Biology subjects

Kikuchi, K.

Publications and source records attributed to Kikuchi, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Optimization of breeding conditions in Danionella cerebrum to advance its use as a vertebrate model

We systematically evaluated tank configuration and spawning-tube parameters to improve egg production and collection efficiency in Danionella cerebrum. A shallow breeding tank with a black bottom significantly increased egg production while facilitating egg collection. Further optimization of spawning-tube parameters revealed a strong effect of tube diameter on reproductive performance, with narrower tubes improving fertilization efficiency and a 4-mm inner diameter yielding the highest egg production. Longer tubes also tended to increase egg production, although the difference between 5- and 10-cm tubes was not significant. While 5-cm tubes facilitated routine egg collection, the trend toward higher egg production and greater water volume of 10-cm tubes enabled short-term in-tube embryo culture, providing an alternative workflow when frequent egg collection is unnecessary. Notably, increasing the number of available spawning tubes did not further enhance egg production; instead, analysis of tube usage revealed a preference for previously used spawning sites. Together, these findings establish practical breeding parameters that improve reproductive output and streamline egg collection and embryo handling in D. cerebrum.

developmental biology↗

bioRxiv2026

In-Cell Protein Crystallization via a Locally Flexible 24-mer Assembly Precursor

In-cell protein crystallization (ICPC) produces ordered protein crystals within living cells, but the mechanisms used by proteins to acquire long-range crystalline order in the cellular environment remains poorly understood. Here, we define the assembly pathway of CipB, a crystalline inclusion protein from Photorhabdus luminescens. CipB crystals formed in cells dissolve under mild acidic conditions into a predominant 24-mer species, supporting a model in which an in-cell crystal is built from a discrete 24-mer assembly precursor rather than through direct packing of smaller oligomeric states. Structural analysis of recrystallized CipB shows that the same 24-mer architecture packs into a body-centered cubic lattice, consistent with the lattice observed for the in-cell crystals. Cryo-EM and molecular dynamics analyses indicate that the 24-mer assembly precursor preserves its overall architecture while retaining local conformational flexibility at the N-terminal and surface-loop regions. Mutation analyses further link the N-terminal region to the formation of the 24-mer precursor and surface residues to lattice assembly. These observations support a stepwise crystallization model in which N-terminal flexibility facilitates the formation of an assembly-competent 24-mer precursor, whereas defined hydrophobic surface contacts subsequently organize these precursors into a long-range-ordered lattice.

biophysics↗

bioRxiv2026

Deformation Gradient Tensor Model of Roll-Spiral Transformation for Protein Assembly Refractile Body

Spiral geometries commonly occur in natural and engineered systems and are fundamentally described by curvature and torsion. In deformation-dominated systems, these variables evolve dynamically, requiring a continuum mechanical framework to link geometry and deformation. This study focused on refractile bodies (R-bodies), protein supramolecular assemblies that undergo reversible roll-spiral transformations in response to stimuli such as pH changes. Although multiple R-body types with distinct morphologies and unrolling behaviours were experimentally identified, their deformation mechanisms lack quantitative theoretical descriptions. We proposed a deformation-gradient-tensor-based continuum model incorporating geometrical mapping from the rolled to spiral state within a unified framework. The model successfully reconstructed macroscopic deformation behaviours of types 51, 7, and Pa R-bodies by capturing differences in unrolling behaviours, tapered geometry, and spatio-temporal evolution. The analysis revealed that deformation proceeds through a coupled process in which the curvature decreases via straightening, while the torsion increases by twisting. Importantly, the framework connected the macroscopic morphology with microscopic lattice deformation, enabling quantitative inference of lattice intervals and angles. The proposed comprehensive geometric model of the R-body roll-spiral transformation offers a general mathematical foundation for understanding deformation-driven spiral transformations in soft matter systems.

biophysics↗

bioRxiv2026

Assembly-pathway regulation dictates pH-responsive actuation in the R-body protein machinery

