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Palacios-Barreto P, Mar-Silva AF, Bayona-Vasquez NJ, Adams DH, Díaz-Jaimes P. Characterization of the complete mitochondrial genome of the brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes, Rhinopteridae) in the western Atlantic and its phylogenetic implications. Mol Biol Rep 2023; 50:4083-4095. [PMID: 36877343 DOI: 10.1007/s11033-023-08272-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. This species is sometimes confused with Rhinoptera bonasus, the only external diagnostic characteristic to distinguish between both species is the number of rows of tooth plates. Both cownose rays overlap geographically from Rio de Janeiro to the western North Atlantic. This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationships and delimitation of these two species. METHODS AND RESULTS The mitochondrial genome sequences of R. brasiliensis was obtained by next-generation sequencing. The length of the mitochondrial genome was 17,759 bp containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. The phylogenetic analysis showed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome as R. steindachneri (GenBank accession number KM364982), differs from multiple mitocondrial DNA sequences of R. steindachneri and is nearly identical to that of R. javanica. CONCLUSION The new mitogenome determined in this study provides new insight into the phylogenetic relationships in Rhinoptera, while providing new molecular data that can be applied to population genetic studies.
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Affiliation(s)
- Paola Palacios-Barreto
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, México.,Fundación colombiana para la investigación y conservación de Tiburones y Rayas, SQUALUS, Cali, Colombia
| | - Adán Fernando Mar-Silva
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, México
| | - Natalia J Bayona-Vasquez
- Division of Natural Science and Mathematics, Oxford College, Emory University, 30054, Oxford, GA, USA
| | - Douglas H Adams
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Indian River Field Laboratory, 32901, Melbourne, FL, USA
| | - Píndaro Díaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México.
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2
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Characterization of mitochondrial genome of Indian Ocean blue-spotted maskray, Neotrygon indica and its phylogenetic relationship within Dasyatidae Family. Int J Biol Macromol 2022; 223:458-467. [PMID: 36347369 DOI: 10.1016/j.ijbiomac.2022.10.277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
The present study characterized complete mitochondrial genome of Blue-spotted maskray, Neotrygon indica and studied the evolutionary relationship of the species within the Dasyatidae family. The total length of the mitogenome was 17,974 bp including 37 genes and a non-coding control region. The average frequency of nucleotides in protein-coding genes was A: 29.1 %, T: 30.2 %, G: 13.0 % and C: 27.7 % with AT content of 59.3 %. The values of AT and GC skewness were -0.018 and -0.338, respectively. Comparative analyses showed a large number of average synonymous substitutions per synonymous site (Ks) in gene NADH4 (5.07) followed by NADH5 (4.72). High values of average number of non-synonymous substitutions per non-synonymous site (Ka) were observed in genes ATPase8 (0.54) and NADH2 (0.44). Genes NADH4L and NADH2 showed high interspecific genetic distance values of 0.224 ± 0.001 and 0.213 ± 0.002, respectively. Heat map analysis showed variation in codon usage among different species of the Dasyatidae family. The phylogenetic tree showed a sister relationship between the Dasyatinae and the Neotrygoninae subfamilies. Neotrygon indica formed as a sister species to the clade consisting of N. varidens and N. orientalis. Based on the present results, Neotrygon indica could have diverged from the common ancestor of the two latter in the Plio-Pleistocene. The present study showed distinct characteristics of N. indica from its congeners through comparative mitogenomics.
