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Kumar A, Negi N, Yadav N, Badola R, Hussain SA, Gupta SK. Genetic diversity, spatial connectivity, and population structure of Asian silurid catfish Wallago attu (Bloch and Schneider, 1801) in the Ganga River System: insights from mitochondrial DNA analysis. Mol Biol Rep 2024; 51:378. [PMID: 38427103 DOI: 10.1007/s11033-024-09323-w] [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: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND The Ganga River System (GRS) is a biodiversity hotspot, its ecological richness is shaped by a complex geological history. In this study, we examined the genetic diversity, spatial connectivity, and population structure of the Asian Silurid catfish, Wallago attu, across seven tributaries of the GRS. METHODS AND RESULTS We employed three mitochondrial DNA (mtDNA) regions: cytochrome c oxidase subunit I (COXI), cytochrome b (Cyt b), and control region (CR). Our comprehensive dataset encompassed 2420 bp of mtDNA, derived from 176 W. attu individuals across 19 sampling sites within the seven rivers of GRS. Our findings revealed high gene diversity (Hd:0.99) within W. attu populations. Analysis of Molecular Variance (AMOVA) highlighted that maximum genetic variations were attributed within the populations, and the observed genetic differentiation among the seven populations of W. attu ranged from low to moderate. Network analysis uncovered the presence of three distinct genetic clades, showing no specific association with seven studied rivers. Bayesian skyline plots provided insights into the demographic history of W. attu, suggesting a recent population expansion estimated to have occurred approximately 0.04 million years ago (mya) during the Pleistocene epoch. CONCLUSIONS These results significantly enhance our understanding of the genetic diversity and spatial connectivity of W. attu, serving as a vital foundation for developing informed conservation strategies and the sustainable management of this economically valuable resource within the Ganga River System.
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Grants
- B-03/2015-16/1077/NMCG National Mission for Clean Ganga (NMCG), Ministry of Jal Shakti, Government of India
- B-03/2015-16/1077/NMCG National Mission for Clean Ganga (NMCG), Ministry of Jal Shakti, Government of India
- B-03/2015-16/1077/NMCG National Mission for Clean Ganga (NMCG), Ministry of Jal Shakti, Government of India
- B-03/2015-16/1077/NMCG National Mission for Clean Ganga (NMCG), Ministry of Jal Shakti, Government of India
- B-03/2015-16/1077/NMCG National Mission for Clean Ganga (NMCG), Ministry of Jal Shakti, Government of India
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Affiliation(s)
- Ajit Kumar
- Wildlife Institute of India, Dehra Dun, P.O. Box # 18, Chandrabani, Uttarakhand, 248001, India
| | - Naveen Negi
- Wildlife Institute of India, Dehra Dun, P.O. Box # 18, Chandrabani, Uttarakhand, 248001, India
| | - Neha Yadav
- Wildlife Institute of India, Dehra Dun, P.O. Box # 18, Chandrabani, Uttarakhand, 248001, India
| | - Ruchi Badola
- Wildlife Institute of India, Dehra Dun, P.O. Box # 18, Chandrabani, Uttarakhand, 248001, India
| | - Syed Ainul Hussain
- Wildlife Institute of India, Dehra Dun, P.O. Box # 18, Chandrabani, Uttarakhand, 248001, India
| | - Sandeep Kumar Gupta
- Wildlife Institute of India, Dehra Dun, P.O. Box # 18, Chandrabani, Uttarakhand, 248001, India.
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Marques-Neto JC, de Lima GM, Maciel CMT, Maciel BR, Abrunhosa FA, Sampaio I, Maciel CR. In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data. BMC Genomics 2023; 24:677. [PMID: 37950193 PMCID: PMC10637016 DOI: 10.1186/s12864-023-09770-y] [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: 07/18/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará. RESULTS Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial). CONCLUSIONS It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.
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Affiliation(s)
- Jerônimo Costa Marques-Neto
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Gabriel Monteiro de Lima
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Carlos Murilo Tenório Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Bruna Ramalho Maciel
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Fernando Araujo Abrunhosa
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Carcinology, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Iracilda Sampaio
- Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Cristiana Ramalho Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
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3
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Yoshitake K, Yanagisawa K, Sugimoto Y, Nakamura H, Mizusawa N, Miya M, Hamasaki K, Kobayashi T, Watabe S, Nishikiori K, Asakawa S. Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers. Funct Integr Genomics 2023; 23:96. [PMID: 36947319 PMCID: PMC10033627 DOI: 10.1007/s10142-023-01013-3] [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: 11/01/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.