Refractile bodies (R-bodies) are protein assemblies that form tightly rolled morphologies in cells and undergo large-scale extension into long spirals in response to environmental stimuli. The type 51 R-body, the focus of this study, is assembled from four Reb proteins and undergoes a rapid repeatable [~]50-fold extension. Although R-bodies were first described more than 70 years ago, it has remained unclear how RebC and RebD contribute to the formation and function of this four-protein machinery even though RebA and RebB have been proposed as its major components. We characterized the wild-type R-body (Rb_WT) and a series of reb gene knockout mutants by combining in-cell, biochemical analyses, small-angle X-ray scattering (SAXS) and attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. We found that RebD is incorporated into Rb_WT as a minor component, while RebC is not detectably incorporated into the final assembly. Mutants lacking either RebA or RebB still form roll-like assemblies but lack pH-dependent extension. In contrast, mutants lacking RebC and/or RebD exhibit a substantially lower propensity for roll formation and instead undergo off-pathway aggregation with increased {beta}-sheet content. SAXS analyses further indicate that roll-like morphology does not ensure formation of the ordered lamellar architecture characteristic of functional Rb_WT. Thus, pH-responsive R-body actuation is dictated not simply by the major proteins that constitute the final architecture, but by a regulated assembly pathway that builds the ordered lamellar architecture required for actuation. These findings establish assembly-pathway regulation as a key principle for constructing dynamic protein architectures capable of stimuli-responsive mechanical actuation.

biophysics↗

bioRxiv2026

Social caste switching triggers emergence of novel cellular identities in Zootermopsis termites

A hallmark of eusocial insects is the specialisation of individuals into castes that share the same genome but present distinct phenotypes. Caste switching can affect gene expression1,2, but can it give rise to entirely new cell types? Here, we generated single-cell transcriptomic atlases of a king, a queen, a soldier, and six workers of the termite Zootermopsis nevadensis to understand whether caste differentiation is accompanied by the emergence of novel cellular identities. Out of 24 annotated termite cell types, 18 of which mirrored homologous Drosophila cell types, one was unique for king, one was almost entirely restricted to the queen, and none were exclusive to nonreproductives. Instead, nonreproductive termites possessed more muscle and neuronal cells and less fat cells than reproductives. Caste-linked transcriptional signatures were detected in most cell types, including rare genes expressed with dual specificity for both cell type and caste. Despite the emergence of new cell types in reproductives, expression of hormones, immune genes, carbohydrate-active enzymes3, and rapidly adapting genes4 were only weakly altered by caste. These findings show that cellular differentiation can be induced anew in adult organisms without dysregulating their key physiologic pathways.

evolutionary biology↗

bioRxiv2026

Rapid chromosomal rearrangements and sex chromosome turnover underlie the evolution of parapatric Pacific Scomber mackerels

Teleost display remarkable species diversity despite relatively conserved karyotypes, suggesting an important role for chromosomal rearrangements in speciation. Yet this hypothesis remains poorly tested in pelagic marine fishes, as genomic studies have predominantly focused on freshwater and coastal taxa. In this study, we investigated the genomic basis of hybrid incompatibility between two parapatric Pacific mackerels, Scomber japonicus and S. australasicus, hypothesizing chromosomal rearrangements as the major driving forces. We generated haplotype-resolved de novo genome assemblies for both Pacific species and assessed genomic rearrangements along with the genome of the Atlantic species, S. scombrus, reconstructed from publicly available data. Comparative genomic analyses revealed extensive chromosomal rearrangements across the genomes. Notably, the rate of chromosomal inversions was approximately sevenfold higher between the two Pacific species than between allopatric lineages. These rearrangements included complex structural changes involving megabase-scale inversions and associated translocations. Our analyses also showed that the sex chromosomes of the three species evolved independently. In the two Pacific species, large recombination-suppression regions (>10 Mb) arose convergently but through distinct mechanisms: tandem chromosomal inversions in S. japonicus and, most likely, transposable element-mediated sequence divergence in S. australasicus. By contrast, recombination suppression in S. scombrus is restricted to a [~]14 kb hemizygous region containing amhr2Y, generated by duplication and translocation. Population-level analyses further revealed ongoing evolution of recombination-suppressed regions in the Pacific species and uncovered multiple Y chromosome lineages in S. australasicus that differ markedly in the extent of recombination suppression. Together, these results demonstrate rapid structural genome evolution in Scomber and provide a genomic framework for understanding how chromosomal rearrangements contribute to reproductive isolation, sex chromosome turnover, and the diversification of pelagic marine fishes.

evolutionary biology↗

bioRxiv2026

Impaired Motor Awareness of Balance Control is Associated with Postural Instability in Parkinson's Disease

BackgroundBalance instability is a major contributor to disability and falls in people with Parkinsons disease (PwP) and is often insufficiently explained by motor impairment alone. Altered awareness of motor control has been suggested to contribute to sensorimotor dysfunction in PwP, but its relationship with balance performance is poorly understood. ObjectiveTo determine whether awareness of balance control, assessed using a control detection task (CDT), differs between healthy controls (HC) and PwP, and whether CDT performance is associated with balance-related measures. MethodsHealthy older adults (n=20) and PwP (n=22) performed a standing version of the CDT based on center-of-pressure (COP) control, using a force plate. CDT accuracy was used as the primary outcome measure. Static balance during quiet standing was assessed using the COP trajectory length and rectangular area. Dynamic standing balance was assessed using the Index of Postural Stability (IPS). Group differences were examined by independent-samples t-tests. Correlations between CDT accuracy and balance measures were analyzed. ResultsThe PwP group showed significantly lower CDT accuracy. Higher CDT accuracy was associated with better static balance in the HC group and the combined sample, and with higher IPS primarily in the PwP group. ConclusionsMotor awareness during postural tasks is altered in PwP and is associated with balance control. These findings suggest that balance instability in Parkinsons disease may involve altered balance-related action-outcome monitoring in addition to motor dysfunction.

neuroscience↗

bioRxiv2026

Kinetic design of reversible probe exchange enables continuous single-molecule tracking beyond the photobleaching limit

Single-molecule fluorescence imaging enables direct tracking of molecular dynamics. Prolonged observation, however, is limited by photobleaching, restricting access to rare events and slow transitions. Exchangeable fluorogenic labeling has been developed to overcome this limitation, yet continuous single-molecule tracking has not been achieved. We define two quantitative kinetic conditions for continuous tracking: pre-bleach dissociation and within-frame rebinding. Mapping reported systems onto a kinetic landscape delineates the regime required for continuous tracking. To reach this regime, we turned to odorant-binding proteins, whose biological role favors rapid ligand capture and release. We paired this scaffold with high-contrast fluorogenic probes to maximize rebinding capacity while preserving rapid dissociation. The resulting system, EverGreen, sustains uninterrupted single-molecule observation for over 24 hours and establishes a general kinetic design framework beyond the photobleaching limit.

biophysics↗

bioRxiv2026

Hypoxia-activated scleraxis a mediates epicardial progenitor differentiation into a unique cardiac perivascular cell type

The epicardium is a crucial source of progenitor cells and paracrine signals that support heart development and regeneration. However, the molecular mechanisms that guide epicardial cell fate decisions remain incompletely understood. Here, we identify the transcription factor Scleraxis a (encoded by scxa) as a key regulator of epicardial progenitor differentiation in zebrafish. Through single-cell transcriptomics, genetic lineage tracing, and cardiac injury models, we show that scxa is transiently induced in activated epicardial progenitor cells (aEPCs) during both heart regeneration and developmental coronary angiogenesis. scxa+ epicardial cells primarily give rise to a previously uncharacterized cardiac population of perivascular cells marked by col18a1a, molecularly distinct from classical pericytes and vascular smooth muscle cells. We refer to this population as epicardial-derived perivascular mesenchymal cells (Epi-PMCs). These Epi-PMCs closely associate with coronary vessels and may contribute to vascular stabilization and remodeling, potentially through the anti-angiogenic but vessel-stabilizing activity of endostatin derived from collagen XVIII. Loss of scxa increases coronary vessel density. Mechanistically, we identify hypoxia and Hif1a signaling as upstream regulators of scxa, with systemic hypoxia or Hif factor stabilization robustly inducing scxa expression in the epicardium. Together, these findings uncover a hypoxia-responsive Scxa-Col18a1a axis that drives epicardial differentiation toward a vascular-supportive fate, offering new insight into the regulation of coronary vessel development and the regenerative potential of the epicardium.

developmental biology↗

bioRxiv2026

Divergence in skeletal muscle growth by differential spatial hyperplastic patterning in teleost fishes

