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Nishimura O, Rozewicki J, Yamaguchi K, Tatsumi K, Ohishi Y, Ohta T, Yagura M, Niwa T, Tanegashima C, Teramura A, Hirase S, Kawaguchi A, Tan M, D'Aniello S, Castro F, Machado A, Koyanagi M, Terakita A, Misawa R, Horie M, Kawasaki J, Asahida T, Yamaguchi A, Murakumo K, Matsumoto R, Irisarri I, Miyamoto N, Toyoda A, Tanaka S, Sakamoto T, Semba Y, Yamauchi S, Yamada K, Nishida K, Kiyatake I, Sato K, Hyodo S, Kadota M, Uno Y, Kuraku S. Squalomix: shark and ray genome analysis consortium and its data sharing platform. F1000Res 2022; 11:1077. [PMID: 36262334 PMCID: PMC9561540 DOI: 10.12688/f1000research.123591.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.
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Affiliation(s)
- Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - John Rozewicki
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Tazro Ohta
- Joint Support-Center for Data Science Research, Database Center for Life Science, Mishima, Shizuoka, 411-8540, Japan
| | - Masaru Yagura
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Taiki Niwa
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Akinori Teramura
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Akane Kawaguchi
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Filipe Castro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal
| | - André Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Ryo Misawa
- Japan Fisheries Research and Education Agency, Hachinohe, Aomori, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Junna Kawasaki
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Takashi Asahida
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Atsuko Yamaguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
| | | | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature-Zoology, Hamburg, 20146, Germany
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sho Tanaka
- School of Marine Science and Technology, Tokai University, Shizuoka, Shizuoka, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi, Japan., Okayama, Japan
| | - Yasuko Semba
- Highly Migratory Resources Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shizuoka, Shizuoka, Japan
| | | | - Kazuyuki Yamada
- Marine Science Museum, Tokai University, Shizuoka, Shizuoka, Japan
| | | | | | - Keiichi Sato
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo,, Kashiwa, Chiba, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan,
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6
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Wyffels JT, George R, Adams L, Adams C, Clauss T, Newton A, Hyatt MW, Yach C, Penfold LM. Testosterone and semen seasonality for the sand tiger shark Carcharias taurus†. Biol Reprod 2021; 102:876-887. [PMID: 31836894 DOI: 10.1093/biolre/ioz221] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/14/2019] [Accepted: 11/12/2019] [Indexed: 11/12/2022] Open
Abstract
Understanding the fundamental reproductive biology of a species is the first step toward identifying parameters that are critical for reproduction and for the development of assisted reproductive techniques. Ejaculates were collected from aquarium (n = 24) and in situ (n = 34) sand tiger sharks Carcharias taurus. Volume, pH, osmolarity, sperm concentration, motility, status, morphology, and plasma membrane integrity were assessed for each ejaculate. Semen with the highest proportion of motile sperm was collected between April and June for both in situ and aquarium sand tiger sharks indicating a seasonal reproductive cycle. Overall, 17 of 30 semen samples collected from aquarium sharks from April through June contained motile sperm compared to 29 of 29 of in situ sharks, demonstrating semen quality differences between aquarium and in situ sharks. Sperm motility, status, morphology, and plasma membrane integrity were significantly higher (P < 0.05) for in situ compared to aquarium sand tiger sharks. Testosterone was measured by an enzyme immunoassay validated for the species. Testosterone concentration was seasonal for both aquarium and in situ sharks with highest concentrations measured in spring and lowest in summer. In situ sharks had higher (P < 0.05) testosterone concentration in spring than aquarium sharks. This study demonstrated annual reproduction with spring seasonality for male sand tiger sharks through marked seasonal differences in testosterone and semen production. Lower testosterone and poorer semen quality was observed in aquarium sharks likely contributing to the species' limited reproductive success in aquariums.
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Affiliation(s)
- Jennifer T Wyffels
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - Lance Adams
- Aquarium of the Pacific, Long Beach, California, USA
| | - Cayman Adams
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - Alisa Newton
- Wildlife Conservation Society's New York Aquarium, Brooklyn, New York, USA
| | - Michael W Hyatt
- Wildlife Conservation Society's New York Aquarium, Brooklyn, New York, USA
| | | | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
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García-Salinas P, Gallego V, Asturiano JF. Reproductive Anatomy of Chondrichthyans: Notes on Specimen Handling and Sperm Extraction. II. Sharks and Chimaeras. Animals (Basel) 2021; 11:ani11082191. [PMID: 34438648 PMCID: PMC8388383 DOI: 10.3390/ani11082191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Sperm extraction and artificial insemination may serve ex situ conservation initiatives for threatened sharks and related species. A comparison of the reproductive anatomy of eight chondrichthyans is presented in this study, emphasizing the important differences when performing these reproductive techniques. Additionally, we show how to obtain sperm samples from both living and dead specimens using cannulation, abdominal massage, or oviducal gland extraction. These tools can improve the success of breeding programs developed in aquaria and research facilities. Abstract The chondrichthyan fishes, which comprise sharks, rays, and chimaeras, are one of the most threatened groups of vertebrates on the planet. Given this situation, an additional strategy for the protection of these species could be the ex situ conservation projects developed in public aquaria and research centers. Nevertheless, to increase sustainability and to develop properly in situ reintroduction strategies, captive breeding techniques, such as sperm extraction and artificial insemination, should be developed. These techniques are commonly used in other threatened species and could be also used in chondrichthyans. However, the different reproductive morphologies found in this group can complicate both processes. Therefore, a comparison of the reproductive anatomy of eight distinct chondrichthyans, with an emphasis on those important differences when performing sperm extraction or artificial insemination, is carried out herein. Sharks and chimaeras belonging to the Scyliorhinidae, Carcharhinidae, Centrophoridae, Etmopteridae, Hexanchidae, and Chimaeridae families were obtained from commercial fisheries, public aquaria, and stranding events. In addition, the process of obtaining viable sperm samples through cannulation, abdominal massage, and oviducal gland extraction is described in detail for both living and dead animals.
