CD, and CSB domains and two AT-rich tandem repeat regions. Most genes are encoded in the heavy strand except the NADH dehydrogenase subunit 6 (ND6) gene and seven tRNA genes. Most PCGs start with the initiation codon ATG, except the COI (Cytochrome Oxidase Subunit-I) gene, which starts with the GTG codon. The present investigation also predicts the distinctive cloverleaf structures of tRNAs except for tRNA-Ser1 and tRNA-Ser-2, which lack a DHU arm. The comparative analysis of Ka/Ks with other 33 species from Order Testudines, in relation to B. kachuga, revealed negative selection in most PCGs, indicating a process of preservation and purification that aids in eliminating undesirable or detrimental substitutes. Phylogenetic analysis of this species has been analysed using the complete mitogenome of 33 turtle species. The maximum likelihood phylogenetic tree strongly supports each family in different clades and also reveals a close relationship between the Pangashura and Batagur genera. Our study suggests the generation of genome-wide molecular data, in terms of mitogenomes, SNPs, and SSRs, is needed to improve the understanding of this species and their phylogenetics and evolutionary relationships, which will help to improve the conservation efforts of this species.
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Affiliation(s)
- Sofia Priyadarsani Das
- Department of Aquaculture, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan; Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India.
| | - Rama Krishnan
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Mohit Sunil
- Bharathidasan University, Trichy, Tamil Nadu, India
| | - Ashutosh Majhi
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India
| | - Yakshita
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India
| | - Fan-Hua Nan
- Department of Aquaculture, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan
| | - Ashutosh Srivastava
- Amity Institute of Marine Science and Technology, Amity University Uttar Pradesh, Sector-125, Noida, India; Siddhart University, Kapilvastu, Siddhart Nagar, Uttar Pradesh, India.
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Zheng S, Zhang C, Zhou J, Zhang S, Liu Y, Jin X, Wang Y, Liu B. Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda. Biochem Genet 2024; 62:3030-3051. [PMID: 38063953 DOI: 10.1007/s10528-023-10594-4] [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: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 07/31/2024]
Abstract
In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.
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Affiliation(s)
- Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China.
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, 510300, Guangdong, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China.
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Yang LM, Xue JF, Zhao XM, Ding K, Liu ZW, Wang ZSY, Chen JB, Huang YK. Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships. Genes (Basel) 2024; 15:893. [PMID: 39062672 PMCID: PMC11276143 DOI: 10.3390/genes15070893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms.
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Affiliation(s)
- Li-min Yang
- School of Materials and Environmental Engineering, Chizhou University, Chizhou 247000, China; (L.-m.Y.); (Z.-w.L.); (Z.-s.-y.W.); (J.-b.C.)
| | - Jing-feng Xue
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource and Environment, Anhui Agricultural University, Hefei 230036, China; (J.-f.X.); (X.-m.Z.)
| | - Xiao-man Zhao
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource and Environment, Anhui Agricultural University, Hefei 230036, China; (J.-f.X.); (X.-m.Z.)
| | - Ke Ding
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines, Anhui University of Science and Technology, Huainan 232001, China;
- State Key Laboratory for Geomechanics and Deep Underground Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Zhao-wen Liu
- School of Materials and Environmental Engineering, Chizhou University, Chizhou 247000, China; (L.-m.Y.); (Z.-w.L.); (Z.-s.-y.W.); (J.-b.C.)
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource and Environment, Anhui Agricultural University, Hefei 230036, China; (J.-f.X.); (X.-m.Z.)
| | - Zhou-si-yu Wang
- School of Materials and Environmental Engineering, Chizhou University, Chizhou 247000, China; (L.-m.Y.); (Z.-w.L.); (Z.-s.-y.W.); (J.-b.C.)
| | - Jian-bing Chen
- School of Materials and Environmental Engineering, Chizhou University, Chizhou 247000, China; (L.-m.Y.); (Z.-w.L.); (Z.-s.-y.W.); (J.-b.C.)
| | - You-kun Huang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource and Environment, Anhui Agricultural University, Hefei 230036, China; (J.-f.X.); (X.-m.Z.)
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Sun Y, Chen J, Liang X, Li J, Ye Y, Xu K. Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea. PeerJ 2024; 12:e17314. [PMID: 38799064 PMCID: PMC11127644 DOI: 10.7717/peerj.17314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Background Despite the Caridean shrimps' vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P. ortmanni, P. izumiae and P. lophotes. Methods The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina's next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank. Results The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species-P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group. Conclusions Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus.
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Affiliation(s)
- Yuman Sun
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Jian Chen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Xinjie Liang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Kaida Xu
- Zhejiang Marine Fishery Research Institute, Zhoushan, Zhejiang Province, China
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs, Zhoushan, Zhejiang Province, China
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Liao X, Shih Y, Jia C, Gao T. Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis. Genes (Basel) 2024; 15:557. [PMID: 38790187 PMCID: PMC11121196 DOI: 10.3390/genes15050557] [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: 03/23/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.