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3
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Hardenstine RS, He S, Cochran JEM, Braun CD, Cagua EF, Pierce SJ, Prebble CEM, Rohner CA, Saenz‐Angudelo P, Sinclair‐Taylor TH, Skomal GB, Thorrold SR, Watts AM, Zakroff CJ, Berumen ML. Pieces in a global puzzle: Population genetics at two whale shark aggregations in the western Indian Ocean. Ecol Evol 2022; 12:e8492. [PMID: 35127024 PMCID: PMC8796955 DOI: 10.1002/ece3.8492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/30/2021] [Accepted: 11/10/2021] [Indexed: 02/01/2023] Open
Abstract
The whale shark Rhincodon typus is found throughout the world's tropical and warm-temperate ocean basins. Despite their broad physical distribution, research on the species has been concentrated at a few aggregation sites. Comparing DNA sequences from sharks at different sites can provide a demographically neutral understanding of the whale shark's global ecology. Here, we created genetic profiles for 84 whale sharks from the Saudi Arabian Red Sea and 72 individuals from the coast of Tanzania using a combination of microsatellite and mitochondrial sequences. These two sites, separated by approximately 4500 km (shortest over-water distance), exhibit markedly different population demographics and behavioral ecologies. Eleven microsatellite DNA markers revealed that the two aggregation sites have similar levels of allelic richness and appear to be derived from the same source population. We sequenced the mitochondrial control region to produce multiple global haplotype networks (based on different alignment methodologies) that were broadly similar to each other in terms of population structure but suggested different demographic histories. Data from both microsatellite and mitochondrial markers demonstrated the stability of genetic diversity within the Saudi Arabian aggregation site throughout the sampling period. These results contrast previously measured declines in diversity at Ningaloo Reef, Western Australia. Mapping the geographic distribution of whale shark lineages provides insight into the species' connectivity and can be used to direct management efforts at both local and global scales. Similarly, understanding historical fluctuations in whale shark abundance provides a baseline by which to assess current trends. Continued development of new sequencing methods and the incorporation of genomic data could lead to considerable advances in the scientific understanding of whale shark population ecology and corresponding improvements to conservation policy.
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Affiliation(s)
- Royale S. Hardenstine
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Song He
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Jesse E. M. Cochran
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Camrin D. Braun
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Edgar Fernando Cagua
- School of Biological SciencesCentre for Integrative EcologyUniversity of CanterburyChristchurchNew Zealand
- WorldFishBayan LepasMalaysia
| | | | - Clare E. M. Prebble
- Marine Megafauna FoundationTruckeeCaliforniaUSA
- National Oceanography CentreUniversity of South HamptonSouth HamtonUK
| | | | - Pablo Saenz‐Angudelo
- Facultad de CienciasInstituo de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | | | - Gregory B. Skomal
- Massachusetts Division of Marine FisheriesNew BedfordMassachusettsUSA
| | - Simon R. Thorrold
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Alexandra M. Watts
- Marine Megafauna FoundationTruckeeCaliforniaUSA
- Ecological Genetics and Conservation LaboratoryManchester Metropolitan UniversityManchesterUK
| | - Casey J. Zakroff
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Michael L. Berumen
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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4
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Gomes-Dos-Santos A, Machado AM, Aranha SG, Dias E, Veríssimo A, Castro LFC, Froufe E. The complete mitochondrial genome of the endemic Iberian pygmy skate Neoraja iberica Stehmann, Séret, Costa, & Baro 2008 (Elasmobranchii, Rajidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:848-850. [PMID: 33796653 PMCID: PMC7971246 DOI: 10.1080/23802359.2021.1884030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Skates, Chondrichthyes fishes from order Rajiformes, are the most species-rich group of all Batoidea. However, their phylogenetic relationships and systematics is still a highly discussed and controversial subject. The use of complete mitogenome has shown to be a promising tool to fill this gap of knowledge. Here, the complete mitogenome of the Iberian pygmy skate Neoraja iberica (Stehmann, Séret, Costa & Baro 2008) was sequenced and assembled. The mitogenome is 16,723 bp long and its gene content (i.e. 13 protein-coding genes, 22 transfer RNA, and 2 ribosomal RNA genes) and arrangement are the expected for Batoidea. Phylogenetic reconstructions, including 89 Rajiformes and two outgroup Rhinopristiformes, recovered family Rajidae as monophyletic, and further divided in the monophyletic tribe Rajini, sister to tribes Amblyrajini and Rostrorajini. The newly sequenced N. iberica mitogenome is the first representative of the tribe Rostrorajini.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal
| | - Sofia Graça Aranha
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Ester Dias
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO - Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal
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Sun CH, Liu HY, Xu N, Zhang XL, Zhang Q, Han BP. Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes. Front Genet 2021; 12:627402. [PMID: 33633787 PMCID: PMC7901900 DOI: 10.3389/fgene.2021.627402] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenomes are circular DNA molecules with sizes of 16,701 bp (Hyphessobrycon amandae; MT484069) and 16,710 bp (Hemigrammus erythrozonus; MT484070); both have a highly conserved structure typical of Characidae, with the start codon ATN (ATG/ATT) and stop codon TAR (TAA/TAG) or an incomplete T--/TA-. Most protein-coding genes of the 11 Characidae mitogenomes showed significant codon usage bias, and the protein-coding gene cox1 was found to be a comparatively slow-evolving gene. Phylogenetic analyses via the maximum likelihood and Bayesian inference methods confirmed that H. amandae and H. erythrozonus belong to the family Characidae. In all Characidae species studied, one genus was well supported; whereas other two genera showed marked differentiation. These findings provide a phylogenetic basis for improved classification of the family Characidae. Determining the mitogenomes of H. erythrozonus and H. amandae improves our understanding of the phylogeny and evolution of fish species.