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Affiliation(s)
- Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Kyohei Yanagisawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Yuma Sugimoto
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Hiroshi Nakamura
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Nanami Mizusawa
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Masaki Miya
- Department of Collection Management, Natural History Museum and Institute, Chiba, 260-8682, Japan
| | - Koji Hamasaki
- Department of Marine Ecosystem Science, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takanori Kobayashi
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Kazuomi Nishikiori
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan.
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4
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Duong T, Nguyen NT, Tran DD, Le TH, Nor SAM. Multiple genetic lineages of anadromous migratory Mekong catfish Pangasius krempfi revealed by mtDNA control region and cytochrome b. Ecol Evol 2023; 13:e9845. [PMID: 36820247 PMCID: PMC9937891 DOI: 10.1002/ece3.9845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/20/2023] Open
Abstract
Population genetic structure of migratory fishes can reflect ecological and evolutionary processes. Pangasius krempfi is a critically important anadromous catfish in the Mekong River, and its migration pathways and genetic structure have attracted much interest. To investigate, we quantified the genetic diversity of this species using the control region (D-loop) and Cytochrome b (Cytb) of the mitochondrial genome. Fish were sampled (n = 91) along the Mekong tributaries from upstream to estuaries and coastal areas in the Mekong Delta and compared to three samples from Pakse (Laos). The D-loop haplotype (0.941 ± 0.014) and nucleotide diversity (0.0083 ± 0.0005) were high in all populations, but that of Cytb was low (0.331 ± 0.059 and 0.00063 ± 0.00011, respectively). No genetic difference was detected between populations, indicating strong gene flow and confirming a long migration distance for this species. Pangasius krempfi was not genetically structured according to geographical populations but was delineated into three haplogroups, suggesting multiple genetic lineages. The presence of haplogroups in each sampling location implies that migration downstream is random but parallel when the fish enter two river tributaries bifurcating from the main Mekong River. Individuals can also migrate along the coast, far from the estuaries, suggesting a longer migration path than previously reported, which is crucial for maintaining diverse genetic origin and migration pathways for P. krempfi.
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Affiliation(s)
- Thuy‐Yen Duong
- College of Aquaculture and FisheriesCan Tho UniversityCan Tho CityVietnam
| | | | - Dac Dinh Tran
- College of Aquaculture and FisheriesCan Tho UniversityCan Tho CityVietnam
| | - Thanh Hoa Le
- Immunology DepartmentInstitute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST)Ho Chi Minh CityVietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST)Ho Chi Minh CityVietnam
| | - Siti Azizah Mohd Nor
- Institute of Marine BiotechnologyUniversiti Malaysia TerengganuTerengganuMalaysia
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5
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Comparative mitogenomics and phylogenetics of the family Carangidae with special emphasis on the mitogenome of the Indian Scad Decapterus russelli. Sci Rep 2022; 12:5642. [PMID: 35379869 PMCID: PMC8980026 DOI: 10.1038/s41598-022-09636-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/23/2022] [Indexed: 11/09/2022] Open
Abstract
Carangids are abundant and commercially important marine fish that contribute to a significant portion of the fisheries in many parts of the world. In the present study, we characterized the complete mitogenome of the Indian scad, Decapterus russelli and performed a comprehensive comparative mitogenomic analysis of the family Carangidae. The comparative mitogenomics provided valuable insights into the structure, variability, and features of the coding and non-coding regions that evolved across species over millions of years. The structural features of tRNAs revealed changes in the frequency of mismatched and wobble base pairs, which is reflected in the base composition of H and L strands. The highly conserved sequence motif of the mTERF binding site in carangids over the ~ 400 MYA of their divergence demonstrated the functional importance of these sites. The control region of carangids was characterized by the presence of discontinuous repeat units with a high rate of sequence divergence in the form of base substitutions, insertions, and deletions. The maintenance of secondary structures in the control region independent of the rapid evolution of primary structure suggested the effect of selective constraints on their maintenance. Maximum likelihood (ML) and Bayesian inference (BI) phylogeny revealed a similar topology consistent with previous taxonomic studies. The extant carangids diverged through the evolutionary events experienced during the Cretaceous, Paleogene, and Neogene periods.
