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Baeza JA, Stephens NC, Baker A, Lyons A, Franks B, Pirro S, Feldheim KA. Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement. Gene 2024; 894:147939. [PMID: 38572145 PMCID: PMC10990291 DOI: 10.1016/j.gene.2023.147939] [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] [Indexed: 04/05/2024]
Abstract
The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.
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Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
- Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile
| | | | - Alyssa Baker
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Andrew Lyons
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | - Bryan Franks
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | | | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, IL, USA
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Devloo‐Delva F, Burridge CP, Kyne PM, Brunnschweiler JM, Chapman DD, Charvet P, Chen X, Cliff G, Daly R, Drymon JM, Espinoza M, Fernando D, Barcia LG, Glaus K, González‐Garza BI, Grant MI, Gunasekera RM, Hernandez S, Hyodo S, Jabado RW, Jaquemet S, Johnson G, Ketchum JT, Magalon H, Marthick JR, Mollen FH, Mona S, Naylor GJP, Nevill JEG, Phillips NM, Pillans RD, Postaire BD, Smoothey AF, Tachihara K, Tillet BJ, Valerio‐Vargas JA, Feutry P. From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator. Ecol Evol 2023; 13:e9837. [PMID: 36844667 PMCID: PMC9944188 DOI: 10.1002/ece3.9837] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.
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Affiliation(s)
- Floriaan Devloo‐Delva
- Oceans and Atmosphere, CSIROHobartTasmaniaAustralia
- Quantitative Marine Science, Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Peter M. Kyne
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | | | - Demian D. Chapman
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Patricia Charvet
- Programa de Pós‐graduação em Sistemática, Uso e Conservação da BiodiversidadeUniversidade Federal do Ceará (PPGSis ‐ UFC)FortalezaBrazil
| | - Xiao Chen
- College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
| | - Geremy Cliff
- KwaZulu‐Natal Sharks Board, Umhlanga 4320, South Africa and School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Ryan Daly
- Oceanographic Research Institute, South African Association for Marine Biological Research, PointDurbanSouth Africa
- South African Institute for Aquatic BiodiversityMkhandaSouth Africa
| | - J. Marcus Drymon
- Coastal Research and Extension CenterMississippi State UniversityBiloxiMississippiUSA
- Mississippi‐Alabama Sea Grant ConsortiumOcean SpringsMississippiUSA
| | - Mario Espinoza
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
| | | | - Laura Garcia Barcia
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Kerstin Glaus
- Faculty of Science, Technology and Environment, School of Marine StudiesThe University of the South PacificSuvaFiji
| | | | - Michael I. Grant
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
| | | | - Sebastian Hernandez
- Biomolecular Laboratory, Center for International ProgramsUniversidad VERITASSan JoséCosta Rica
- Sala de Colecciones, Facultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research InstituteUniversity of TokyoKashiwa, ChibaJapan
| | - Rima W. Jabado
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
- Elasmo ProjectDubaiUnited Arab Emirates
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Grant Johnson
- Department of Industry, Tourism and Trade, Aquatic Resource Research UnitDarwinNorthern TerritoryAustralia
| | | | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - James R. Marthick
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesParisFrance
- EPHEPSL Research UniversityParisFrance
| | - Gavin J. P. Naylor
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | | | - Nicole M. Phillips
- School of Biological, Environmental and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | | | - Bautisse D. Postaire
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Amy F. Smoothey
- NSW Department of Primary Industries, Fisheries ResearchSydney Institute of Marine ScienceMosmanNew South WalesAustralia
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of ScienceUniversity of Ryukyus, NishiharaOkinawaJapan
| | - Bree J. Tillet
- Translational Research Institute, University of Queensland Diamantina InstituteBrisbaneQueenslandAustralia
| | - Jorge A. Valerio‐Vargas
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
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Wang C, Lai T, Ye P, Yan Y, Feutry P, He B, Huang Z, Zhu T, Wang J, Chen X. Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae. Gene 2022; 820:146232. [PMID: 35114282 DOI: 10.1016/j.gene.2022.146232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 01/08/2023]
Abstract
In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.
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Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China
| | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Peiyuan Ye
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yunrong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
| | - Pierre Feutry
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7000, Australia
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning 530000, China
| | | | - Ting Zhu
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; Guangxi Mangrove Research Center, Beihai 536000, China.
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Laurrabaquio-Alvarado NS, Díaz-Jaimes P, Hinojosa-Álvarez S, Blanco-Parra MDP, Adams DH, Pérez-Jiménez JC, Castillo-Géniz JL. Mitochondrial DNA genome evidence for the existence of a third divergent lineage in the western Atlantic Ocean for the bull shark (Carcharhinus leucas). JOURNAL OF FISH BIOLOGY 2021; 99:275-282. [PMID: 33559201 DOI: 10.1111/jfb.14698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/06/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
We report for the first time a highly divergent lineage in the Caribbean Sea for the bull shark (Carcharhinus leucas) based on the analysis of 51 mitochondrial DNA genomes of individuals collected in the western North Atlantic. When comparing the mtDNA control region obtained from the mitogenomes to sequences reported previously for Brazil, the Caribbean lineage remained highly divergent. These results support the existence of a discrete population in Central America due to a phylogeographic break separating the Caribbean Sea from the western North Atlantic, Gulf of Mexico and South America.
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Affiliation(s)
| | - Píndaro Díaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, UNAM, Mexico City, Mexico
| | - Silvia Hinojosa-Álvarez
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Monterrey, Mexico
| | - Maria Del Pilar Blanco-Parra
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico
- División de Ciencias e Ingeniería, Universidad de Quintana Roo, Chetumal, Mexico
- Fundación internacional para la naturaleza y la sustentabilidad, Chetumal, Mexico
| | - Douglas H Adams
- Florida Fish & Wildlife Conservation Commission, Fish & Wildlife Research Institute, Melbourne, Florida, USA
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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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Blower DC, Ovenden JR. The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:923-4. [PMID: 24938089 DOI: 10.3109/19401736.2014.926487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33× average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA's, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.
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Affiliation(s)
- Dean C Blower
- a School of Biological Sciences, The University of Queensland , St. Lucia , Australia and
| | - Jennifer R Ovenden
- a School of Biological Sciences, The University of Queensland , St. Lucia , Australia and.,b Molecular Fisheries Laboratory , The University of Queensland , St. Lucia , Australia
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