Skeletal muscle plays important locomotive and metabolic functions, yet its formation and maintenance are processes remaining largely unclear mechanistically in any animal. Teleost fishes display extraordinary muscle growth due to their ability to undergo both hyperplasia and hypertrophy throughout life. These phenomena vary greatly even between closely related species, providing opportunities to elucidate growth dynamics and underlying mechanisms through cross-species comparisons. Using histological and genetic approaches, we compared muscle growth dynamics in three closely related danionin species with distinct growth capacities: the giant danio (Devario malabaricus), the zebrafish (Danio rerio), and Danionella cerebrum, as well as the more distantly related African turquoise killifish (Nothobranchius furzeri). Our study reveals alterations in spatial patterning of muscle hyperplasia and developmental timing to be major contributors to observed differences in muscle growth between examined species. Single-cell RNA profiling, in situ hybridization chain reaction and cell type-specific mutagenesis revealed muscle stem cell-specific expression of extracellular matrix genes that mediate stem cell activity, which in turn may drive growth differences between species. Taken together, our findings highlight autonomous regulation of muscle stem cells as a conserved but adaptable mechanism governing muscle patterning and diversification.

evolutionary biology↗

bioRxiv2025

Peculiar Pigment Pattern and Population Profile of a Poisonous Pufferfish

Pufferfish are well-known for their toxicity, yet they also exhibit a remarkable diversity of pigment patterns. Mushifugu (Takifugu exascurus) is a pufferfish endemic to Japans coastal waters and is characterized by conspicuous labyrinthine patterns. Despite being recorded along both the Sea of Japan and the Pacific coasts, it has a limited distribution and is infrequently observed. Aside from its unique body pattern, mushifugu shows little to no morphological differences from other Takifugu species, often leading to speculation that it may be an interspecific hybrid. In addition, previous theoretical and empirical studies have shown that complex camouflage-like labyrinthine patterns can emerge through the pattern blending caused by hybridization between spotted species, providing support for this possibility. Here, we investigate the phylogenetic origin of mushifugu and its distinctive pattern through population structure analysis and demographic inference in comparison with its closest spotted relative, komonfugu (T. flavipterus). Mitochondrial DNA (mtDNA) analysis revealed two regional haplogroups within mushifugu--one in the Sea of Japan (SJ) and the other in the Pacific Ocean (PO). In the haplotype network, the SJ haplogroup formed a distinct cluster, whereas the PO haplogroup appeared as its own cluster connected to the komonfugu haplogroup. By contrast, genome-wide SNP analyses indicated limited structure between the SJ and PO mushifugu populations, while clearly separating mushifugu from komonfugu. Coalescent-based demographic inference suggested that the two species diverged following a bottleneck event in the early Pleistocene. These results confirm that mushifugu is a distinct species rather than a recent interspecific hybrid. Nevertheless, evidence of introgression was detected in both mitochondrial and nuclear genomes, suggesting multiple episodes of past hybridization between mushifugu and komonfugu, highlighting the potentially complex evolutionary processes shaping Takifugu species and their pigment patterns.

evolutionary biology↗

bioRxiv2025

MAP7-driven cytoskeletal cross-talk establishes Sertoli cell polarity crucial for germ cell meiotic progression

How specialized apical membrane domains are assembled in vivo remains poorly understood. In the mouse testis, Sertoli cells build a luminal apical domain after birth that organizes the seminiferous epithelium and supports germ cell differentiation, distinct from fetal polarity established during cord formation. Here, we identify the microtubule-associated protein MAP7 as a key regulator of cytoskeletal organization during apical domain formation. MAP7 preferentially localizes to apical microtubules in Sertoli cells, showing limited overlap with stable microtubule markers. Native-tissue imaging indicates that MAP7-decorated microtubules, initially lacking obvious directionality, become increasingly aligned along the tubule axis as the apical domain matures. In Map7-deficient testes, microtubule abundance is maintained, but higher-order organization is disrupted and accompanied by persistent luminal F-actin accumulation. These defects compromise apical domain maturation and lumen formation during the first wave of spermatogenesis and are associated with altered tight-junction patterning. Proteomic analysis identifies the non-muscle myosin II heavy chains MYH9 and MYH10 among MAP7-associated proteins. MYH9 becomes enriched at luminal regions where microtubules and F-actin converge, but remains diffuse in Map7-deficient Sertoli cells despite ectopic luminal cytoskeletal assemblies, suggesting that MAP7 helps establish a cytoskeletal context that supports spatially restricted NMII enrichment. Single-cell RNA sequencing shows that Sertoli transcriptional differentiation largely proceeds without MAP7, whereas germ cells exhibit delayed meiotic progression with expansion of pachytene-stage subpopulations. Together, these findings establish MAP7-dependent microtubule remodeling as an organizing mechanism for postnatal apical domain maturation and suggest how epithelial cytoskeletal architecture shapes a niche that helps pace developmental progression of neighboring germ cells.