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6
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Luz SCS, Montes MA, Farias RS, Lima RV, Torres RA, Ferreira EJG, Severi W, Coimbra MRM. Reduced genetic diversity and the success of the invasive peacock bass (Cichliformes: Cichlidae). BRAZ J BIOL 2021; 84:e248656. [PMID: 34730686 DOI: 10.1590/1519-6984.248656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/10/2021] [Indexed: 11/22/2022] Open
Abstract
Several species of Cichla successfully colonized lakes and reservoirs of Brazil, since the 1960's, causing serious damage to local wildlife. In this study, 135 peacock bass were collected in a reservoir complex in order to identify if they represented a single dominant species or multiple ones, as several Cichla species have been reported in the basin. Specimens were identified by color pattern, morphometric and meristic data, and using mitochondrial markers COI, 16S rDNA and Control Region (CR). Overlapping morphological data and similar coloration patterns prevented their identification using the taxonomic keys to species identification available in the literature. However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. A single haplotype was observed for the 16S and CR, while three were detected for COI, with a dominant haplotype present in 98.5% of the samples. The extreme low diversity of the transplanted C. kelberi evidenced a limited number of founding maternal lineages. The success of this colonization seems to rely mainly on abiotic factors, such as increased water transparency of lentic environments that favor visual predators that along with the absence of predators, have made C. kelberi a successful invader of these reservoirs.
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Affiliation(s)
- S C S Luz
- Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Pesca e Aquicultura, Recife, PE, Brasil
| | - M A Montes
- Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Biologia, Recife, PE, Brasil
| | - R S Farias
- Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Pesca e Aquicultura, Recife, PE, Brasil
| | - R V Lima
- Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Pesca e Aquicultura, Recife, PE, Brasil
| | - R A Torres
- Universidade Federal de Pernambuco - UFPE, Departamento de Zoologia, Recife, PE, Brasil
| | - E J G Ferreira
- Instituto Nacional de Pesquisas da Amazônia - INPA, Coordenação de Biodiversidade, Manaus, AM, Brasil
| | - W Severi
- Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Pesca e Aquicultura, Recife, PE, Brasil
| | - M R M Coimbra
- Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Pesca e Aquicultura, Recife, PE, Brasil
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7
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Yin X, Li X, Chen J, Tian K, Zhang H, Yuan P. Characterization of the complete mitochondrial genome of Chrysochir aureus and phylogenetic studies of Sciaenidae. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:444-446. [PMID: 33659703 PMCID: PMC7872559 DOI: 10.1080/23802359.2020.1870900] [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: 10/28/2022]
Abstract
The complete mitochondrial genome of Chrysochir aureus was sequenced. The full length of the mitochondrial genome was 16,501 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.95% A, 29.99% C, 26.29% T, and 16.77% G. Twelve PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of C. aureus described in this study could be a useful basis for management of this species and laid a foundation for further research involved with phylogenetic relationship within Sciaenidae.
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Affiliation(s)
- Xiaolong Yin
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences, Guangzhou, China.,Zhoushan Fisheries Research Institute of Zhejiang Province, Zhoushan, China
| | - Xuepeng Li
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China.,College of Life Sciences, Yantai University, Yantai, China
| | - Jian Chen
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Kuo Tian
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Hua Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences, Guangzhou, China
| | - Pengxiang Yuan
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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8
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Sun Y. Characterization of the complete mitochondrial genome of Ostorhinchus novemfasciatus and phylogenetic studies of Apogoninae. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:31-32. [PMID: 33490591 PMCID: PMC7801025 DOI: 10.1080/23802359.2020.1845579] [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: 10/31/2022]
Abstract
The complete mitochondrial genome of Ostorhinchus novemfasciatus was first presented in this study. The full length of the mitochondrial genome was 16,779 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.0% A, 30.2% C, 26.2% T and 17.5% G. 12 PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of O. novemfasciatus described in this study could be a useful basis for the management of this species and laid a foundation for further research involved with phylogenetic relationship within Apogoninae.
