Shigehiro Kuraku

Tandem repeats (TRs) and transposable elements (TEs) occupy substantial fractions of eukaryotic genomes, yet how repeat detection programs affect downstream expression analyses remains poorly explored. Here, we present an improved chromosome-scale assembly of the African turquoise killifish, Nothobranchius furzeri . The assembly matches experimentally estimated genome size and chromosome number. It resolves highly expanded TRs that occupy up to 28.0% of the whole genome. Using this assembly and other complete vertebrate genome assemblies, we compared TR and TE-derived regions across combinations of TR detection programs and TE consensus library construction workflows under a standardized TE classification scheme. Choices in TR detection reshaped the apparent TE landscape. TE workflows shared a broad core of TE-derived regions but recovered complementary sets of age- and sex-associated TE loci, evaluated with a sex-balanced killifish multi-tissue aging cohort. Together, the combinatorial use of adaptable programs supports robust, locus-aware detection of complex repeats across genome assemblies.

Background: Pacific saury Cololabis saira is one of the important food resources drawing attention for its recent rapid decline of catch. Their life cycle and embryonic development have been largely unknown. It is important to clarify how the habitat and reproduction of this species have been affected by the global changes of the aquatic environment. Results: We obtained fertilized eggs of C. saira by spontaneous spawning and artificial fertilization and observed the embryonic development up to larval stages. Embryonic stages are documented with major periods of developmental events: cleavage, gastrulation (epiboly), and somitogenesis and organogenesis. Remarkably, segmentation of somites starts in the middle of epiboly, unlike other well‐documented teleost species such as zebrafish and medaka. Morphological changes in the larval stage up to feeding juvenile are also described. Growth speed of larval Pacific saury is dramatically rapid in comparison to closely related beloniform fish such as medaka. Conclusions: In comparison to medaka, early embryogenesis of saury proceeds relatively slowly, but is followed by an earlier onset of somitogenesis, revealing a distinct developmental timetable. Despite reaching adult body length exceeding 20 cm in only half a year, the developmental basis of the remarkable growth of saury remains unclear. The developmental staging framework established here provides a foundation for future studies investigating the molecular mechanisms underlying saury development, as well as the effects of environmental factors, including ocean warming, on embryonic development and early life‐history traits.

Sweet taste guides animals to consume carbohydrate-rich foods, and many different vertebrate groups, from fish to mammals, rely on sugar-rich fruits or nectar produced by flowering plants (angiosperms). Although the genes encoding T1R2-T1R3, the receptor pair that mammals use to sense sugars, exist in the genomes of many vertebrates, their functions are unclear—and whether sugar sensing arose once early in vertebrate evolution or independently in different lineages after angiosperms evolved is currently unknown. Here, we combined ancestral reconstruction and receptor functional profiling to examine the evolutionary history of T1R taste receptors—including recently-described non-canonical receptors—across all major vertebrate clades. Our results pinpoint the origin of sugar sensing to before the emergence of angiosperms and uncover a myriad of alternative T1R-based sugar-sensing mechanisms, suggesting multiple independent T1R trajectories and revealing uncharted sensory diversity across vertebrates.

Meiotic entry in vertebrates has been viewed as a transcriptional switch driven by the MEIOSIN–STRA8 axis, but whether this represents the ancestral regulatory logic of meiosis has remained unclear. Here we combine comparative genomics with genetic and single-cell analyses in zebrafish and mice to show that MEIOSIN retains an intrinsic STRA8-independent activity. We identify Meiosin orthologs in zebrafish and hagfish, vertebrate lineages that lack Stra8, and show that these proteins retain the HMG domain but have lost the bHLH domain required for the canonical MEIOSIN–STRA8 interaction. In zebrafish, meiosin is transiently induced at meiotic entry in both sexes, yet its loss selectively disrupts the female germline, causing failure of oogenesis and female-to-male sex reversal. In mice, MEIOSIN lacking the bHLH domain still initiates key features of meiotic entry and partially activates meiotic target genes, although it fails to support full meiotic progression. Together, these findings support a model in which HMG-containing MEIOSIN provides a conserved core activity for meiotic gene activation, whereas STRA8 and the bHLH-mediated MEIOSIN–STRA8 interaction reinforce the efficiency and robustness of this program in lineages that retain the canonical module.

