Squalomix: Shark and ray genome analysis consortium and its data sharing platform

Shigehiro Kuraku; Osamu Nishimura; John Rozewicki; Kazuaki Yamaguchi; Kaori Tatsumi; Yuta Ohishi; Tazro Ohta; Masaru Yagura; Taiki Niwa; Chiharu Tanegashima; Akinori Teramura; Shotaro Hirase; Akane Kawaguchi; Milton Tan; Salvatore D'Aniello; Filipe Castro; André Machado; Mitsumasa Koyanagi; Akihisa Terakita; Ryo Misawa; Masayuki Horie; Junna Kawasaki; Takashi Asahida; Atsuko Yamaguchi; Kiyomi Murakumo; Rui Matsumoto; Iker Irisarri; Norio Miyamoto; Atsushi Toyoda; Sho Tanaka; Tatsuya Sakamoto; Yasuko Semba; Shinya Yamauchi; Kazuyuki Yamada; Kiyonori Nishida; Itsuki Kiyatake; Keiichi Sato; Susumu Hyodo; Mitsutaka Kadota; Yoshinobu Uno

doi:10.12688/f1000research.123591.1

Squalomix: Shark and ray genome analysis consortium and its data sharing platform

Shigehiro Kuraku, Osamu Nishimura, John Rozewicki, Kazuaki Yamaguchi, Kaori Tatsumi, Yuta Ohishi, Tazro Ohta, Masaru Yagura, Taiki Niwa, Chiharu Tanegashima, Akinori Teramura, Shotaro Hirase, Akane Kawaguchi, Milton Tan, Salvatore D'Aniello, Filipe Castro, André Machado, Mitsumasa Koyanagi, Akihisa Terakita, Ryo MisawaMasayuki Horie, Junna Kawasaki, Takashi Asahida, Atsuko Yamaguchi, Kiyomi Murakumo, Rui Matsumoto, Iker Irisarri, Norio Miyamoto, Atsushi Toyoda, Sho Tanaka, Tatsuya Sakamoto, Yasuko Semba, Shinya Yamauchi, Kazuyuki Yamada, Kiyonori Nishida, Itsuki Kiyatake, Keiichi Sato, Susumu Hyodo, Mitsutaka Kadota, Yoshinobu Uno

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Article number	1077
Journal	F1000Research
Volume	11
DOIs	https://doi.org/10.12688/f1000research.123591.1
State	Published - 2022
Externally published	Yes

Keywords

Biodiversity genomics
Chimaera
Karyotype
Ray
Shark
Whole genome sequencing

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology
General Pharmacology, Toxicology and Pharmaceutics

Online availability

10.12688/f1000research.123591.1

Library availability

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Cite this

Kuraku, S., 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., ... Uno, Y. (2022). Squalomix: Shark and ray genome analysis consortium and its data sharing platform. F1000Research, 11, Article 1077. https://doi.org/10.12688/f1000research.123591.1

Kuraku, S, 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 2022, 'Squalomix: Shark and ray genome analysis consortium and its data sharing platform', F1000Research, vol. 11, 1077. https://doi.org/10.12688/f1000research.123591.1

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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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AU - Nishimura, Osamu

AU - Rozewicki, John

AU - Yamaguchi, Kazuaki

AU - Tatsumi, Kaori

AU - Ohishi, Yuta

AU - Ohta, Tazro

AU - Yagura, Masaru

AU - Niwa, Taiki

AU - Tanegashima, Chiharu

AU - Teramura, Akinori

AU - Hirase, Shotaro

AU - Kawaguchi, Akane

AU - Tan, Milton

AU - D'Aniello, Salvatore

AU - Castro, Filipe

AU - Machado, André

AU - Koyanagi, Mitsumasa

AU - Terakita, Akihisa

AU - Misawa, Ryo

AU - Horie, Masayuki

AU - Kawasaki, Junna

AU - Asahida, Takashi

AU - Yamaguchi, Atsuko

AU - Murakumo, Kiyomi

AU - Matsumoto, Rui

AU - Irisarri, Iker

AU - Miyamoto, Norio

AU - Toyoda, Atsushi

AU - Tanaka, Sho

AU - Sakamoto, Tatsuya

AU - Semba, Yasuko

AU - Yamauchi, Shinya

AU - Yamada, Kazuyuki

AU - Nishida, Kiyonori

AU - Kiyatake, Itsuki

AU - Sato, Keiichi

AU - Hyodo, Susumu

AU - Kadota, Mitsutaka

AU - Uno, Yoshinobu

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Squalomix: Shark and ray genome analysis consortium and its data sharing platform

Abstract

Keywords

ASJC Scopus subject areas

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