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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.
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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
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Venuti I, Ceruso M, Muscariello T, Ambrosio RL, Di Pinto A, Pepe T. Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud. Foods 2023; 12:3441. [PMID: 37761149 PMCID: PMC10530232 DOI: 10.3390/foods12183441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Dentex gibbosus (Pink dentex) is a fish species of increasing economic interest in the Mediterranean Sea that is consumed both whole and processed. The growing value of this sparid in European markets is responsible for its substitution with fraudulent species. The distinctive morphologic feature of D. gibbosus is the conspicuous hump on the forehead in the older and larger specimens. However, the head is regularly convex in young individuals, requiring high skills and competencies for correct identification. Authentication becomes even more challenging in the case of prepared and processed products. Therefore, the molecular characterization of Pink dentex plays a crucial role in preventing commercial fraud with species substitution. This paper proposes a comparative mitogenome analysis between 19 sparid species of commercial interest as a tool to accurately design species-specific primers targeting a fragment of the NAD2 gene for the identification of D. gibbosus. We successfully detected Pink dentex DNA both using endpoint and real-time PCR. The findings showed the high specificity of the designed primers, demonstrating this a suitable, fast, and cost-effective method that could be used for the unambiguous identification of Pink dentex. This innovative approach for sparid authentication is expected to contribute to seafood traceability, public health assurance, integrity, and the credibility of the seafood industry.
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Affiliation(s)
- Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Tiziana Muscariello
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Rosa Luisa Ambrosio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
| | - Angela Di Pinto
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, Km 3, Valenzano, 70010 Bari, Italy;
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via F. Delpino, n. 1, 80137 Naples, Italy; (I.V.); (T.M.); (R.L.A.); (T.P.)
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3
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Ceruso M, Mascolo C, De Luca P, Venuti I, Smaldone G, Biffali E, Anastasio A, Pepe T, Sordino P. A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds. Foods 2020; 9:E1397. [PMID: 33023115 PMCID: PMC7600753 DOI: 10.3390/foods9101397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.
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Affiliation(s)
- Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Giorgio Smaldone
- Department Agricultural Sciences, University of Naples Federico II, via Università, n.100, Portici, 80055 Naples, Italy;
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
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Łukasik P, Chong RA, Nazario K, Matsuura Y, Bublitz DAC, Campbell MA, Meyer MC, Van Leuven JT, Pessacq P, Veloso C, Simon C, McCutcheon JP. One Hundred Mitochondrial Genomes of Cicadas. J Hered 2020; 110:247-256. [PMID: 30590568 DOI: 10.1093/jhered/esy068] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 12/21/2018] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.
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Affiliation(s)
- Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Rebecca A Chong
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI
| | - Katherine Nazario
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Yu Matsuura
- Tropical Biosphere Research Center, University of the Ryukyus, Japan
| | - De Anna C Bublitz
- Division of Biological Sciences, University of Montana, Missoula, MT
| | | | - Mariah C Meyer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | | | - Pablo Pessacq
- Centro de Investigaciones Esquel de Montaña y Estepa Patagónicas (CIEMEP), Esquel, Chubut, Argentina
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT
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5
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Ceruso M, Mascolo C, Anastasio A, Pepe T, Sordino P. Frauds and fish species authentication: Study of the complete mitochondrial genome of some Sparidae to provide specific barcode markers. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.03.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Rapid divergence, molecular evolution, and morphological diversification of coastal host-parasite systems from southern Brazil. Parasitology 2019; 146:1313-1332. [PMID: 31142390 DOI: 10.1017/s0031182019000556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study assessed the role of historical processes on the geographic isolation, molecular evolution, and morphological diversification of host-parasite populations from the southern Brazilian coast. Adult specimens of Scleromystax barbatus and Scleromystax macropterus were collected from the sub-basin of the Nhundiaquara River and the sub-basin of the Paranaguá Bay, state of Paraná, Brazil. Four species of Gyrodactylus were recovered from the body surface of both host species. Morphometric analysis of Gyrodactylus spp. and Scleromystax spp. indicated that subpopulations of parasites and hosts could be distinguished from different sub-basins and locations, but the degree of morphological differentiation seems to be little related to geographic distance between subpopulations. Phylogenetic relationships based on DNA sequences of Gyrodactylus spp. and Scleromystax spp. allowed distinguishing lineages of parasites and hosts from different sub-basins. However, the level of genetic structuring of parasites was higher in comparison to host species. Evidence of positive selection in mtDNA sequences is likely associated with local adaptation of lineages of parasites and hosts. A historical demographic analysis revealed that populations of Gyrodactylus and Scleromystax have expanded in the last 250 000 years. The genetic variation of parasites and hosts is consistent with population-specific selection, population expansions, and recent evolutionary co-divergence.
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Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes. Int J Biol Macromol 2019; 135:609-618. [PMID: 31132441 DOI: 10.1016/j.ijbiomac.2019.05.139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/30/2019] [Accepted: 05/21/2019] [Indexed: 11/20/2022]
Abstract
Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. 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 duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.
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8
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Comparison of mitochondrial DNA enrichment and sequencing methods from fish tissue. Food Chem 2019; 294:333-338. [PMID: 31126471 DOI: 10.1016/j.foodchem.2019.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023]
Abstract
Sparid fish species have different commercial values related to their organoleptic features. Mitochondrial (mt) DNA provides a potential tool to distinguish species, but the enrichment of high-quality mtDNA from total genomic DNA is critical to obtain entire mtDNA sequences. Conventional mtDNA isolation is relatively low-cost and proficient. However, high numbers of PCR cycles can lead to artefacts (10-6 mutations/bp). We describe a rapid protocol for mtDNA extraction and enrichment from fish tissues, based on conventional miniprep columns and paramagnetic bead-based purification, without the need to employ PCR amplification. This newly described method generates a substrate for next-generation sequencing (NGS) analysis and is likely to have wider applications for mitochondrial studies in other fish families to help ensure traceability and differentiation of fish with high commercial values.
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Zhao L, Dong J, Sun C, Tian Y, Hu J, Ye X. Phylogenetic analysis of sooty grunter and other major freshwater fishes in the suborder Percoidei based on mitochondrial DNA. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:234-248. [PMID: 30451556 DOI: 10.1080/24701394.2018.1482283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Perciformes is the largest order of fishes and vertebrates. Sooty grunter (Hephaestus fuliginosus) is an economic fish species in the Terapontidae family of Percoidei, a suborder within Perciformes. To conduct molecular-level analysis of the phylogenetic relationships between sooty grunter and major freshwater fishes in Percoidei, we analysed the entire sooty grunter mitochondrial genome sequence and obtained the mitochondrial genome information of 19 fishes from Terapontidae, Serranidae, and Centrarchidae families in Percoidei from GenBank. The complete length of the sooty grunter mitochondrial genome was 16,770 bp; it encoded 13 proteins, 2 rRNAs, 22 tRNAs, and a displacement loop (D-loop). Other than ND6 and eight tRNA genes that are encoded by the light strand, the majority of genes are encoded by the heavy strand. The sequence and distribution of sooty grunter mitochondrial-encoded genes and non-coding segment were similar to those of most vertebrates. The results of neighbour joining, maximum parsimony, and Bayesian inference analyses of the complete mitochondrial genome and six genes, including cytochrome oxidase I, cytochrome B, 12S rRNA, ND2, ND4, and ND5, were consistent. In the phylogenetic trees, fishes in Terapontidae and Centrarchidae formed monophyletic clades, whereas those in Serranidae were divided into two clades, each containing Lateolabrax and Siniperca species. Among the three freshwater fish species in Terapontidae, the freshwater Terapontidae were more closely related to jade perch than with silver perch, suggesting that freshwater Terapontidae fishes originate from marine fishes. In addition, the phylogenetic results indicated that Micropterus salmoides salmoides and Micropterus salmoides floridanus in Centrarchidae should be designated as two independent species, and Siniperca in Serranidae should be considered an independent family. The sooty grunter mitochondrial genome sequence obtained in this study could be used to conduct population genetic diversity and germplasm resource studies. Furthermore, the phylogenetic analysis results of freshwater fishes in Percoidei could provide a molecular basis for cross-breeding.
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Affiliation(s)
- Lixiang Zhao
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b College of Fisheries and Life Science , Shanghai Ocean University , Shanghai , China
| | - Junjian Dong
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China
| | - Chengfei Sun
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b College of Fisheries and Life Science , Shanghai Ocean University , Shanghai , China
| | - Yuanyuan Tian
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China
| | - Jie Hu
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China
| | - Xing Ye
- a Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture , Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b College of Fisheries and Life Science , Shanghai Ocean University , Shanghai , China
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Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics 2018; 19:354. [PMID: 29747572 PMCID: PMC5946542 DOI: 10.1186/s12864-018-4717-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. RESULTS In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. CONCLUSIONS The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
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Affiliation(s)
- Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shanqun Jiang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
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11
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Gong L, Chen W, Liu LQ, Lü ZM. The complete mitochondrial genome of Gymnogobius Petschiliensis (Gobiiformes; Gobiidae; Gobionellinae) and its phylogenetic implications. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:816-818. [PMID: 33473994 PMCID: PMC7799598 DOI: 10.1080/23802359.2017.1398609] [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: 11/25/2022]
Abstract
Of the goby fishes, many Gymnogobius species have been poor recognized mainly because of the absence of enough molecular information and clear phylogenetic framework. In this study, the complete mitochondrial genome of Gymnogobius petschiliensis was determined and described. The mitogenome is 16,422 bp in length and consists of 22 tRNAs, 13 protein-coding genes, two rRNAs, one control region and a light strand replication origin (OL). The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 27.5%, 29.5%, 26.1%, and 16.9%, for A, T, C, and G, respectively, with a slight bias on A + T content (57.0%). The 13 protein-coding genes use the initiation codon ATG except COI, which uses GTG. Most of them use TAA or TAG as the stop codon, while COII, COIII, and Cyt b use an incomplete T or TA and ND4 uses an unusual AGA. The maximum-likelihood phylogeny tree of 19 Gobionellinae species demonstrated that G. petschiliensis had a very closely relationship with the same genus G. urotaenia. This study is expected to contributing to the phylogenetic evolution of G. petschiliensis and further phylogenetic relationship of Gobionellinae and Gobiiformes.