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Affiliation(s)
- Cheng-He Sun
- Department of Ecology, Jinan University, Guangzhou, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Yi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xiao-Li Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Qun Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Bo-Ping Han
- Department of Ecology, Jinan University, Guangzhou, China
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6
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Zhu T, Li Y, Pang Y, Han Y, Li J, Wang Z, Liu X, Li H, Hua Y, Jiang H, Teng H, Quan J, Liu Y, Geng M, Li M, Hui F, Liu J, Qiu Q, Li Q, Ren Y. Chromosome-level genome assembly of Lethenteron reissneri provides insights into lamprey evolution. Mol Ecol Resour 2020; 21:448-463. [PMID: 33053263 DOI: 10.1111/1755-0998.13279] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 11/29/2022]
Abstract
The reissner lamprey Lethenteron reissneri, belonging to the class Cyclostomata, serves as a bridge between invertebrates and jawed vertebrates, and is considered the sister group of jawed vertebrates. However, despite this evolutionary significance, the genetic mechanisms underlying the adaptive evolution of the lamprey lineage remain unclear. Here, we assembled a 1.06 Gb chromosome-level draft genome of L. reissneri, with 72 chromosomes (ranging in length from 4.5 Mb to 25.9 Mb) and a scaffold N50 length of 13.23 Mb. Genome quality comparisons revealed that the reissner lamprey genome has higher completeness and contiguity than the previously published sea lamprey and Japanese lamprey genomes. Moreover, reissner lamprey, sea lamprey, and Japanese lamprey species share similar transposable element profiles and Hox gene cluster compositions, suggesting that a burst of transposable element activity and whole genome duplication occurred before their divergence. Additionally, the Lip gene copy numbers, which have been studied for their functions in the host defence system, were found to be expanded uniquely in lamprey lineages, suggesting key roles for these genes in lamprey evolution and adaptation. We also identified two neural-related genes, Nrn1 and Unc13a, with copy number expansions in jawed vertebrates, which may be functionally relevant to the origin of lamprey brains. Hence, this study not only provides the first chromosome-level reference genome for Cyclostomata, but also highlights features of the unique biology and adaptive evolution of the lamprey lineage.