cell biology↗

bioRxiv2025

Evaluation of Conditional Treatment Effect of Salt Stress on Tomato Sugar Content Using Causal Machine Learning: A Pilot Study

Exposing tomatoes to salt stress has been reported to increase the fruit sugar content ({degrees}Brix); however, this treatments causal impact under varying environmental conditions remains unclear. In this pilot study, a causal inference analysis was conducted using a Causal Tree to analyze the factors that influence the effect of salt-stress treatment on improving the {degrees}Brix in tomatoes. Data were collected from a single greenhouse using one cultivar over multiple cultivation periods, totaling 707 fruits. Propensity score matching was applied to reduce the covariate imbalance between the salt (NaCl) treatment and control groups. Using a Causal Tree, conditional average treatment effects were then estimated to assess heterogeneity in treatment impact based on environmental variables, such as temperature, humidity, and illumination. Treatment with NaCl significantly increased {degrees}Brix compared to the control, but the magnitude of the effect varied depending on the environmental conditions. The Causal Tree analysis based on the accumulated cultivation data identified specific combinations of environmental factors under which the impact of NaCl treatment on {degrees}Brix enhancement was more pronounced. For example, the estimated Conditional Average Treatment Effect (CATE) reached as high as 0.88 when humidity was [≥]75%, illuminance was [≥]8144 lx, and categorical variable C3 was F1 or F2. In contrast, the CATE dropped to as low as 0.036 under low humidity (<79%) and high temperature (<24{degrees}C). These findings highlight humidity as the most influential factor, whose impact was modulated by interactions with temperature and light conditions.

plant biology↗

bioRxiv2025

Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones

Structural variation is increasingly recognized as a pivotal contributor to genomic diversity in marine invertebrates, yet its extent and evolutionary significance remain poorly characterized in many species. Haplotype-phased genome assembly is an excellent method for studying such variations by comparing homologous chromosomes. In this study, we constructed a haplotype-phased genome assembly for the western Pacific abalone, Haliotis gigantea, using high-fidelity (HiFi) long-read sequencing and high-resolution chromosome conformation capture (Hi-C) data. The primary and alternative assemblies each comprised 18 long scaffolds (>50 Mb), consistent with the species diploid chromosome number (2n = 36), and contained 96.5% and 96.2% complete single-copy Metazoa Benchmarking Universal Single-Copy Orthologs genes, respectively, indicating high assembly quality. Comparative analysis of the two haplotypes revealed three homologous chromosomes with large-scale non-syntenic regions caused by extensive segmental duplications, with each enriched in distinct gene domains. These non-syntenic chromosomes likely originated in abalone evolution, as they were conserved across both closely and distantly related species. Our findings highlight the evolutionary importance of non-syntenic structural variation in shaping genome architecture and suggest that such variation may play a broader role in functional diversification across abalones.

genomics↗

bioRxiv2025

Inhibition of NF-κB signaling pathway in astrocytes facilitates amyloid-β clearance by kallikrein-related peptidase 7

Alzheimer disease (AD) is characterized by the deposition of amyloid-{beta} peptide (A{beta}). Decreased A{beta} clearance is observed in sporadic AD patients, suggesting that enhancing A{beta} clearance is a potential therapeutic approach for AD. We identified kallikrein-related peptidase 7 (KLK7) as an astrocyte-derived A{beta}-degrading protease, and its mRNA expression is reduced in AD brains. Memantine, an N-methyl-D-aspartate (NMDA) receptor antagonist, upregulates KLK7 expression in astrocytes; however, the regulatory mechanism remains unclear. Here, we show that the NMDA receptor signaling negatively regulates KLK7 mRNA expression via nuclear factor-{kappa}B (NF-{kappa}B). Inhibition of NF-{kappa}B signaling pathway in astrocytes increases KLK7 expression and promotes A{beta} degradation. Moreover, the mRNA expression level of the NF-{kappa}B family is elevated in AD brains and shows a negative correlation with KLK7 mRNA expression. Finally, the injection of an NF-{kappa}B inhibitor significantly upregulates Klk7 expression and reduces A{beta} levels in vivo. These findings suggest that the NMDA receptor-NF-{kappa}B signaling axis in astrocytes negatively regulates KLK7 expression and modulates KLK7-mediated A{beta} clearance.

