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Squalomix: shark and ray genome analysis consortium and its data sharing platform.
Nishimura, Osamu; Rozewicki, John; Yamaguchi, Kazuaki; Tatsumi, Kaori; Ohishi, Yuta; Ohta, Tazro; Yagura, Masaru; Niwa, Taiki; Tanegashima, Chiharu; Teramura, Akinori; Hirase, Shotaro; Kawaguchi, Akane; Tan, Milton; D'Aniello, Salvatore; Castro, Filipe; Machado, André; Koyanagi, Mitsumasa; Terakita, Akihisa; Misawa, Ryo; Horie, Masayuki; Kawasaki, Junna; Asahida, Takashi; Yamaguchi, Atsuko; Murakumo, Kiyomi; Matsumoto, Rui; Irisarri, Iker; Miyamoto, Norio; Toyoda, Atsushi; Tanaka, Sho; Sakamoto, Tatsuya; Semba, Yasuko; Yamauchi, Shinya; Yamada, Kazuyuki; Nishida, Kiyonori; Kiyatake, Itsuki; Sato, Keiichi; Hyodo, Susumu; Kadota, Mitsutaka; Uno, Yoshinobu; Kuraku, Shigehiro.
Affiliation
  • Nishimura O; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
  • Rozewicki J; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
  • Yamaguchi K; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
  • Tatsumi K; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
  • Ohishi Y; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
  • Ohta T; Joint Support-Center for Data Science Research, Database Center for Life Science, Mishima, Shizuoka, 411-8540, Japan.
  • Yagura M; Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
  • Niwa T; Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
  • Tanegashima C; Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan.
  • Teramura A; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
  • Hirase S; Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan.
  • Kawaguchi A; Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan.
  • Tan M; Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
  • D'Aniello S; Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA.
  • Castro F; Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy.
  • Machado A; Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
  • Koyanagi M; Faculty of Sciences, University of Porto, Porto, Portugal.
  • Terakita A; Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
  • Misawa R; Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan.
  • Horie M; Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan.
  • Kawasaki J; Japan Fisheries Research and Education Agency, Hachinohe, Aomori, Japan.
  • Asahida T; Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan.
  • Yamaguchi A; Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan.
  • Murakumo K; School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan.
  • Matsumoto R; Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.
  • Irisarri I; Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan.
  • Miyamoto N; Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan.
  • Toyoda A; Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature-Zoology, Hamburg, 20146, Germany.
  • Tanaka S; X-STAR, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan.
  • Sakamoto T; Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
  • Semba Y; School of Marine Science and Technology, Tokai University, Shizuoka, Shizuoka, Japan.
  • Yamauchi S; Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi, Japan., Okayama, Japan.
  • Yamada K; Highly Migratory Resources Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shizuoka, Shizuoka, Japan.
  • Nishida K; Aquamarine Fukushima, Iwaki, Fukushima, Japan.
  • Kiyatake I; Marine Science Museum, Tokai University, Shizuoka, Shizuoka, Japan.
  • Sato K; Osaka Aquarium Kaiyukan, Osaka, Osaka, Japan.
  • Hyodo S; Osaka Aquarium Kaiyukan, Osaka, Osaka, Japan.
  • Kadota M; Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan.
  • Uno Y; Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo,, Kashiwa, Chiba, Japan.
  • Kuraku S; Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
F1000Res ; 11: 1077, 2022.
Article in En | MEDLINE | ID: mdl-36262334
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Sharks Limits: Animals Language: En Journal: F1000Res Year: 2022 Document type: Article Affiliation country:
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Sharks Limits: Animals Language: En Journal: F1000Res Year: 2022 Document type: Article Affiliation country: