Below you find opportunities of presentation at international conferences and workshops from our lab
August 17-21, 2024
18th International Zebrafish Conference in Kyoto, Japan
Why can't we simply call them all 'fish'? – insights from shark genome evolution
Shigehiro Kuraku
Extant ‘fishes’, categorized in jawless, cartilaginous, actinopterygian, or sarcopterygian fishes, comprise a non-monophyletic group of vertebrates from which tetrapods are excluded, and are therefore paraphyletic. Recent advances in whole-genome sequencing have shed light on phylogenetic relationships, divergence times, and the molecular basis of their phenotypic diversity among those different 'fish' lineages. In the interchange of these themes, the presenter's research group has not only led the Squalomix consortium (https://github.com/Squalomix/info) to conduct whole genome sequencing and analysis for elasmobranchs (sharks and rays) but also provided genome-wide data for medaka biology (e.g., in MedakaBase - https://medakabase.nbrp.jp/) as a part of the national bioresource project (NBRP) of Japan. Above all, the former activity revealed distinct signatures of genome structural properties of sharks and rays, such as genome size, karyotype organization, and repetitive element compositions (Hara et al., Nat Ecol Evol, 2018. 2: 1761-1771). The new findings include contrasting patterns of gene repertoire evolution between cartilaginous fishes and teleost fishes, observed in various gene families including vitellogenins (VTG) and Hox, opsins, and aquaporins (AQP) (Ohishi et al., Genome Biol Evol, 2023. 15: evad028; reviewed in Kuraku et al., Ichthyo Res, 2024. 71: 1-12). By covering these topics from our research, this presentation will disentangle the evolutionary diversification of the different 'fish' lineages from which the molecular basis of cellular and developmental characters of zebrafish and medaka has been derived.
October 22-24, 2024
Developmental gene landscape in shark and ray genome sequences
Shigehiro Kuraku
Sharks and rays, classified within the taxon Elasmobranchii, represent one of the long-established evolutionary lineages of vertebrates, yet they remain vastly understudied at the molecular level. This gap arises from challenges such as their elusive nature, low fecundity, and the complexity of their relatively large and repetitive genomes (reviewed in Kuraku, 2021. Dev. Biol. 477: 262-272). Previously, we provided initial insights into shark genomics, presenting interim findings from genome analyses of three species (brownbanded bamboo shark, cloudy catshark, and whale shark), alongside tissue-specific gene expression profiles and epigenomic data on the chromatin regulator CTCF (Hara et al., 2018. Nat. Ecol. Evol. 2: 1761-1771). More recently, through the collaborative efforts of the Squalomix consortium (https://github.com/Squalomix/info), we employed PacBio HiFi genome sequencing and Hi-C scaffolding to achieve chromosome-scale assemblies for multiple shark and ray genomes. These sequences were validated with karyotype data obtained from cell culturing (Uno et al., 2020. Commun. Biol. 3:652). Our growing dataset enables us to analyze genomic trends in developmental gene repertoires, sometimes shedding light on the patterns that were not observed in many other vertebrates. Particularly noteworthy in emerging shark genome sequences with enhanced continuity is the presence of Hox C genes previously thought to be absent in some elasmobranchs. These findings not only deepen our understanding of ancestral vertebrate genomes but also may offer insights into the phenotypic diversity of sharks and rays.
