Biology subjects

Kon-Nanjo, K.

Publications and source records attributed to Kon-Nanjo, K..

7 recordsLinked to original sources

bioRxiv2026

Histo-anatomical atlas and thermal tolerance of Garra rufa: A novel small teleost model adaptable to human body temperature

Garra rufa, commonly known as the doctor fish, is a small freshwater cyprinid notable for its exceptional tolerance to high temperatures, surviving even at around the human body temperature of 37 {degrees}C, and has emerging potential as a novel laboratory model for human cancer xenotransplantation and infectious disease research. To establish a foundation for its experimental use, we conducted comprehensive anatomical and histological analyses across major organ systems. The overall body organization and tissue architecture of G. rufa are broadly similar to those of zebrafish (Danio rerio), indicating a conserved cyprinid body plan. However, several organ systems in G. rufa exhibited species-specific differences compared with zebrafish, including a well-developed adhesive disc around the oral region, a long and coiled intestine, and a distinct dark pigmentation of the peritoneum. These species-specific traits may reflect ecological and behavioral adaptations of G. rufa, including benthic scraping in warm, flowing habitats. Physiological assays confirmed that G. rufa maintains high survival rates and normal swimming activity at 37 {degrees}C, whereas zebrafish exhibit significant mortality and reduced locomotion under the same conditions. Collectively, this work provides a comprehensive histo-anatomical atlas of G. rufa, highlighting its unique morphological specializations while establishing an essential reference for the development of this species as a novel experimental fish model.

zoology↗

bioRxiv2026

Comparative genomics reveals signatures of distinct metabolic strategies and gene loss associated with Hydra immortality

Hydra is a freshwater cnidarian genus that provides a unique comparative model for aging research, contrasting the immortal H. vulgaris with the aging-inducible H. oligactis. Here, we report a high-quality, chromosome-level genome assembly of H. vulgaris strain AEP.JNIG. Our assembly is comparable in quality to existing resources, facilitating the analysis of genomic diversity across laboratory strains. Epigenomic profiling revealed that gene-body hypermethylation correlates with transcriptional stability and the suppression of spurious transcription in evolutionary conserved genes, suggesting an epigenetic mechanism for genomic integrity. Furthermore, comparative genomics demonstrated that while Hydra conserves fundamental Hallmarks of Aging pathways, the immortal H. vulgaris paradoxically lacks canonical anti-aging genes (e.g., Klotho, NAMPT) found in the aging-inducible H. oligactis. Instead, H. vulgaris exhibits a distinct metabolic signature related to mitochondrial energy production and NTP synthesis. Collectively, our comparative genomics results suggest multiple potential mechanisms associated with the H. vulgaris immortality and the aging traits of H. oligactis, providing novel targets for future functional studies. Significance statementWhy do some organisms age while others appear not to? The freshwater animal Hydra provides a unique opportunity to investigate this question, as closely related species display contrasting aging phenotypes. We generated a high-quality genome assembly for a new strain of a non-aging species and conducted comparative analyses with related strains and an aging species. Even closely related strains can accumulate substantial genetic divergence over time, and stable DNA modification patterns were associated with consistent gene activity, suggesting a mechanism that may help maintain cellular balance. Surprisingly, several well-known longevity genes are present in the aging species but absent in the non-aging one. This suggests that extended lifespan may not simply depend on possessing more "anti-aging" genes, but instead may reflect differences in how core biological processes are organized. Our study provides new insights into the genetic basis of aging and highlights Hydra as a powerful model for understanding longevity.

genomics↗

bioRxiv2025

Chromosomal fusions and subsequent rearrangements shaped octopus genomes

Why some animal groups retain ancestral chromosomal complements while others change significantly is a fundamental question in evolutionary genomics. Few systems exist where accumulations of chromosomal changes can be studied in the context of morphological innovation. In coleoid cephalopods (octopus, squid, cuttlefish), an ancient coleoid chromosomal rearrangement event (ACCRE) has led to a substantial increase in the chromosome number and a new set of chromosomal homologies. Compared to typical molluscan or bilaterian genomes, ACCRE has enabled the origin of many novel regulatory regions in coleoid cephalopods. However, the discrepancies between extant octopodiform (octopus, [~]30 chromosomes) and decapodiform (squid and cuttlefish, [~]46 chromosomes) karyotypes and the direction of these evolutionary changes remain unexplained. Here we provide a draft genome assembly of the vampire squid Vampyroteuthis sp., the largest cephalopod genome sequenced to-date (over 10 gigabasepairs). Through syntenic comparisons, we infer that this basally branching octopodiform species shows partial retention of the chromosomal complement of Decapodiformes, indicating its more ancestral state and the derived nature of the octopod karyotype. Together with the analysis of a new chromosome-level assembly of the pelagic octopod Argonauta hians, we identified irreversible chromosomal fusion-with-mixing events followed by inter-chromosomal translocations in octopods. We show that this secondary reduction and mixing within octopod chromosomes has enabled the origin of a more entangled genomic configuration, shedding light onto the early evolutionary transitions within the clade. Our results offer broader insights into general patterns of chromosomal evolution following large-scale rearrangement events in animal genomes. Significance statementHow changes to the ancient animal synteny result in novel chromosomal homologies is difficult to dissect due to the lack of intermediate states. Here we report that the genome of Vampyroteuthis, one of the largest animal genomes sequenced to-date (over 11 gigabasepairs), despite its phylogenetic position within the octopodiform cephalopods, partially retains squid and cuttlefish chromosomal complement, reflecting an ancestral karyotypic state that existed at the time of divergence between these cephalopod lineages. Our findings reveal karyotype reductions through chromosomal fusions were followed by inter-chromosomal translocations in octopods, leading to a more specialized genomic and gene regulatory architecture. These data show how chromosomal fusions can act as drivers of further inter-chromosomal rearrangements in animal genomes.