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Affiliation(s)
- Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wei Chen
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Li-Qin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Zhen-Ming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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12
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Complete mitochondrial genome of the Pleuronichthys lighti (Pleuronectiformes, Pleuronectidae) with phylogenetic consideration. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0570-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Gong L, Du X, Lü ZM, Liu LQ. The complete mitochondrial genome characterization of Tridentiger obscurus (Gobiiformes: Gobiidae) and phylogenetic analyses of Gobionellinae. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:662-663. [PMID: 33473938 PMCID: PMC7800103 DOI: 10.1080/23802359.2017.1375874] [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: 11/15/2022]
Abstract
The dusky tripletooth goby, Tridentiger obscurus, is a good model organism for the small in size and reaching maturity within a single year. Previous studies mainly focused on the annual reproductive cycle, social behavior and life history, but little information is available of the mitochondrial genome and phylogenetic evolution of this gobioid fish. In this article, we described the complete mitogenome of T. obscurus and reconstructed the phylogenetic relationship of the relative species of Gobionellinae. The genome is 16,501 bp in length including 13 protein-coding, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region and an L-strand replication origin. The overall base composition is 28.1%, 27.0%, 28.0% and 16.9% for A, T, C and G, respectively. This result is expected for better understanding the systematic evolution of the genus Tridentiger and further phylogenetic study of Gobiiformes.
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Affiliation(s)
- Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Xun Du
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Zhen-Ming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Li-Qin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Mascolo C, Ceruso M, Sordino P, Palma G, Anastasio A, Pepe T. Development of a Method to Extract and Amplify the Complete Mitogenome of Some Sparidae Species. Ital J Food Saf 2017; 6:6154. [PMID: 28713786 PMCID: PMC5505091 DOI: 10.4081/ijfs.2017.6154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/13/2017] [Indexed: 11/28/2022] Open
Abstract
Previous studies showed that fish mitochondrial DNA (mtDNA) is set up by a closed circular molecule of 16-17 kilobases (kb), comprising 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), 13 protein-coding genes and 2 non-coding regions. The analysis of single mtDNA genes, such as Cytb, COI, 16S and 12S, or short segment of them, has been widely used against species substitution in both fresh and processed fish products. The analysis of the complete mitochondrial genome of fishery products allows to better study and characterise fish species. The aim of this research was to extract and amplify the complete mtDNA of some fish species of commercial interest belonging to the Sparidae family. The studied species were Dentex dentex, Dentex gibbosus, Dentex nufar, Pagellus acarne and Pagellus erythrinus. The entire mitogenome was obtained by gene amplification using long polymerase chain reactions. The analysis of the complete mitochondrial sequences will allow to gain further insights on these species and to find polymorphic sites that assess the degree of genetic variability of the species belonging to the family Sparidae.
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Affiliation(s)
- Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy.,Biology and Evolution of Marine Organisms, Research Centre Anton Dohrn Zoological Station, Naples, Italy
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms, Research Centre Anton Dohrn Zoological Station, Naples, Italy
| | | | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
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15
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Wei M, Liu Y, Guo H, Zhao F, Chen S. Characterization of the complete mitochondrial genome of Cynoglossus gracilis and a comparative analysis with other Cynoglossinae fishes. Gene 2016; 591:369-75. [PMID: 27312953 DOI: 10.1016/j.gene.2016.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 11/29/2022]
Abstract
Mitochondrial genomes can provide basic information for phylogenetic analysis and evolutionary studies. We present here the mitochondrial genome of Cynoglossus gracilis, which is 16,565bp in length. Numerous distinct regions were identified, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, a light-strand replication origin, and a control region. Interestingly, we detected rearrangement of genes in C. gracilis, including a control region translocation, tRNA(Gln) gene inversion, and tRNA(Ile) gene shuffling. Additionally, a phylogenetic analysis based on the nucleotide sequences of the 13 PCGs using maximum likelihood and Bayesian inference methods reveals that C. gracilis is closely related to Cynoglossus semilaevis. This study provides important mitogenomic data for analyzing phylogenetic relationships in the Cynoglossinae.
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Affiliation(s)
- Min Wei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Yang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Hua Guo
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Fazhen Zhao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Songlin Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China.
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16
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Complete mitochondrial genome of the Himalayan serow (Capricornis thar) and its phylogenetic status within the genus Capricornis. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Shi W, Gong L, Wang SY, Miao XG, Kong XY. Tandem Duplication and Random Loss for mitogenome rearrangement in Symphurus (Teleost: Pleuronectiformes). BMC Genomics 2015; 16:355. [PMID: 25943439 PMCID: PMC4430869 DOI: 10.1186/s12864-015-1581-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/24/2015] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial genomes (mitogenomes) of flatfishes (Pleuronectiformes) exhibit highly diversified types of large-scale gene rearrangements. We have reported that the mitogenomes of Crossorhombus azureus (Bothidae), Samariscus latus (Samaridae) and Cynoglossus fishes (Cynoglossidae) show different types of gene rearrangements. Results In the present study, the complete mitogenomes of two Symphurus species (Cynoglossidae), Symphurus plagiusa and Symphurus orientalis, were determined. The gene order in the S. plagiusa mitogenome is the same as that of a typical vertebrate (without any gene rearrangements). Surprisingly, large-scale gene rearrangements have occurred in S. orientalis. In the rearranged fragment from the control region (CR) to the WANCY tRNA cluster (tRNA cluster of tRNA-W, tRNA-A, tRNA-N, tRNA-C and tRNA-Y) in the S. orientalis mitogenome, tRNA-V and tRNA-M have been translocated to the 3’ end of the 16S rRNA gene, with six large intergenic spacers over 20 bp in length. In addition, an origin for light-strand replication (OL) structure that is typically located in the WANCY region was absent in both the S. plagiusa and S. orientalis mitogenomes. It is generally recognized that a sequence in the WANCY region that encodes tRNAs forms a hairpin structure (OL-like structure) and can act as the OL when the typical locus is lost. Moreover, an additional OL-like structure was identified near the control region in the S. plagiusa mitogenome. Conclusions The positions of the intergenic spacers and the rearranged genes of the S. orientalis mitogenome strongly indicate that the mechanism underlying the rearrangement of this mitogenome was Tandem Duplication and Random Loss. Additionally, two OL-like regions substituting for the typical locus were found in the S. plagiusa mitogenome. We speculate that the ancestral mitogenomes of S. plagiusa and S. orientalis also had this characteristic, such that if both OL-like structures functioned during mitochondrial replication, they could initiate duplicate replications of the light strand (L-strand), leading to duplication of the region between the two structures. We consider that this mechanism may account for the gene duplication that occurred during the gene rearrangement process in the evolution of the ancestral mitogenome to the S. orientalis mitogenome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1581-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Li Gong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Shu-Ying Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Xian-Guang Miao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Xiao-Yu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
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18
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Zhou CL, Tian J, Yang CG. The complete mitochondrial genome sequence of Hemibagrus sp. (Siluriformes: Bagridae), molecular data for species identification. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1914-5. [PMID: 25319298 DOI: 10.3109/19401736.2014.971284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we determined and described the complete mitogenome sequence of Hemibagrus sp. for the first time, which is 16,513 bp in length, and contains 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 origin of replication on the light-strand (OL) and a putative control region. The overall base composition was 31.1% A, 26.9% T, 26.9% C, 15.1% G, with a slight AT bias (58.0%). All protein-coding genes shared the start codon ATG, except for COI, which began with GTG. The tRNA-Ser(UGC) couldn't be folded into the typical cloverleaf secondary structure because its dihydrouridine arm is replaced by a simple loop. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of Bagridae and Siluriformes.
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Affiliation(s)
- Can-Lin Zhou
- a College of Life Science and Technology, Xinjiang University , Urumqi , P.R. China .,b Basic Medical College, Xinjiang Medical University , Urumqi , P.R. China
| | - Juan Tian
- c The Fifth Affiliated Hospital of Xinjiang Medical University , Urumqi , P.R. China , and
| | - Chang-Geng Yang
- d Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , P.R. China
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Dray L, Neuhof M, Diamant A, Huchon D. The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:781-2. [PMID: 24963773 DOI: 10.3109/19401736.2014.928861] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the gilthead seabream Sparus aurata Linnaeus 1758, one of the world's most important mariculture species, was sequenced using next generation sequencing technology. The genome sequence is comprised of 16,652 bp exhibiting the canonical vertebrate mitochondria gene order. Regions of gene overlap, tRNA length, as well as start and stop codon were similar to those observed in other Sparidae. Phylogenetic reconstructions based on mitochondrial protein coding genes corroborate the view that Sparidae is paraphyletic and includes Centracanthidae.
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Affiliation(s)
- Liran Dray
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Moran Neuhof
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Arik Diamant
- b National Center for Mariculture, Israel Oceanographic and Limnological Research , Eilat Israel
| | - Dorothée Huchon
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
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20
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Shi W, Miao XG, Kong XY. A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes). BMC Genomics 2014; 15:352. [PMID: 24885702 PMCID: PMC4035078 DOI: 10.1186/1471-2164-15-352] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 04/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements. RESULTS In the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained. CONCLUSIONS We propose a "Double Replications and Random Loss" model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.