Gcm1 and Gcm2 are paralogous transcription factors in vertebrates that play key roles in the development of pharyngeal‐derived epithelia, yet their deployment across vertebrate lineages remains incompletely understood. While Gcm2 shows deeply conserved pharyngeal expression across gnathostomes, Gcm1 has been mainly characterized in mammals, where it exhibits broader expression patterns. How Gcm1 is deployed in non‐mammalian vertebrates has remained unexplored. Here, we performed a comparative analysis of Gcm1 expression in cartilaginous fishes, non‐teleost actinopterygians, and amphibians. RNA in situ hybridization revealed conserved Gcm1 expression in gill epithelia across these taxa. Parallel analyses showed that Gcm2 is also expressed in gill epithelia, with overlapping but distinct spatial patterns. In addition, Gcm1 showed lineage‐specific expression in bichir embryos, including strong expression in external gills and scattered epithelial cells in the yolk‐sac membrane. In the external gills, Gcm1 ‐positive cells possess vacuole‐like cytoplasmic structures, suggesting a previously unrecognized epithelial cell population. Together, our findings indicate that Gcm1 and Gcm2 share ancestral expression in pharyngeal epithelia but have followed distinct evolutionary trajectories, with Gcm1 exhibiting greater lineage‐specific diversification.

The relevance of protein structural flexibility in function remains contested, but experimental and computational evidence continues to accumulate. Many efforts to address this investigate intrinsic disorder, which commonly refers to peptide segments or entire protein sequences that presumably lack structure and exhibit high flexibility/conformational heterogeneity under physiological conditions. These efforts face challenges such as conflicting computational predictions and ambiguous relationships among intrinsic disorder locations and other protein properties. We address these challenges at a genome-wide scale in Drosophila melanogaster using residue-level predictions for various protein properties. We employ single and consensus approaches to quantify the prevalence of intrinsic disorder and attempt to infer function by testing for differences along protein sequences. Intrinsic disorder is likely more common at terminals than internal regions, and amino acid frequencies can vary substantially between regions in a manner that plausibly reflects functions of intrinsic disorder, rather than only proteome-wide effects. Tertiary structure potentially underlies the prevalence of intrinsic disorder along protein sequences; this prevalence varies more in a putatively solvent-exposed context than a solvent-buried one. Protein-binding appears to be a main function of intrinsic disorder, and we find support consistent with the notion that structural flexibility fosters binding plasticity, and show that location and protein length are factors in this relationship. Nucleic acid-binding and linker are ostensibly less common disorder functions than protein-binding, but nucleic acid-binding seems more localized at terminals. Residue-level estimates of selection pressure indicate that disordered regions generally evolve under weaker sequence constraints than structured regions, except at the N-terminal region. Biases in disorder prediction are a considerable factor in many of the observations, but unlikely a full explanation. The findings strengthen support for functional relevance of flexibility, offer insight into protein architecture and function, and lend impetus for experimental inquiry.

Medaka (Oryzias latipes) is a small freshwater teleost widely used as a vertebrate model organism. Existing medaka reference genomes, however, contain many gaps and unresolved repetitive regions, hindering precise genome annotation and comparative analyses. Here we present one complete and two near-complete genome assemblies for three inbred medaka strains derived from geographically distant populations. These assemblies provide a comprehensive view of highly repetitive sequences and chromosome-scale genome architecture in medaka. The fully resolved centromeres reveal an intriguing sequence organization characterized by short, distinct SF1+3 satellite arrays flanked by larger homogenized repeats. These short arrays are putatively hypomethylated and conserved across all acrocentric chromosomes, suggesting a functional role in centromere stability. The reconstructed 121 copies of the giant mobile element Teratorn retain complete genes of both a transposon and a herpesvirus, highlighting its unique persistence and impact on host genomes. Moreover, our assemblies reveal extensive structural divergence of medaka Y Chromosomes, yet identify a small (~24 kb) conserved region encompassing Dmy that may suffice for male determination. Collectively, these (near-)complete medaka genomes provide a powerful resource for exploring the biology of uncharacterized repetitive regions and the molecular basis of phenotypic diversity in vertebrates.