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Affiliation(s)
- Ying Sun
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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9
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Tea YK, Gill AC, Senou H. Two New Species of Pseudojuloides from Western Australia and Southern Japan, with a Redescription of Pseudojuloides elongatus (Teleostei: Labridae). COPEIA 2020. [DOI: 10.1643/ci-19-316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia; (YKT) . Send reprint requests to YKT
| | - Anthony C. Gill
- Ichthyology, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
| | - Hiroshi Senou
- Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Odawara, Kanagawa 250-0031, Japan;
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10
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Tea Y, Van Der Wal C, Ludt WB, Gill AC, Lo N, Ho SYW. Boomeranging around Australia: Historical biogeography and population genomics of the anti‐equatorial fish
Microcanthus strigatus
(Teleostei: Microcanthidae). Mol Ecol 2019; 28:3771-3785. [DOI: 10.1111/mec.15172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Yi‐Kai Tea
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
| | - William B. Ludt
- National Museum of Natural History, Smithsonian Institution Washington DC USA
- Natural History Museum of Los Angeles County Los Angeles CA USA
| | - Anthony C. Gill
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- Australian Museum Research Institute, Australian Museum Sydney NSW Australia
- Macleay Museum University of Sydney Sydney NSW Australia
| | - Nathan Lo
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
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11
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Wang Z, Miao Z, Yin X, Chen J, Ying X. Phylogenetic analysis of the complete mitochondrial genome of Dysomma anguillare (Anguilliformes, Synaphobranchidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1602006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Zuhao Wang
- Department of Food Science and Pharmacy, Key Laboratory of Aquatic Products Processing of Zhejiang Province, Zhejiang Ocean University, Zhoushan, PR China
| | - Zengliang Miao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, PR China
| | - Xiaolong Yin
- Zhoushan Fisheries Research Institute of Zhejiang Province, Zhoushan, PR China
| | - Jian Chen
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, PR China
| | - Xiaoguo Ying
- Department of Food Science and Pharmacy, Key Laboratory of Aquatic Products Processing of Zhejiang Province, Zhejiang Ocean University, Zhoushan, PR China
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12
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Niu W, Kong L, Ma H, Gao Y. Characterization and phylogenetic analysis of the complete mitochondrial genome of Bodianus oxycephalus (Perciformes, Labridae). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0857-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Siva C, Kumar R, Sharma L, Laskar MA, Sumer S, Barat A, Sahoo PK. The complete mitochondrial genome of a stream loach (Schistura reticulofasciata) and its phylogeny. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0941-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Genetic legacy of tertiary climatic change: a case study of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi, in Hong Kong. Heredity (Edinb) 2017; 119:360-370. [PMID: 28792491 DOI: 10.1038/hdy.2017.47] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 11/08/2022] Open
Abstract
The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant ΦST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.
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15
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Xu B, Wang Y, Zhou H, Gou C, Dong W, Wang Y, Gao Y, Ma H. Complete mitochondrial genome of Japanese bigeye ( Pristigenys niphonia): genome characterization and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:886-888. [PMID: 33473666 PMCID: PMC7800645 DOI: 10.1080/23802359.2016.1258339] [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: 11/02/2022]
Abstract
The Japanese bigeye (Pristigenys niphonia) is a species in the genus Pristigenys and in the family Priacanthidae. To understand the phylogenetic relationship of Japanese bigeye in teleost, we firstly determined the complete mitochondrial genome of Japanese bigeye. The entire mitochondrial genome of Japanese bigeye is 16,519bp in length, including 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNAs), and 2 main non-coding regions. The overall base composition is 24.9% of T, 30.6% of C, 27.7% of A, and 16.8% of G. The gene arrangement, base composition, and tRNA structures of the complete mitochondrial genome of Japanese bigeye is consistent with those of other teleost. The complete mitochondrial genome of Japanese bigeye was used to construct phylogenetic tree, which shows that Japanese bigeye is clustered with the fishes of the order Perciformes. We expect that the availability of mitochondrial genome of Japanese bigeye will facilitate the further investigations of the taxonomic resolution, biogeography, and molecular systematic.
