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Squalomix: shark and ray genome analysis consortium and its data sharing platform
Osamu Nishimura1, John Rozewicki1, Kazuaki Yamaguchi1
1Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan.
F1000Research
|October 20, 2022
Summary
The Squalomix Consortium is developing crucial genomic resources for sharks and rays (Elasmobranchii) to address challenges like elusive species and complex genomes. This initiative provides valuable molecular data for understanding these vital aquatic vertebrates.
Area of Science:
- * Evolutionary Biology
- * Genomics
- * Marine Vertebrate Zoology
Background:
- * Elasmobranchii (sharks and rays) represent an ancient vertebrate lineage with significant ecological roles.
- * Limited molecular resources hinder research on elasmobranchs due to challenges like elusiveness, low fecundity, large repetitive genomes, and difficulties in cell culturing for karyotyping.
Purpose of the Study:
- * To establish a comprehensive suite of molecular resources for sharks and rays.
- * To overcome existing bottlenecks in elasmobranch research through advanced genomic and cytological techniques.
- * To provide accessible data for the scientific community.
Main Methods:
- * Development of in-house cytological techniques for cell culturing and karyotyping.
- * Chromatin preparation for High-Chromosome Conformation Capture (Hi-C) data acquisition.
- * High-fidelity long-read sequencing for genome assembly.
Main Results:
- * Generation of genome and transcriptome sequences for selected elasmobranch species.
- * Creation of a JBrowse2-powered genome browser for visualizing sequence alignments.
- * Compilation of extensive gene expression profiles.
Conclusions:
- * The Squalomix Consortium is successfully generating vital genomic and transcriptomic resources for sharks and rays.
- * These resources will significantly advance research into elasmobranch evolution, biology, and conservation.
- * Accessible data and tools are provided via GitHub for broad scientific utilization.
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