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Affiliation(s)
| | | | - Xiao-Yu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China.
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21
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Li N, Song N, Gao T. The complete mitochondrial genome of Japanese Ammodytes personatus (Perciformes, Ammodytidae). MITOCHONDRIAL DNA 2014; 26:781-2. [PMID: 24409904 DOI: 10.3109/19401736.2013.855750] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial genome of Japanese Ammodytes personatus is a circular molecule of 16,527 bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions (control region and L-strand replication origin OL). The mitogenome exhibits the canonical gene arrangement as those of most vertebrates, the nucleotide composition of which reveals an obvious anti-G bias. In the control region, we identified the termination-associated sequence domain, the central conserved sequence block domains (F, E, D, C, B and A), and CSB domains (1, 2 and 3).
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Affiliation(s)
- Ning Li
- a Institute of Evolution and Marine Biodiversity, Ocean University of China , Qingdao , People's Republic of China
| | - Na Song
- a Institute of Evolution and Marine Biodiversity, Ocean University of China , Qingdao , People's Republic of China
| | - Tianxiang Gao
- a Institute of Evolution and Marine Biodiversity, Ocean University of China , Qingdao , People's Republic of China
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22
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Singh RK, Mohindra V, Pathak A, Lal KK, Jena JK. Complete sequence and characterization of mitochondrial genome in great snakehead, Channa marulius (Hamilton, 1822). ACTA ACUST UNITED AC 2013; 26:473-4. [PMID: 24047162 DOI: 10.3109/19401736.2013.834429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete nucleotide sequence of mitogenome of the great snakehead, Channa marulius (Channidae), was determined and found to be 16,569 base pairs in length. The content and arrangement of different genes on the mitogenome was found similar to other typical teleosts. The overall base composition of the L-strand was found to be T (19.1%), C (31.5%), A (34.8%) and G (14.6%). The control region was 915 nt long and without any repetitive region. The mitogenome sequence data would be useful for studying phylogenetic relationship of C. marulius with other perciform species.
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Affiliation(s)
- Rajeev K Singh
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Indian Council of Agricultural Research , Lucknow, Uttar Pradesh , India
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23
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Shi W, Dong XL, Wang ZM, Miao XG, Wang SY, Kong XY. Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes. BMC Evol Biol 2013; 13:173. [PMID: 23962312 PMCID: PMC3751894 DOI: 10.1186/1471-2148-13-173] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/12/2013] [Indexed: 11/19/2022] Open
Abstract
Background Few mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed changes in mitogenome structure. Mitochondrial gene rearrangements are usually explained by the recombination model or tandem duplication and random loss model. Results In this study, the complete mitochondrial genomes of four flatfishes, Crossorhombus azureus (blue flounder), Grammatobothus krempfi, Pleuronichthys cornutus, and Platichthys stellatus were determined. A striking finding is that eight genes in the C. azureus mitogenome are located in a novel position, differing from that of available vertebrate mitogenomes. Specifically, the ND6 and seven tRNA genes (the Q, A, C, Y, S1, E, P genes) encoded by the L-strand have been translocated to a position between tRNA-T and tRNA-F though the original order of the genes is maintained. Conclusions These special features are used to suggest a mechanism for C. azureus mitogenome rearrangement. First, a dimeric molecule was formed by two monomers linked head-to-tail, then one of the two sets of promoters lost function and the genes controlled by the disabled promoters became pseudogenes, non-coding sequences, and even were lost from the genome. This study provides a new gene-rearrangement model that accounts for the events of gene-rearrangement in a vertebrate mitogenome.
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Affiliation(s)
- Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
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Zhuang X, Qu M, Zhang X, Ding S. A comprehensive description and evolutionary analysis of 22 grouper (perciformes, epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PLoS One 2013; 8:e73561. [PMID: 23951357 PMCID: PMC3739747 DOI: 10.1371/journal.pone.0073561] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholisargus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes' control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus, and Aethaloperca to genus Cephalopholis.
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Affiliation(s)
- Xuan Zhuang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Meng Qu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Xiang Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
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25
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Wei T, Zhang B, Sun Y. Structure comparison of control region in Stromateoidei and complete mitochondrial genome of the bluefin driftfish Psenes pellucidus (Perciformes, Nomeidae). ACTA ACUST UNITED AC 2013; 25:355-6. [PMID: 23815326 DOI: 10.3109/19401736.2013.803091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, the complete mitochondrial genome of the bluefin driftfish Psenes pellucidus was determined first. The genome was 16,572 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 2 main non-coding regions. The mitochondrial genome of bluefin driftfish had common features about gene arrangement, base composition and tRNA structures compared with those of most of the bony fishes. In the control region, a termination-associated sequence, the central conserved block (CSB-F, CSB-E and CSB-D) and the conserved sequence blocks (CSB-1, CSB-2 and CSB-3) were determined. Meanwhile, the conserved motif 5'-GCCGG-3' was identified in the origin of light strand replication of bluefin driftfish. This mitogenome sequence data would play key role in phylogenetic analysis of Stromateoidei.