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Affiliation(s)
- Bo Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yingzhe Wang
- Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Haizhu Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Changlong Gou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Wenlong Dong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yu Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yunhang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Hongxia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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16
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Firidin S, Eroglu O, Altinok I. Genetic characterization of brown meagre (Sciaena umbra) and Shi Drum (Umbrina cirrosa) populations. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Valenzuela-Quiñonez F, De-Anda-Montañez JA, Gilbert-Horvath E, Garza JC, García-De León FJ. Panmixia in a Critically Endangered Fish: The Totoaba (Totoaba macdonaldi) in the Gulf of California. J Hered 2016; 107:496-503. [PMID: 27466386 DOI: 10.1093/jhered/esw046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/24/2016] [Indexed: 01/26/2023] Open
Abstract
Conservation of the evolutionary legacy of endangered species is a key component for long-term persistence. Totoaba is a long-lived fish endemic to the Gulf of California and is considered critically endangered. There is currently a debate concerning its conservation status and whether it can be used as a fishery resource. Unfortunately, basic information on biological and genetic population structure of the species is lacking. We sampled 313 individuals and employed 16 microsatellite loci and 3 mitochondrial DNA markers (16S, 547 pb; COI, 619 pb; control region, 650 pb) to assess population structure and demography of totoaba in the Gulf of California, with samples from locations that encompass nearly all of its recognized geographic distribution. We could not reject a hypothesis of panmixia for totoaba, using nuclear or mitochondrial markers. Demographic analysis of mtDNA suggests a sudden population expansion model. The results have important implications for totoaba conservation because poaching is a significant conservation challenge and could have additive negative effects over the single population of totoaba in the Gulf of California.
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Affiliation(s)
- Fausto Valenzuela-Quiñonez
- From the CONACYT-Centro de Investigaciones Biológicas de Noroeste (CIBNOR), Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez); Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and García-De León); Laboratorio de Recursos Bentónicos y Modelación Bioeconómica, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and De-Anda-Montañez); and Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060 (Gilbert-Horvath and Garza)
| | - Juan A De-Anda-Montañez
- From the CONACYT-Centro de Investigaciones Biológicas de Noroeste (CIBNOR), Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez); Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and García-De León); Laboratorio de Recursos Bentónicos y Modelación Bioeconómica, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and De-Anda-Montañez); and Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060 (Gilbert-Horvath and Garza)
| | - Elizabeth Gilbert-Horvath
- From the CONACYT-Centro de Investigaciones Biológicas de Noroeste (CIBNOR), Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez); Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and García-De León); Laboratorio de Recursos Bentónicos y Modelación Bioeconómica, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and De-Anda-Montañez); and Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060 (Gilbert-Horvath and Garza)
| | - John Carlos Garza
- From the CONACYT-Centro de Investigaciones Biológicas de Noroeste (CIBNOR), Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez); Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and García-De León); Laboratorio de Recursos Bentónicos y Modelación Bioeconómica, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and De-Anda-Montañez); and Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060 (Gilbert-Horvath and Garza)
| | - Francisco J García-De León
- From the CONACYT-Centro de Investigaciones Biológicas de Noroeste (CIBNOR), Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez); Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and García-De León); Laboratorio de Recursos Bentónicos y Modelación Bioeconómica, Centro de Investigaciones Biológicas de Noroeste, Calle IPN 195, La Paz, B.C.S. 23096, Mexico (Valenzuela-Quiñonez and De-Anda-Montañez); and Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060 (Gilbert-Horvath and Garza).
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18
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Reid K, Hoareau TB, Graves JE, Potts WM, Dos Santos SMR, Klopper AW, Bloomer P. Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone. Heredity (Edinb) 2016; 117:307-315. [PMID: 27436525 DOI: 10.1038/hdy.2016.51] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022] Open
Abstract
The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (FST 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.