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Affiliation(s)
- Pablo García-Salinas
- Grupo de Acuicultura y Biodiversidad, Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 València, Spain; (P.G.-S.); (V.G.)
- Associació LAMNA per a L’estudi dels Elasmobranquis a la Comunitat Valenciana, Fraules 10, 13, 46020 València, Spain
| | - Victor Gallego
- Grupo de Acuicultura y Biodiversidad, Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 València, Spain; (P.G.-S.); (V.G.)
| | - Juan F. Asturiano
- Grupo de Acuicultura y Biodiversidad, Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 València, Spain; (P.G.-S.); (V.G.)
- Correspondence: ; Tel.: +34-96-387-93-85
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8
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García-Salinas P, Gallego V, Asturiano JF. Reproductive Anatomy of Chondrichthyans: Notes on Specimen Handling and Sperm Extraction. I. Rays and Skates. Animals (Basel) 2021; 11:ani11071888. [PMID: 34202036 PMCID: PMC8300314 DOI: 10.3390/ani11071888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Many species of rays and skates are endangered, and ex situ conservation programs developed by research centers and public aquaria could improve this situation. To reproduce these species in captivity, scientists need to know how to extract their sperm and how to conduct their artificial insemination; however, the anatomical diversity of the reproductive organs of this group of animals is a handicap. A comparison of the reproductive anatomies of 11 distinct species is presented here, emphasizing the important differences between the species when performing sperm extraction or artificial insemination. In addition, the process of obtaining sperm samples from both live and dead males is described in detail, using both cannulation and abdominal massage. Abstract The superorder Batoidea (rays, skates, and relatives), constitutes one of the most threatened group of vertebrates. Strengthening ex situ conservation programs developed in research centers and public aquaria could be a way of addressing this situation. However, captive breeding programs must be improved to prevent the capture of wild animals and to develop proper in situ reintroduction strategies. Sperm extraction and artificial insemination are two techniques commonly used in other threatened species, which could also be used in rays and the like. However, the different reproductive morphologies present within this group of animals may hamper both processes. Here, we present a comparison of the reproductive anatomies of 11 distinct batoid species, emphasizing the important differences between the species when performing sperm extraction or artificial insemination. Both male and female animals, belonging to the Rajidae, Dasyatidae, Torpedinidae and Myliobatidae families, from the Mediterranean Sea were studied. In addition, we describe the procedure to extract sperm using both cannulation and abdominal massage, either from live or dead batoids Finally, the obtention of motile sperm recovered from the oviducal gland of females is described. These techniques generate a new range of possibilities for the conservation of these threatened species.
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Affiliation(s)
- Pablo García-Salinas
- Grupo de Acuicultura y Biodiversidad, Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 Valencia, Spain; (P.G.-S.); (V.G.)
- Associació LAMNA per a l’estudi dels elasmobranquis a la Comunitat Valenciana, Fraules 10, 46020 Valencia, Spain
| | - Victor Gallego
- Grupo de Acuicultura y Biodiversidad, Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 Valencia, Spain; (P.G.-S.); (V.G.)
| | - Juan F. Asturiano
- Grupo de Acuicultura y Biodiversidad, Instituto de Ciencia y Tecnología Animal, Universitat Politècnica de València, 46022 Valencia, Spain; (P.G.-S.); (V.G.)
- Correspondence: ; Tel.: +34-96-3879385
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11
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Nielsen J, Hedeholm RB, Lynghammar A, McClusky LM, Berland B, Steffensen JF, Christiansen JS. Assessing the reproductive biology of the Greenland shark (Somniosus microcephalus). PLoS One 2020; 15:e0238986. [PMID: 33027263 PMCID: PMC7540863 DOI: 10.1371/journal.pone.0238986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 08/27/2020] [Indexed: 11/18/2022] Open
Abstract
The Greenland shark (Somniosus microcephalus, Squaliformes: Somniosidae) is a long-lived Arctic top predator, which in combination with the high historical and modern fishing pressures, has made it subject to increased scientific focus in recent years. Key aspects of reproduction are not well known as exemplified by sparse and contradictory information e.g. on birth size and number of pups per pregnancy. This study represents the first comprehensive work on Greenland shark reproductive biology based on data from 312 specimens collected over the past 60 years. We provide guidelines quantifying reproductive parameters to assess specific maturation stages, as well as calculate body length-at-maturity (TL50) which was 2.84±0.06 m for males and 4.19±0.04 m for females. From the available information on the ovarian fecundity of Greenland sharks as well as a meta-analysis of Squaliform reproductive parameters, we estimate up to 200-324 pups per pregnancy (depending on maternal size) with a body length-at-birth of 35-45 cm. These estimates remain to be verified by future observations from gravid Greenland sharks.
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Affiliation(s)
- Julius Nielsen
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | | | - Arve Lynghammar
- Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Leon M. McClusky
- Faculty of Health Sciences, UiT The Arctic University of Norway, Narvik, Norway
| | | | | | - Jørgen S. Christiansen
- Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
- Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
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