Genomes have maintained relatively stable gene sets during evolution, while chromosome organization and genome size vary drastically, even among vertebrates. Changes in genome size are often attributed to variable amounts of repetitive sequences, including transposable elements. However, it remains poorly understood what allows such drastic changes and how they affect various components of the genome and their functions. Elasmobranchs, including sharks, rays, and skates, exhibit high among-species variation of genome size and high within-species variation of chromosome length, offering a unique study system. In this study, we present the first whole genome sequences of the whitebelly skate with relatively small genome size among elasmobranchs (2.2 Gb) and the red stingray. These chromosome-scale assemblies enable the assessment of genomic compositions including centromeres and non-coding elements, which reveal notable profiles of tRNA loci and unbiased intragenomic distribution of transposons in elasmobranch genomes. Comparative analyses across these species reveal a shared genomic architecture characterized by correlations of intergenic and intronic sequence lengths with chromosome sizes, with repetitive element accumulation in elongated regions. To assess whether elements beyond repetitive elements scale with genome size, we analyze tandem gene duplications and find they also tend to increase with genome expansion. In the quest of tandem genes, we characterize the first batoid HoxC cluster supported by transcriptional evidence in the red stingray genome, which has undergone extensive repetitive element invasion to unexpectedly co-localize with the HoxB cluster on a sex chromosome. Our study demonstrates an inclusive analysis encompassing both coding and non-coding regions, adaptable to diverse vertebrate taxa and a basis for molecular-level understanding on phenotypic diversity of elasmobranchs.

The Greenland shark ( Somniosus microcephalus ) is known for its slow metabolism and deep-sea habitat. It is thought to be the longest-lived vertebrate on Earth, with an estimated lifespan of 392 ± 120 y. Despite its remarkable longevity and unusual lifestyle, no genomic studies are yet available for this species. Here, we report a chromosome-level assembly of the Greenland shark genome, which is 5.9 Gb in size with an N50 length of 233 Mb and a completeness score of 96.7%. Our analyses of gene family expansion and positive selection revealed classical longevity-related mechanisms, including immune enhancement, cancer resistance, and DNA repair, as well as additional features potentially associated with extended lifespan limits. Unique amino acid substitutions in the globular domain of linker histone H1.0 are predicted to enhance chromatin stability, and the species’ distinctive gene repertoire provides a framework for generating hypotheses potentially linking ferroptosis to exceptional longevity. We also elucidate the dynamics of the effective population size ( N _e ) of the Greenland shark and its close relative, the Pacific sleeper shark ( Somniosus pacificus ). These genomic analyses offer insights into the molecular basis of the exceptional longevity of the Greenland shark and highlight potential genetic mechanisms that could inform future research into longevity.

The effective management of threatened shark populations relies on accurate demographic data, particularly operational sex ratios. While sex identification in intact shark bodies is straightforward through the presence of external male organs, namely claspers, it remains impossible for processed fins in the illegal wildlife trade, early-stage embryos in breeding programs, or archived tissue fragments and blood samples where morphological traits are lost. Here, we present a robust molecular sexing framework leveraging recently identified sequences from shark sex chromosomes, consistently organized in the XY system, to our current knowledge. Our approach consists of two distinct methodologies tailored to the the current identification status of sex chromosome sequences in the target species. For the whale shark Rhincodon typus and the brownbanded bamboo shark Chiloscyllium punctatum , we employed end-point PCR assays targeting male-specific Y-linked markers. For the cloudy catshark Scyliorhinus torazame , we developed a quantitative PCR (qPCR) assay targeting differential X chromosome dosage. In this dosage-based system, females (XX) are distinguished by an amplification profile approximately one cycle earlier than males (XY). By integrating X-linked dosage quantification, our framework provides a critical internal control that significantly enhances reliability, allowing researchers to distinguish true females from PCR failures. This toolkit offers a versatile solution for diverse applications, ranging from the study of sex determination mechanisms in pre-phenotypic embryos to the reconstruction of sex ratios from space-constrained tissue archives and global wildlife forensics, thereby contributing to the comprehensive conservation of shark biodiversity.