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Affiliation(s)
- Tao Wei
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University , 316000 Zhoushan , P.R. China
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26
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Liang R, Zheng W, Zou Q, Zeng Y, Zhu S, Zou J. The complete mitochondrial genome of black grunt Hapalogenys nigripinnis. MITOCHONDRIAL DNA 2012; 23:444-6. [PMID: 22928817 DOI: 10.3109/19401736.2012.710221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete sequence of the mitochondrial genome of Hapalogenys nigripinnis was determined in this study. The genome was 16,478 bp in size with a base composition of 28.6% A, 15.8% G, 27.4% T, and 28.2% C, containing a typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 noncoding control region. The genomic composition, organization, and gene order of H. nigripinnis was similar to that obtained in most vertebrates. These results may provide molecular information on the future phylogenetic relationships of H. nigripinnis and its position within the suborder Percoidei.
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Affiliation(s)
- Rishen Liang
- College of Animal Science, South China Agricultural University, Guangzhou, PR China
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27
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Cheng Y, Xu T, Jin X, Shi G, Wang R. The complete mitochondrial genome of silver croaker Argyrosomus argentatus (Perciforems; Sciaenidae): Genome characterization and phylogenetic consideration. Mol Biol 2012. [DOI: 10.1134/s0026893312020215] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Chen DX, Chu WY, Liu XL, Nong XX, Li YL, Du SJ, Zhang JS. Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences. ACTA ACUST UNITED AC 2012; 23:70-6. [PMID: 22409749 DOI: 10.3109/19401736.2011.653799] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sinipercids are a group of 12 species of freshwater percoid fish endemic to East Asia and their phylogenetic placements have perplexed generations of taxonomists. We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three sinipercid fishes (Siniperca chuatsi, S. kneri, and S. scherzeri) to characterize and compare their mitochondrial genomes. The mitochondrial genomes of S. chuatsi, S. kneri, and S. scherzeri were 16,496, 17,002, and 16,585 bp in length, respectively. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major non-coding control region. Among the 13 protein-coding genes of all the three sinipercid fishes, three reading-frame overlaps were found on the same strand. There is an 81-bp tandem repeat cluster at the end of CSB-3 in the S. scherzeri control region. The complete mitochondrial genomes of the three sinipercids should be useful for the evolutionary studies of sinipercids and other vertebrate species.
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Affiliation(s)
- Dun-Xue Chen
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, People's Republic of China
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Cheng J, Ma GQ, Song N, Gao TX. Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae. Gene 2011; 491:210-23. [PMID: 21989484 DOI: 10.1016/j.gene.2011.09.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 09/20/2011] [Accepted: 09/20/2011] [Indexed: 11/25/2022]
Abstract
The monophyly and phylogenetic relationships of Pseudosciaeniae have long been controversial. Here we describe the mitochondrial genome (mitogenome) sequence of Collichthys niveatus. It is a circular double-stranded DNA molecule of 16,450 base pairs (bp) in length with a standard set of 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes as well as a non-coding control region. The mitogenome of C. niveatus shared common features with those of other bony fishes in terms of gene arrangement, base composition, and tRNA structures. The C. niveatus mitogenome exhibited pronounced strand-specific asymmetry in nucleotide composition, which was also reflected in the codon usage of genes oriented in opposite directions. Contrary to the typical structure of the control region, the central conserved blocks (CSB-D, -E, and -F) could not be detected in C. niveatus mitogenome. Phylogenetic analysis based on whole mitogenome sequences provided strong support for the monophyly of Pseudosciaeniae, and sister-group relationships of C. niveatus+Collichthys lucidus and Larimichthys crocea+Larimichthys polyactis, which was consistent with the traditional taxonomy. Unexpected divergence was found in two C. niveatus mitogenomes and several hypotheses were proposed to explain this observation including misidentification and introgressive hybridization between C. niveatus and L. polyactis, and polyphyletic origin of C. niveatus. We considered species misidentification to be the main hypothesis. However, additional data is essential to test these proposed hypotheses.