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Affiliation(s)
- Ting Zhu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jun Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yishan Hua
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Hui Jiang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hongming Teng
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jian Quan
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yu Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Ming Geng
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Meiao Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Fan Hui
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jinzhao Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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Afriyie G, Wang Z, Dong Z, Ayisi Larbi C, Asiedu B, Guo Y. Complete mitochondrial genome and assembled DNA barcoding analysis of Lutjanus fulgens (Valenciennes, 1830) and its comparison with other Lutjanus species. Ecol Evol 2020; 10:7971-7980. [PMID: 32788954 PMCID: PMC7417232 DOI: 10.1002/ece3.6542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 11/10/2022] Open
Abstract
Lutjanus fulgens (Valenciennes, 1830) is a teleost species classified under the family Lutjanidae which is a native of the Eastern Atlantic Ocean. Though highly commercialized due to its abundance and good taste, the production output has declined in recent years. This is an indication of the need for effective management and conservation measures. However, accurate species identification will ensure strategic management and conservation measure. DNA-based species identification has proven its reliability in this regard via precise species identification. Several researchers have confirmed the accuracy of DNAbarcode as a species identification tool as well as species phylogeny analysis based on both the complete mitogenome and COI gene. Currently, nine specimens of L. fulgens were sampled from Ghana and subjected to DNA-based analysis, namely, complete mitochondrial DNAand COI gene (DNA barcoding) analyses. The mitogenomic result revealed that L. fulgens is made up of a 16,500 base pairs (bp) mtDNA which consists of 22 transfer RNAs, 13 protein-coding genes, and two ribosomal RNAs (GenBank Accession Number: MN398650). Furthermore, a sequence polymorphism analysis of the COIgene (MN986442-MN986450) detected two haplotypes. These haplotypes were both collected from the same fish landing site which suggests a possible cryptic linage diversity in the L. fulgens population at Vodza. According to the phylogeny examination, a close taxonomic relationship exists between L. fulgens and Lutjanus buccanella caused by a recent evolution termed as sympatric speciation. This study serves as a novel study for this species, building the foundation for future molecular-based study for this species and as a DNA barcode reference data.
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Affiliation(s)
- Gyamfua Afriyie
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic AnimalsFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Christian Ayisi Larbi
- Department of Fisheries and Aquatic Resources ManagementUniversity for Development StudiesTamaleGhana
| | - Berchie Asiedu
- Department of Fisheries and AquacultureUniversity of Energy and Natural ResourcesSunyaniGhana
| | - Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
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Mukundan LP, Sukumaran S, Sebastian W, Gopalakrishnan A. Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus lepturus (Trichiuridae): Insights into Special Characteristics. Biochem Genet 2020; 58:430-451. [DOI: 10.1007/s10528-020-09956-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/05/2020] [Indexed: 12/01/2022]
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But GWC, Wu HY, Shao KT, Shaw PC. Rapid detection of CITES-listed shark fin species by loop-mediated isothermal amplification assay with potential for field use. Sci Rep 2020; 10:4455. [PMID: 32157111 PMCID: PMC7064571 DOI: 10.1038/s41598-020-61150-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/20/2020] [Indexed: 11/24/2022] Open
Abstract
Shark fin is a delicacy in many Asian countries. Overexploitation of sharks for shark fin trading has led to a drastic reduction in shark population. To monitor international trade of shark fin products and protect the endangered species from further population decline, we present rapid, user-friendly and sensitive diagnostic loop-mediated isothermal amplification (LAMP) and effective polymerase chain reaction (PCR) assays for all twelve CITES-listed shark species. Species-specific LAMP and PCR primers were designed based on cytochrome oxidase I (COI) and NADH2 regions. Our LAMP and PCR assays have been tested on 291 samples from 93 shark and related species. Target shark species could be differentiated from non-target species within three hours from DNA extraction to LAMP assay. The LAMP assay reported here is a simple and robust solution for on-site detection of CITES-listed shark species with shark fin products.
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Affiliation(s)
- Grace Wing-Chiu But
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hoi-Yan Wu
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kwang-Tsao Shao
- Systematics and Biodiversity Information Division, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pang-Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.
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10
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Liu X, Li W, Ye Z, Zhu Y, Hong X, Zhu X. Morphological characterization and phylogenetic relationships of Indochinese box turtles-The Cuora galbinifrons complex. Ecol Evol 2019; 9:13030-13042. [PMID: 31871627 PMCID: PMC6912918 DOI: 10.1002/ece3.5680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/10/2019] [Accepted: 09/05/2019] [Indexed: 11/29/2022] Open
Abstract
The members of the Indochinese box turtle complex, namely Cuora galbinifrons, Cuora bourreti, and Cuora picturata, rank the most critically endangered turtle species on earth after more than three decades of over-harvesting for food, traditional Chinese medicine, and pet markets. Despite advances in molecular biology, species boundaries and phylogenetic relationships, the status of the C. galbinifrons complex remains unresolved due to the small number of specimens observed and collected in the field. In this study, we present analyses of morphologic characters as well as mitochondrial and nuclear DNA data to reconstruct the species boundaries and systematic relationships within the C. galbinifrons complex. Based on principal component analysis (PCA) and statistical analysis, we found that phenotypic traits partially overlapped among galbinifrons, bourreti, and picturata, and that galbinifrons and bourreti might be only subspecifically distinct. Moreover, we used the mitochondrial genome, COI, and nuclear gene Rag1 under the maximum likelihood criteria and Bayesian inference criteria to elucidate whether C. galbinifrons could be divided into three separate species or subspecies. We found strong support for a sister relationship between picturata and the other two species, and consequently, we recommend maintaining picturata as a full species, and classifying bourreti and galbinifrons as subspecies of C. galbinifrons. These findings provide evidence for a better understanding of the evolutionary histories of these critically endangered turtles.
