F1000Research (Sep 2022)
Squalomix: shark and ray genome analysis consortium and its data sharing platform [version 1; peer review: 2 approved]
- John Rozewicki,
- Kazuaki Yamaguchi,
- Osamu Nishimura,
- Ryo Misawa,
- Takashi Asahida,
- Mitsumasa Koyanagi,
- Akihisa Terakita,
- Filipe Castro,
- André Machado,
- Milton Tan,
- Salvatore D'Aniello,
- Shotaro Hirase,
- Akane Kawaguchi,
- Chiharu Tanegashima,
- Akinori Teramura,
- Masaru Yagura,
- Taiki Niwa,
- Kaori Tatsumi,
- Yuta Ohishi,
- Susumu Hyodo,
- Mitsutaka Kadota,
- Itsuki Kiyatake,
- Keiichi Sato,
- Kazuyuki Yamada,
- Kiyonori Nishida,
- Yasuko Semba,
- Shinya Yamauchi,
- Sho Tanaka,
- Tatsuya Sakamoto,
- Norio Miyamoto,
- Atsushi Toyoda,
- Rui Matsumoto,
- Iker Irisarri,
- Atsuko Yamaguchi,
- Tazro Ohta,
- Kiyomi Murakumo,
- Junna Kawasaki,
- Masayuki Horie,
- Yoshinobu Uno,
- Shigehiro Kuraku
Affiliations
- 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
- Osamu Nishimura
- ORCiD
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
- Ryo Misawa
- ORCiD
- Japan Fisheries Research and Education Agency, Hachinohe, Aomori, Japan
- Takashi Asahida
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
- 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
- Filipe Castro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- André Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- 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
- 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
- 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
- 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
- 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
- Susumu Hyodo
- ORCiD
- 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
- Itsuki Kiyatake
- Osaka Aquarium Kaiyukan, Osaka, Osaka, Japan
- Keiichi Sato
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
- Kazuyuki Yamada
- Marine Science Museum, Tokai University, Shizuoka, Shizuoka, Japan
- Kiyonori Nishida
- Osaka Aquarium Kaiyukan, Osaka, Osaka, Japan
- Yasuko Semba
- Highly Migratory Resources Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shizuoka, Shizuoka, Japan
- Shinya Yamauchi
- Aquamarine Fukushima, Iwaki, Fukushima, 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
- 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
- Rui Matsumoto
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
- Iker Irisarri
- ORCiD
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature-Zoology, Hamburg, 20146, Germany
- Atsuko Yamaguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
- Tazro Ohta
- ORCiD
- Joint Support-Center for Data Science Research, Database Center for Life Science, Mishima, Shizuoka, 411-8540, Japan
- Kiyomi Murakumo
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
- Junna Kawasaki
- ORCiD
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Masayuki Horie
- ORCiD
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
- Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Tokyo, Japan
- Shigehiro Kuraku
- ORCiD
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
- Journal volume & issue
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Vol. 11
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.
