Toward bona fide "whole-genome"

Even without rowing out to sea, the research materials obtained from aquariums and the resulting genomic data help us understand the mechanisms of life. Our research interests have extended to the iconic manta rays, and just today, we witnessed a rare case of shark embryonic development occurring right here in our aquarium tank at NIG. I will share those details another time.

Although some time has passed since its publication, following our genomic analyses of the elephant fish (Teramura et al., DNA Res 2026) and the Greenland shark (Yang et al., PNAS 2026), our team, involving reliable collaborators, has published a new paper reporting the genome assemblies of two batoid (rays and skate) species:

Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium. Genome Res. August 2026, Vol. 36, No. 8

Figure 1: The red stingray individual at a local aquarium. After dissection, the specimen used for genome sequencing in this study was donated as a voucher specimen to the Museum of Nature and Human Activities, Hyogo. The whitebelly skate specimen was likewise deposited into the Fisheries Research Agency [FRA] fish specimen collection. I would like to express my deepest gratitude to everyone who facilitated the specimen procurement and data acquisition.)

Let me start with some background on how this publication came together. In a prior study on sex chromosomes (Niwa et al., PNAS 2025), we revealed that the red stingray (Hemitrygon akajei) possesses two X chromosomes  (X1 and X2), but we did not formally report the full genome assembly in that prior paper. To accomplish this, we framed this new paper around two batoid species under the umbrella of the Squalomix Consortium. We focused on genome size dynamics, a theme highlighted especially by interspecies comparison. This organization allowed us to credit the contributors who provided specimens and sequencing data, while allowing each laboratory member to showcase their analytical expertise.

By integrating optical mapping data from the BioNano Saphyr system, the red stingray genome assembly likely provides the first clear structural resolution of centromeres in cartilaginous fishes (these repetitive regions were presumably missing from most previous assemblies). Meanwhile, our second focal species, the whitebelly skate Rhinoraja longicauda, exhibited the smallest genome size documented so far among sequenced elasmobranchs (approximately 2.2 Gb). During the manuscript revision process, we also incorporated the cloudy catshark Scyliorhinus torazame, which possesses a ~6.6 Gb genome, allowing us to span a three-fold difference in genome size.

Fiigure 2. The coastal view in Shiogama City, Miyagi Prefecture, right before we dissected the whitebelly skate specimen.

In many genomic studies, the entire genome is sequenced, yet only a tiny fraction of the sequence data is actually utilized. Approaches like analyzing conserved synteny to compare functional gene positions, or scanning for signatures of natural selection via the comparison of synonymous and non-synonymous substitution rates, bypass introns and intergenic regions—which typically account for over 90% of the genome. Our stance in this study was different. Beyond the obvious necessity of resolving chromosome-scale structures, we deliberately explored the expansive "wilderness" of non-coding (i.e. intronic and intergenic) regions. Our goal was to understand the fundamental architecture of vertebrate genomes by encompassing non-coding regions. We incorporated this philosophy into the title of the paper with the phrase "inclusive" sequence analysis.

Cartilaginous fish karyotypes frequently present a bioinformatic challenge (that is not widely recognized by genomicists working on mammals and teleost fishes): how do we confidently verify whether short assembled sequences are genuine small chromosomes, rather than unassembled fragments of larger chromosomes? And how exactly should we identify centromeres in chromosomal sequences? We provided practical, previously undocumented strategies to address these questions. We also profiled rDNA and tRNA genes, discovering that tRNA locus numbers are exceptionally high in elasmobranchs. Furthermore, we demonstrated that transposable element (TE) distribution remains largely uniform across both intronic and intergenic regions, and we reaffirmed that the expansion and contraction of TEs is one major driver of genome size variation. As a methodological note, during the revision process, we implemented an analytical pipeline tweak: rather than jumping straight into TE detection, we first computationally detected and masked tandem repeats (which are generally easier to define) before proceeding to TE detection.

Additionally, we proposed what I believe has not been shown explicitly for vertebrate genomes: species with larger genome sizes tend to harbor higher tandem gene copy numbers. We highlighted the V2R (vomeronasal type-2 receptor) gene cluster as a concrete example. It points to a rather straightforward evolutionary trend—as the genome expands (even in the absence of whole-genome duplication events), the gene repertoire increases, thereby providing a broader array of functional gene variants that can serve as raw material for phenotypic evolution. This hypothesis will certainly require further validation across a wider range of species.

We also investigated another classic tandem array: the Hox gene clusters. Crucially, we identified the HoxC cluster in the red stingray—a cluster previously assumed to be absent in batoids (rays and skates). To my knowledge, this is the first time the HoxC cluster has been reported in a ray alongside gene expression evidence. Conversely, we could not find the HoxC cluster in the order Rajiformes (which includes the whitebelly skate); it appears they have deleted the entire cluster. In the red stingray, not only HoxC but also the HoxB cluster is somewhat buried within highly repetitive, difficult-to-read regions, and we reported that both of these Hox clusters reside on the X chromosome. Among vertebrates, elasmobranchs might be unique in harboring Hox clusters on sex chromosomes. (For our previous work on shark and ray Hox genes, you can search the keyword "Hox" on our Publications page).

Ultimately, our initial objective of providing supplementary genomic context for a previous paper (Niwa et al., PNAS 2025) expanded significantly. We ended up addressing a wide array of biological topics, resulting in a manuscript that we regard as a profound stepping stone for our next phase of research incorporating even more diverse species. Moving forward, we will continue to leverage the rigorous analytical frameworks of molecular evolution to clarify exactly what defines sharks and rays, as well as other major vertebrate taxa, at the molecular level. I am always open to inquiries from motivated researchers and students who wish to join us and apply their expertise and excitement for molecular evolution, zoology, or fisheries science to these challenges.