neuroscience↗

bioRxiv2025

Deep exploration of transcriptomic cellular identities over evolutionary time

Whole-organism cell atlases have painted the cellular landscapes of individual species; however, comparing cells across the tree of life remains challenging. Most cross-species analyses are restricted to orthologous genes, while the complexity of atlas data constitutes an access barrier for many researchers. We developed a computational strategy to accelerate the exploration of cellular identities at scale. We integrated 30 atlases detailing the expression of 861,013 genes by 2,645,508 animal and plant cells and trained a universal model of cellular transcriptomes to track cell type diversification over evolutionary times. Transfer learning achieved cell type annotation of a de novo atlas of the insect Cryptocercus punctulatus within minutes. We devised a generative artificial intelligence approach to construct virtual cell atlases from genome sequences and used it to synthesise an atlas of the Tasmanian tiger, extinct since 1936. We then reduced the footprint of extant atlases by 100 times while retaining crucial information and developed interfaces to answer dozens of query types within seconds, boosting atlas exploration by [~]50,000 times.

evolutionary biology↗

bioRxiv2024

Identification of the sex determination region and the development of a marker to distinguish males and females in megai abalone (Haliotis gigantea)

Sex identification markers are of considerable value to aquaculture and fisheries as they enable pre-maturity prediction of the genotypic sex of individuals as well as of the sex ratio in offspring. For these reasons, extensive investigations of the mechanisms of sex determination have been conducted in commercially important finfish species, resulting in the development of sex identification markers for many of these. However, research on shellfish is still in its infancy stage. In this study, we investigated the genomic basis of sex determination in megai abalone (Haliotis gigantea), a gastropod species of economic importance in fisheries and aquaculture in East Asia, with the aim of developing a sex identification marker. Initially, we examined the applicability of sex identification markers reported for two other Haliotis species, but found they were not transferable to H. gigantea. We then analyzed the sex chromosomes in H. gigantea using a whole-genome resequencing approach. By calculating the fixation index value between 10 females and 10 males, we identified a genomic region spanning approximately 2 Mb that exhibited nucleotide sequence divergence between the sexes (from the position 260,372 bp to 1,930,278 bp in chromosome 18). This region was located next to the pseudoautosomal region which is characterized by an absence of sequence differentiation between the sexes. In the divergent region, male-specific SNPs were identified but no female-specific SNPs were detected, indicating that this species has an XX-XY sex determination system. By exploring Indel polymorphisms in the divergent region, we successfully developed a codominant PCR marker for sex identification that could be applied to wild individuals from geographically distant locations. A cross-species analysis suggested that the sex determination region in H. gigantea was unlikely to be shared with the closely related species H. discus hannai. This raises the possibility of a widespread, rapid turnover of sex chromosomes or sex determination regions in abalones, similar to certain vertebrate lineages such as finfish.

genomics↗

bioRxiv2024

Silver chimaera genome assembly and identification of the holocephalan sex chromosome sequence

Cartilaginous fishes are divided into holocephalans and elasmobranchs, and comparative studies involving them are expected to elucidate how variable phenotypes and distinctive genomic properties were established in those ancient vertebrate lineages. To date, molecular-level studies on holocephalans have concentrated on the family Callorhinchidae, with a chromosome-scale genome assembly of Callorhinchus milii available. In this study, we focused on the most species-rich holocephalan family Chimaeridae and sequenced the genome of its member, silver chimaera (Chimaera phantasma). We report the first chromosome-scale genome assembly of the Chimaeridae, with high continuity and completeness, which exhibited a large intragenomic variation of chromosome lengths, which is correlated with intron size. This pattern is observed more widely in vertebrates and at least partly accounts for cross-species genome size variation. A male-female comparison identified a silver chimaera genomic scaffold with a double sequence depth for females, which we identify as an X chromosome fragment. This is the first DNA sequence-based evidence of a holocephalan sex chromosome, suggesting a male heterogametic sex determination system. This study, allowing the first chromosome-level comparison among holocephalan genomes, will trigger in-depth understanding of the genomic diversity among vertebrates as well as species population genetic structures based on the genome assembly of high completeness.

genomics↗