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Affiliation(s)
- K Reid
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - T B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - J E Graves
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Williamsburg, VA, USA
| | - W M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - S M R Dos Santos
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - A W Klopper
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - P Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
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19
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Liu J, Kong L, Gao Y, Wu C. Complete mitochondrial genome of black-banded trevally (Seriolina nigrofasciata): Genome characterization and phylogenetic considerations. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4701-4703. [PMID: 26678379 DOI: 10.3109/19401736.2015.1106509] [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
The black-banded trevally (Seriolina nigrofasciata) is a species of the family Carangidae and the only known member of genus Seriolina. To understand the phylogenetic relationship of black-banded trevally in teleost, we first determined the complete mitochondrial genome of black-banded trevally. The entire mitochondrial genome of black-banded trevally is 16 531 bp in length, containing 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNAs), and 2 main non-coding regions. The overall base composition is T 25.8%, C 30.0%, A 26.7%, and G 17.5%. The gene arrangement, base composition, and tRNA structures of black-banded trevally are consistent with those of other teleost. Two of the central conserved sequence blocks (CSB-2 and CSB-3) were identified and the core sequence (TACATGTATGTA) of terminal-associated sequences was recognized in the control region. Meanwhile, the conserved motif 5'-GCCGG-3' was identified in the origin of light-strand replication of black-banded trevally. The complete mitochondrial genome of black-banded trevally was used to construct phylogenetic tree, which shows that black-banded trevally is clustered with the fishes of the genus Seriola. We expect that the availability of the mitochondrial genome of black-banded trevally will facilitate the further investigations of molecular systematic and phylogenetic analysis of the Carangidae.
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Affiliation(s)
- Jiang Liu
- a National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University , Zhoushan , China , and
| | - Lingcong Kong
- b College of Animal Science and Veterinary Medicine, Jilin Agriculture University , Changchun , China
| | - Yunhang Gao
- b College of Animal Science and Veterinary Medicine, Jilin Agriculture University , Changchun , China
| | - Changwen Wu
- a National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University , Zhoushan , China , and
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20
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Luz LA, Reis LL, Sampaio I, Barros MC, Fraga E. Genetic differentiation in the populations of red piranha, Pygocentrus nattereri Kner (1860) (Characiformes: Serrasalminae), from the river basins of northeastern Brazil. BRAZ J BIOL 2015; 75:838-45. [PMID: 26675902 DOI: 10.1590/1519-6984.00214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 07/18/2014] [Indexed: 11/21/2022] Open
Abstract
The red piranha, Pygocentrus nattereri, is an important resource for artisanal and commercial fisheries. The present study determines the genetic differentiation among P. nattereri populations from the northeastern Brazilian state of Maranhão. The DNA was isolated using a standard phenol-chloroform protocol and the Control Region was amplified by PCR. The PCR products were sequenced using the didesoxyterminal method. A sequence of 1039 bps was obtained from the Control Region of 60 specimens, which presented 33 polymorphic sites, 41 haplotypes, һ =0.978 and π =0.009. The neutrality tests (D and Fs) were significant (P < 0.05) for most of the populations analyzed. The AMOVA indicated that most of the molecular variation (72%) arises between groups. The fixation index was highly significant (FST = 0.707, P < 0.00001). The phylogenetic analyses indicated that the specimens represented a monophyletic group. Genetic distances between populations varied from 0.8% to 1.9%, and were <0.5% within populations. The degree of genetic differentiation found among the stocks of P. nattereri indicates the need for the development of independent management plans for the different river basins in order to preserve the genetic variability of their populations.
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Affiliation(s)
- L A Luz
- Centro de Ciências Agrárias, Universidade Estadual do Maranhão, São Luís, MA, Brazil
| | - L L Reis
- Centro de Ciências Agrárias, Universidade Estadual do Maranhão, São Luís, MA, Brazil
| | - I Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, PA, Brazil
| | - M C Barros
- Centro de Ciências Agrárias, Universidade Estadual do Maranhão, São Luís, MA, Brazil
| | - E Fraga
- Centro de Ciências Agrárias, Universidade Estadual do Maranhão, São Luís, MA, Brazil
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21
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Sukumaran S, Sebastian W, Gopalakrishnan A. Population genetic structure of Indian oil sardine, Sardinella longiceps along Indian coast. Gene 2015; 576:372-8. [PMID: 26494160 DOI: 10.1016/j.gene.2015.10.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 11/30/2022]
Abstract
Genetic stock structure and historical demography of Indian oil sardine, a commercially and ecologically important small pelagic fish, was studied using mitochondrial control region and Cytochrome C Oxidase I (COI) sequences. A 758 bp portion of the control region in 287 individuals and a 576 bp portion of the COI gene in 291 individuals from 10 locations along the distribution range were amplified resulting in 236 and 84 haplotypes, respectively. The high haplotype and low nucleotide diversity values (0.99 and 0.19 for control region and 0.85 and 0.004 for COI, respectively) are characteristic of populations having undergone a demographic expansion. Genetic differentiation, ΦST, was low and insignificant between populations using both control region and COI gene markers. Mismatch analysis showed a recent demographic and spatial expansion coinciding with the late Pleistocene epoch. Mantel tests revealed the lack of isolation by distance which is attributable either to high levels of migration overriding the effect of genetic drift or to insufficient time for accomplishing a balance between migration and drift after a recent range expansion.