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Affiliation(s)
- Xianhui Liao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Yijia Shih
- Fisheries College, Jimei University, Xiamen 361021, China;
| | - Chenghao Jia
- School of Ecology and Environment, Hainan University, Haikou 570228, China;
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
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Yang T, Liu Y, Ning Z. Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals (Basel) 2023; 13:ani13030362. [PMID: 36766251 PMCID: PMC9913227 DOI: 10.3390/ani13030362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The family Ophichthidae has the largest number and the most various species (about 359 valid species) in the order Anguilliformes worldwide. Both morphological and molecular characteristics have been used to assess their taxonomic status. However, due to the ambiguous morphological features, molecular data such as mitochondrial DNA sequences have been implemented for the correct identification and classification of these fishes. In this study, the gene arrangement and structure characteristics of two Ophichthidae mitochondrial genomes were investigated for the first time. The total mitogenome lengths of O. evermanni and O. erabo were 17,759 bp and 17,856 bp, respectively. Comparing with the ancestral mitochondrial gene order, the irregular gene rearrangement happened between ND6 and tRNA-Pro (P) genes with another similar control region emerging between tRNA-Thr (T) and ND6 genes, which could be explained by the tandem duplication and random loss (TDRL) model appropriately. ML phylogenetic tree demonstrated that the family Ophichthidae was monophyletic origin, but genus Ophichthus might be polyphyletic because of the confused cluster relationships among different species.
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications. Genes (Basel) 2022; 13:genes13112128. [DOI: 10.3390/genes13112128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
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.
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Zhang C, Zhang K, Peng Y, Zhou J, Liu Y, Liu B. Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae. Front Genet 2022; 13:922634. [PMID: 35754812 PMCID: PMC9213810 DOI: 10.3389/fgene.2022.922634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.
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Affiliation(s)
- Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
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Wang C, Lai T, Ye P, Yan Y, Feutry P, He B, Huang Z, Zhu T, Wang J, Chen X. Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae. Gene 2022; 820:146232. [PMID: 35114282 DOI: 10.1016/j.gene.2022.146232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 01/08/2023]
Abstract
In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.
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Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China
| | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Peiyuan Ye
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yunrong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
| | - Pierre Feutry
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7000, Australia
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning 530000, China
| | | | - Ting Zhu
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; Guangxi Mangrove Research Center, Beihai 536000, China.
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Ye YY, Miao J, Guo YH, Gong L, Jiang LH, Lü ZM, Xu KD, Guo BY. The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea. Sci Rep 2021; 11:14446. [PMID: 34262102 PMCID: PMC8280103 DOI: 10.1038/s41598-021-93946-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
The complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (- 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.
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Affiliation(s)
- Ying-Ying Ye
- Marine Fishery Institute of Zhejiang Province, Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Ocean University, Zhoushan, 316021, People's Republic of China.
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China.
| | - Jing Miao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Ya-Hong Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Li Gong
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Li-Hua Jiang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Zhen-Ming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Kai-da Xu
- Marine Fishery Institute of Zhejiang Province, Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhejiang Ocean University, Zhoushan, 316021, People's Republic of China.
| | - Bao-Ying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, People's Republic of China
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Zhang K, Zhu K, Liu Y, Zhang H, Gong L, Jiang L, Liu L, Lü Z, Liu B. Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes. Sci Rep 2021; 11:2411. [PMID: 33510193 PMCID: PMC7844273 DOI: 10.1038/s41598-021-81622-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023] Open
Abstract
The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.
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Affiliation(s)
- Kun Zhang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Kehua Zhu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Yifan Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Hua Zhang
- grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Li Gong
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Lihua Jiang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Liqin Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Zhenming Lü
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Bingjian Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
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Sharma A, Siva C, Ali S, Sahoo PK, Nath R, Laskar M, Sarma D. The complete mitochondrial genome of the medicinal fish, Cyprinion semiplotum: Insight into its structural features and phylogenetic implications. Int J Biol Macromol 2020; 164:939-948. [DOI: 10.1016/j.ijbiomac.2020.07.142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 01/24/2023]
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Li Z, Li M, Xu S, Liu L, Chen Z, Zou K. Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations. Int J Mol Sci 2020; 21:E4685. [PMID: 32630142 PMCID: PMC7370159 DOI: 10.3390/ijms21134685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/31/2022] Open
Abstract
Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.
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Affiliation(s)
- Zhenhai Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Min Li
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shannan Xu
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Zuozhi Chen
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China
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15
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Liu ZQ, Shen YZ, Zhao M, Wang W, Chen W, Ma CY, Zhang FY, Ma LB. Characterization of the complete mitochondrial DNA sequence of the Ariosoma meeki (Anguilliformes, Congridae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2539-2541. [PMID: 33457855 PMCID: PMC7782183 DOI: 10.1080/23802359.2020.1781557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
In this study, the complete mitochondrial genome of Ariosoma meeki was sequenced, assembled and annotated. The circular genome is 16,154 bp in length with nucleotide composition is 28.42% A, 26.53% T, 19.65% G, and 25.40% C and contains 13 protein-coding genes (PCGs), 21 transfer RNA genes (tRNAs), 2 ribosomal RNA unit genes and a large non-coding region (putative control region). To further explore the evolution relationship of the Anguilliformes, we constructed the phylogenetic tree and found that the A. meeki had closer relationship with Ariosoma shiroanago. This study provided the valuable evidence on phylogenetic relationship of the A. meeki at the molecular level and essential resource for further study the molecular phylogenetic, biogeography and adaptive evolution of this lineage.
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Affiliation(s)
- Zhi-Qiang Liu
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Yao-Zhong Shen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Ming Zhao
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Wang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Wei Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Chun-Yan Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Feng-Ying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Ling-Bo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
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16
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Novel gene rearrangement pattern in Cynoglossus melampetalus mitochondrial genome: New gene order in genus Cynoglossus (Pleuronectiformes: Cynoglossidae). Int J Biol Macromol 2020; 149:1232-1240. [DOI: 10.1016/j.ijbiomac.2020.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 11/24/2022]
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17
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Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History. Int J Mol Sci 2020; 21:ijms21051874. [PMID: 32182936 PMCID: PMC7084342 DOI: 10.3390/ijms21051874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.
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