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Affiliation(s)
- Jiao Cheng
- Fisheries College, Ocean University of China, Yushan Road, 5, Qingdao 266003, China
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30
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Zhang J, Wu X, Xie M, Xu X, Li A. The mitochondrial genome ofPolylabris halichoeres(Monogenea: Microcotylidae). ACTA ACUST UNITED AC 2011; 22:3-5. [DOI: 10.3109/19401736.2011.588223] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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Oh DJ, Oh BS, Jung MM, Jung YH. Complete mitochondrial genome of three Branchiostegus (Perciformes, Malacanthidae) species: genome description and phylogenetic considerations. ACTA ACUST UNITED AC 2011; 21:151-9. [PMID: 20958223 DOI: 10.3109/19401736.2010.503241] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three tilefishes (Branchiostegus albus, Branchiostegus argentatus, and Branchiostegus japonicus) to characterize and compare their mitochondrial genomes (mitogenomes). The mitogenomes of B. albus, B. argentatus, and B. japonicus were 16,532, 16,550, and 16,541 bp long, respectively, and all consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA (tRNAs)), which are typical for vertebrate mtDNA. As in other bony fishes, most genes were encoded on the H-strand, except for the nad6 and eight tRNA genes that were encoded on the L-strand. Among the 13 protein-coding genes of all three tilefishes, 2 reading-frame overlaps were found on the same strand: atp8 and atp6 overlapped by 10 nucleotides, and nad4L and nad4 overlapped by 7 nucleotides. The identity of the nad4 gene between B. albus and B. argentatus was the lowest at 87%. Conversely, the identity of the nad6 gene between B. albus and B. japonicus was the highest at 99%. Most tRNA genes were similar in length among the three species, while the tRNA-Ser((AGY)) of B. japonicus was 9 bp longer than those of B. albus and B. argentatus. The control region of the mitogenome spanned 853, 862, and 856 bp in B. albus, B. argentatus, and B. japonicus, respectively. A maximum likelihood tree constructed using 11,035 sites contained five independent groups with bootstrap values of 100% in support of their divergence. All three tilefishes examined were clustered with the Pomacanthidae species in Group II.
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Affiliation(s)
- Dae-Ju Oh
- Jeju Biodiversity Research Institute, Jeju HiDI, Seogwipo, Jeju, Republic of Korea
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Cheng Y, Wang R, Xu T. The mitochondrial genome of the spinyhead croaker Collichthys lucida: genome organization and phylogenetic consideration. Mar Genomics 2011; 4:17-23. [PMID: 21429461 DOI: 10.1016/j.margen.2010.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/01/2010] [Accepted: 12/03/2010] [Indexed: 11/29/2022]
Abstract
The complete mitochondrial genome of the spiny head croaker Collichthys lucida was determined in the present study. The mitochondrial DNA was 16,442 base pairs in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major non-coding control region, with the content and order of genes being similar to those in typical teleosts. Most of the genes of C. lucida were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pairs of genes overlapped: ATPase 8 and 6 and ND4L and ND4 by ten and seven nucleotides, respectively. The control region was unusually short at only 768bp, and absence of typical conserved blocks (CSB-D, CSB-E, and CSB-F). Phylogenetic analyses indicated that C. lucida was located in the cluster of fish species from the family Sciaenidae, supporting the traditional taxonomic classification of fish, and in the cluster of Serranidae, the divergence time in Plectropomus leopardus is longer than that among its coordinal species. On the other hand, phylogenetic analyses do not support the monophyletic of family Centracanthidae and genera Larimichthys and Collichthys, which is against the morphological results.
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Affiliation(s)
- Yuanzhi Cheng
- Key Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan 316000, PR China
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The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciformes, Sciaenidae): structure of control region and phylogenetic considerations. Mol Biol Rep 2010; 38:4673-85. [DOI: 10.1007/s11033-010-0602-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 11/22/2010] [Indexed: 11/26/2022]
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34
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Species delineation in Pampus (Perciformes) and the phylogenetic status of the Stromateoidei based on mitogenomics. Mol Biol Rep 2010; 38:1103-14. [DOI: 10.1007/s11033-010-0207-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/11/2010] [Indexed: 11/26/2022]
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35
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Catanese G, Manchado M, Infante C. Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species. Gene 2009; 452:35-43. [PMID: 20035845 DOI: 10.1016/j.gene.2009.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 12/11/2009] [Accepted: 12/12/2009] [Indexed: 11/29/2022]
Abstract
Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.
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Affiliation(s)
- Gaetano Catanese
- IFAPA Centro El Toruño, Junta de Andalucía, 11500 El Puerto de Santa María (Cádiz), Spain
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Kong X, Dong X, Zhang Y, Shi W, Wang Z, Yu Z. A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion. Genome 2009; 52:975-84. [PMID: 19953125 DOI: 10.1139/g09-069] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The organization of fish mitochondrial genomes (mitogenomes) is quite conserved, usually with the heavy strand encoding 12 of 13 protein-coding genes and 14 of 22 tRNA genes, and the light strand encoding ND6 and the remaining 8 tRNA genes. Currently, there are only a few reports on gene reorganization of fish mitogenomes, with only two types of rearrangements (shuffling and translocation) observed. No gene inversion has been detected in approximately 420 complete fish mitogenomes available so far. Here we report a novel rearrangement in the mitogenome of Cynoglossus semilaevis (Cynoglossinae, Cynoglossidae, Pleuronectiformes). The genome is 16 371 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 main noncoding regions, the putative control region and the light-strand replication origin. A striking finding of this study is that the tRNAGln gene is translocated from the light to the heavy strand (Q inversion). This is accompanied by shuffling of the tRNAIle gene and long-range translocation of the putative control region downstream to a site between ND1 and the tRNAGln gene. The remaining gene order is identical to that of typical fish mitogenomes. Additionally, unique characters of this mitogenome, including a high A+T content and length variations of 8 protein-coding genes, were found through comparison of the mitogenome sequence with those from other flatfishes. All the features detected and their relationships with the rearrangements, as well as a possible rearrangement pathway, are discussed. These data provide interesting information for better understanding the molecular mechanisms of gene reorganization in fish mitogenomes.