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Affiliation(s)
- Sandhya Sukumaran
- Central Marine Fisheries Research Institute, Post Box No: 1603, Ernakulam North P.O., Kochi, Kerala, India, Pin-682018.
| | - Wilson Sebastian
- Central Marine Fisheries Research Institute, Post Box No: 1603, Ernakulam North P.O., Kochi, Kerala, India, Pin-682018
| | - A Gopalakrishnan
- Central Marine Fisheries Research Institute, Post Box No: 1603, Ernakulam North P.O., Kochi, Kerala, India, Pin-682018
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22
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Sahoo PK, Goel C, Kumar R, Dhama N, Ali S, Sarma D, Nanda P, Barat A. The complete mitochondrial genome of threatened chocolate mahseer (Neolissochilus hexagonolepis) and its phylogeny. Gene 2015; 570:299-303. [DOI: 10.1016/j.gene.2015.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 07/01/2015] [Accepted: 07/09/2015] [Indexed: 11/30/2022]
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23
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Kumar R, Goel C, Kumari Sahoo P, Singh AK, Barat A. Complete mitochondrial genome organization of Tor tor (Hamilton, 1822). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2541-2. [DOI: 10.3109/19401736.2015.1038795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Rohit Kumar
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Nainital, Uttarakhand, India
| | - Chirag Goel
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Nainital, Uttarakhand, India
| | - Prabhati Kumari Sahoo
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Nainital, Uttarakhand, India
| | - Atul K Singh
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Nainital, Uttarakhand, India
| | - Ashoktaru Barat
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Nainital, Uttarakhand, India
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Jin X, Wang R, Wei T, Tang D, Xu T. Complete mitochondrial genome sequence of Tridentiger bifasciatus and Tridentiger barbatus (Perciformes, Gobiidae): a mitogenomic perspective on the phylogenetic relationships of Gobiidae. Mol Biol Rep 2014; 42:253-65. [PMID: 25260906 DOI: 10.1007/s11033-014-3768-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 09/20/2014] [Indexed: 10/24/2022]
Abstract
The fishes of suborder Gobioidei is the largest group of those in present living Perciformes, which contains about 2,200 species belonging to 270 genera of 9 families in the world. The monophyly and phylogenetic relationships of gobies have been controversial and disputable for a long time. In the present study, the complete mitochondrial genome of the shimofuri goby Tridentiger bifasciatus (T. bifasciatus) and shokihaze goby Tridentiger barbatus (T. barbatus) were firstly determined. The two mitochondrial genomes were both consisted of 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one major control region (CR). They shared similar features with those of other gobies in terms of gene arrangement, base composition, and tRNA structures. The CR was absence of typical conserved blocks (CSB-E, and CSB-F) respectively for the T. bifasciatus and T. barbatus. Phylogenomic analyses, which based on 12 concatenated protein-coding genes and complete mitochondrial genome sequences, revealed that there were two groups within the Gobiidae. A large group consisted of the Amblyopinae, Gobionellinae, Oxudercinae and Sicydiinae, and Amblyopinae was nested in Oxudercinae and they were both paraphyletic to Sicydiinae. The other group was the Gobiinae. As a whole, our phylogenetic data was different from the traditionally classification of Gobiidae, but supported the new phylogenetic taxonomy view of Thacker (Copeia 2009:93-104, 2009).
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Affiliation(s)
- Xiaoxiao Jin
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
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