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 journalArticlepeer-review


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 languageEnglish (US)
Article number1077
StatePublished - 2022
Externally publishedYes


  • Biodiversity genomics
  • Chimaera
  • Karyotype
  • Ray
  • Shark
  • Whole genome sequencing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)


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