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Affiliation(s)
- Xiaoli Liu
- Key Laboratory of Aquatic GenomicsMinistry of AgricultureKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
| | - Wei Li
- Key Laboratory of Aquatic GenomicsMinistry of AgricultureKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
| | - Zhaoyang Ye
- Key Laboratory of Aquatic GenomicsMinistry of AgricultureKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- College of Life Science and FisheriesShanghai Ocean UniversityShanghaiChina
| | - Yanyu Zhu
- Key Laboratory of Aquatic GenomicsMinistry of AgricultureKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- College of Life Science and FisheriesShanghai Ocean UniversityShanghaiChina
| | - Xiaoyou Hong
- Key Laboratory of Aquatic GenomicsMinistry of AgricultureKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
| | - Xinping Zhu
- Key Laboratory of Aquatic GenomicsMinistry of AgricultureKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
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11
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Doane MP, Kacev D, Harrington S, Levi K, Pande D, Vega A, Dinsdale EA. Mitochondrial recovery from shotgun metagenome sequencing enabling phylogenetic analysis of the common thresher shark (Alopias vulpinus). Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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12
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Zhu KC, Liang YY, Wu N, Guo HY, Zhang N, Jiang SG, Zhang DC. Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile). Sci Rep 2017; 7:15299. [PMID: 29127415 PMCID: PMC5681689 DOI: 10.1038/s41598-017-15702-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022] Open
Abstract
To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.
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Affiliation(s)
- Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Yin-Yin Liang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Na Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, Guangdong Province, The People's Republic of China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China.
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
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Read TD, Petit RA, Joseph SJ, Alam MT, Weil MR, Ahmad M, Bhimani R, Vuong JS, Haase CP, Webb DH, Tan M, Dove ADM. Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828. BMC Genomics 2017; 18:532. [PMID: 28709399 PMCID: PMC5513125 DOI: 10.1186/s12864-017-3926-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. RESULTS We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. CONCLUSIONS This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.
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Affiliation(s)
- Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Robert A Petit
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Sandeep J Joseph
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Md Tauqeer Alam
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - M Ryan Weil
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Maida Ahmad
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Ravila Bhimani
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Jocelyn S Vuong
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Chad P Haase
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - D Harry Webb
- , Georgia Aquarium, 225 Baker Street, Atlanta, GA, 30313, USA
| | - Milton Tan
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA. .,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
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Villela LCV, Alves AL, Varela ES, Yamagishi MEB, Giachetto PF, da Silva NMA, Ponzetto JM, Paiva SR, Caetano AR. Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree. Genetica 2017; 145:51-66. [DOI: 10.1007/s10709-016-9945-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/22/2016] [Indexed: 01/08/2023]
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Santaquiteria A, Nielsen J, Klemetsen T, Willassen NP, Præbel K. The complete mitochondrial genome of the long-lived Greenland shark (Somniosus microcephalus): characterization and phylogenetic position. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-016-0676-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Sigsgaard EE, Nielsen IB, Bach SS, Lorenzen ED, Robinson DP, Knudsen SW, Pedersen MW, Jaidah MA, Orlando L, Willerslev E, Møller PR, Thomsen PF. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nat Ecol Evol 2016; 1:4. [DOI: 10.1038/s41559-016-0004] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/11/2016] [Indexed: 11/09/2022]
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Gaitán-Espitia JD, Solano-Iguaran JJ, Tejada-Martinez D, Quintero-Galvis JF. Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- CSIRO Oceans & Atmosphere; GPO Box 1538 Hobart 7001 TAS Australia
| | - Jaiber J. Solano-Iguaran
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Daniela Tejada-Martinez
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
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Díaz-Jaimes P, Bayona-Vásquez NJ, Adams DH, Uribe-Alcocer M. Complete mitochondrial DNA genome of bonnethead shark, Sphyrna tiburo, and phylogenetic relationships among main superorders of modern elasmobranchs. Meta Gene 2016; 7:48-55. [PMID: 27014583 PMCID: PMC4794228 DOI: 10.1016/j.mgene.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
Elasmobranchs are one of the most diverse groups in the marine realm represented by 18 orders, 55 families and about 1200 species reported, but also one of the most vulnerable to exploitation and to climate change. Phylogenetic relationships among main orders have been controversial since the emergence of the Hypnosqualean hypothesis by Shirai (1992) that considered batoids as a sister group of sharks. The use of the complete mitochondrial DNA (mtDNA) may shed light to further validate this hypothesis by increasing the number of informative characters. We report the mtDNA genome of the bonnethead shark Sphyrna tiburo, and compare it with mitogenomes of other 48 species to assess phylogenetic relationships. The mtDNA genome of S. tiburo, is quite similar in size to that of congeneric species but also similar to the reported mtDNA genome of other Carcharhinidae species. Like most vertebrate mitochondrial genomes, it contained 13 protein coding genes, two rRNA genes and 22 tRNA genes and the control region of 1086 bp (D-loop). The Bayesian analysis of the 49 mitogenomes supported the view that sharks and batoids are separate groups.
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Key Words
- ATP, Adenosine triphosphate
- Bonnethead
- CO, Cytochrome oxidase
- Cytb, Cytochrome B
- D-loop, Control region
- Hypnosqualea hypothesis
- ML, Maximum likelihood
- Mitogenome
- ND, Nicotine adenine dehydrogenase
- PCR, Polymerase chain reaction
- Phylogeny
- bp, Base pairs
- mt, Mitochondrial
- myr, Million years
- rRNA, Ribosomal RNA
- tRNA, Transference RNA
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Affiliation(s)
- Píndaro Díaz-Jaimes
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Natalia J. Bayona-Vásquez
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Douglas H. Adams
- Florida Fish and Wildlife Conservation Commission, Fish and
Wildlife Research Institute, 1220 Prospect Avenue, Suite 285, Melbourne, FL
32901, USA
| | - Manuel Uribe-Alcocer
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
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Murienne J, Jeziorski C, Holota H, Coissac E, Blanchet S, Grenouillet G. PCR-free shotgun sequencing of the stone loach mitochondrial genome (Barbatula barbatula). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4211-4212. [PMID: 26000945 DOI: 10.3109/19401736.2015.1022744] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The complete mitochondrial genome of the stone loach Barbatula barbatula (Linnaeus, 1758) (Actinopterygii: Cypriniformes: Nemacheilidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2500 platform. The mitochondrial genome of B. barbatula was determined to be 16,630 bp long and presents an organization typical of vertebrate mitogenomes. The mean coverage was 82× with a minimum coverage of 33× for the control region and 52× for the remaining part of the genome. A phylogenetic analysis of the Nemacheilidae family shows the monophyly of the Barbatula genus with strong support.
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Affiliation(s)
- Jérôme Murienne
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Céline Jeziorski
- b INRA, UAR1209, Département de Génétique Animale , INRA Auzeville , Castanet-Tolosan , France.,c GeT-PlaGe, Genotoul, INRA Auzeville , Castanet-Tolosan , France
| | - Hélène Holota
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
| | - Eric Coissac
- d Laboratoire d'Ecologie Alpine , CNRS UMR , Grenoble , France , and
| | - Simon Blanchet
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France.,e Station Expérimentale du CNRS à Moulis, U.S.R , Moulis , France
| | - Gaël Grenouillet
- a CNRS, Université de Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) , Toulouse , France
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