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Affiliation(s)
- Xiaoyu Kong
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Xiaoli Dong
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Yanchun Zhang
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Wei Shi
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Zhongming Wang
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Ziniu Yu
- Marine Biodiversity Collection of South China Sea, Laboratory of Marine Bioresource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China
- Laboratory of Mariculture Research, College of Fisheries, Ocean University of China, 5 Yushan Road, Qingdao, China
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Álvarez V, Medina I, Prego R, Aubourg SP. Lipid and mineral distribution in different zones of farmed and wild blackspot seabream (Pagellus bogaraveo). EUR J LIPID SCI TECH 2009. [DOI: 10.1002/ejlt.200800282] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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The complete mitochondrial genome sequence of the cutlassfish Trichiurus japonicus (Perciformes: Trichiuridae): Genome characterization and phylogenetic considerations. Mar Genomics 2009; 2:133-42. [PMID: 21798182 DOI: 10.1016/j.margen.2009.07.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Revised: 07/09/2009] [Accepted: 07/23/2009] [Indexed: 11/22/2022]
Abstract
Mitochondrial genome sequence and structure analysis has become a powerful tool for studying molecular evolution and phylogenetic relationships. To understand the systematic status of Trichiurus japonicus in suborder Scombroidei, we determined the complete mitochondrial genome (mitogenome) sequence using the long-polymerase chain reaction (long-PCR) and shotgun sequencing method. The entire mitogenome is 16,796bp in length and has three unusual features, including (1) the absence of tRNA(Pro) gene, (2) the possibly nonfunctional light-strand replication origin (O(L)) showing a shorter loop in secondary structure and no conserved motif (5'-GCCGG-3'), (3) two sets of the tandem repeats at the 5' and 3' ends of the control region. The three features seem common for Trichiurus mitogenomes, as we have confirmed them in other three T. japonicus individuals and in T. nanhaiensis. Phylogenetic analysis does not support the monophyly of Trichiuridae, which is against the morphological result. T. japonicus is most closely related to those species of family Scombridae; they in turn have a sister relationship with Perciformes members including suborders Acanthuroidei, Caproidei, Notothenioidei, Zoarcoidei, Trachinoidei, and some species of Labroidei, based on the current dataset of complete mitogenome. T. japonicus together with T. brevis, T. lepturus and Aphanopus carbo form a clade distinct from Lepidopus caudatus in terms of the complete Cyt b sequences. T. japonicus mitogenome, as the first discovered complete mitogenome of Trichiuridae, should provide important information on both genomics and phylogenetics of Trichiuridae.
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39
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Oh DJ, Kim SJ, Jung YH. Comparison of the mitochondrial genomes of East AsianPseudolabrusfishes. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/19401730802449204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Chiba SN, Iwatsuki Y, Yoshino T, Hanzawa N. Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses. Genes Genet Syst 2009; 84:153-70. [DOI: 10.1266/ggs.84.153] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Satoru N. Chiba
- Graduate school of Science and Engineering, Yamagata University
| | - Yukio Iwatsuki
- Division of Fisheries Science, Faculty of Agriculture, University of Miyazaki
| | - Tetsuo Yoshino
- Department of Marine Sciences, Faculty of Science, University of the Ryukyus
| | - Naoto Hanzawa
- Graduate school of Science and Engineering, Yamagata University
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Cui Z, Liu Y, Li CP, You F, Chu KH. The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): unusual features of its control region and the phylogenetic position of the Sciaenidae. Gene 2008; 432:33-43. [PMID: 19100818 DOI: 10.1016/j.gene.2008.11.024] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 11/20/2008] [Accepted: 11/24/2008] [Indexed: 11/26/2022]
Abstract
To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L. crocea individuals and two L. polyactis individuals. Interestingly, all seven CR sequences from L. crocea were identical while the three sequences from L. polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L. crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L. crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys.
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Affiliation(s)
- Zhaoxia Cui
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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Breines R, Ursvik A, Nymark M, Johansen SD, Coucheron DH. Complete mitochondrial genome sequences of the Arctic Ocean codfishes Arctogadus glacialis and Boreogadus saida reveal oriL and tRNA gene duplications. Polar Biol 2008. [DOI: 10.1007/s00300-008-0463-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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