genomics↗

bioRxiv2025

A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores

Siphonophores (Cnidaria:Hydrozoa) are pelagic colonial marine invertebrates with many highly specialized bodies (zooids) within a single colony. Their unique biology and ecological importance have made them of particular interest. Recent work revealed siphonophore genomes to be larger than in most other cnidarians. To investigate siphonophores genome biology and develop resources for future studies, we sequenced the genome of a single Nanomia septata to chromosome scale. The haploid genome is 1.5GB across 8 chromosomes, a reduction relative to the 15 chromosomes seen in closely related hydrozoan genomes, and is highly rearranged, consistent with multiple mixing events. Genome expansion occurred through intergenic repeat expansion, with protein-coding genes shorter than in most cnidarians. We found no genomic features clearly associated with siphonophores exceptional colony-level complexity. Gene families that play critical roles in cnidarian development have not expanded, and gene proximity was not generally correlated to their expression across zooids, except in male gonophores. To contextualize these observations, we genome sequenced 20 additional Nanomia specimens across the globe and mapped them to our chromosome-scale reference. Population genomic analyses support three previously recognized species of Nanomia, and at least one additional undescribed species. Overlapping geographic distribution of some Nanomia species suggest reproductive isolation in sympatry. Phylogenetic analyses of genome size indicate Nanomia septata and Nanomia cara have similarly large genomes between 1.5-1.7GB, while Nanomia bijuga and an undescribed species show a secondary reduction to 0.7GB. These results highlight how genomic factors have shaped colony organization and genome diversity within Nanomia.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of the doctor fish (Garra rufa)

Garra rufa, commonly known as doctor fish, is a small freshwater cyprinid fish recognized for its high-temperature tolerance. G. rufa is primarily known for its role in ichthyotherapy, in which it helps remove keratinized skin from human hands and feet. However, in recent years, its high-temperature tolerance has attracted attention owing to its potential use as a model for human disease research, including infectious diseases and cancer xenograft models. Despite this interest, the genomic basis underlying high-temperature tolerance remains largely unexplored, primarily because of the limited availability of genomic resources, which hinders its development as an experimental model. In the present study, a high-quality chromosome-level genome assembly of G. rufa was generated using a combination of PacBio HiFi long-read sequencing and Hi-C technology. We generated a chromosome-level genome assembly with 25 chromosomes, 1.38 Gb in total length, and scaffold N50 of 49.3 Mb. Approximately 59% of the genome comprises repetitive elements, with DNA and LTR elements being particularly abundant. In total, 27,352 protein-coding genes were annotated, of which 26,900 genes (98.3%) were functionally annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark for genome assembly and gene annotation demonstrated 94.5% and 94.7% of complete BUSCOs, respectively. We identified two heat shock transcription factor (HSF) and 239 heat shock protein (HSP)-related genes. Heat shock elements, which are HSF-binding motifs, were present within 3 kb upstream of 944 genes, with statistically significant enrichment of HSP-related genes in this set. Furthermore, molecular phylogenetic analysis and whole-genome comparisons revealed that G. rufa is evolutionarily closely related to species in the Labeoninae subfamily of the Cyprinidae family. This chromosome-level reference genome provides a valuable resource for future research aimed at elucidating the molecular mechanisms underlying high-temperature tolerance in G. rufa and establishing it as a model organism for human biomedical studies.

genomics↗

bioRxiv2024

Expansion of a single Helitron subfamily in Hydractinia symbiolongicarpus suggests a shared mechanism of cnidarian chromosomal extension

Helitrons are rolling-circle transposons that amplify through rolling-circle replication mechanism. Since Helitrons were relatively recently identified, their impact on genome evolution is still not fully understood. Here, we describe that a single Helitron subfamily specifically accumulates in the subtelomeric regions of Hydractinia symbiolongicarpus, a colonial hydrozoan cnidarian. Based on the sequence divergence, it is suggested that the Helitron subfamily underwent a burst of activity in the species recent history. Additionally, there is a IS3EU DNA element accumulation at the putative centromeric regions, as well as minisatellite sequences of approximately 200 bp in length extending from the telomere-side end of the Helitron towards the telomere. Phylogenetic analysis of Helitrons in the H. symbiolongicarpus genome suggests that the Helitrons underwent local propagation at the subtelomeric regions. The single Helitron subfamily, along with the consecutive minisatellite, accounts for 26.1% of the genome coverage (126 Mb of the 483 Mb genome), which collectively contribute to the genome size increase observed in H. symbiolongicarpus compared with other cnidarians. Homologous sequences of Helitron in H. symbiolongicarpus were identified in the genomes of other cnidarians, suggesting that Helitrons in hydractinia were present in at least the common ancestor of Cnidaria. Furthermore, in Nematostella vectensis, an anthozoan cnidarian, Helitrons were also accumulated at the subtelomeric regions. All these findings suggest that Helitrons constitute a common cnidarian mechanism of chromosomal extension through local amplification in subtelomeric regions, driving diverse genome expansions within the clade.

genomics↗

bioRxiv2024

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes

Many animal genomes are characterized by highly conserved chromosomal homologies that pre-date the ancient origin of this clade. Despite such conservation, the evolutionary forces behind the retention, expansion, and contraction of chromosomal elements, and the resulting macro-evolutionary implications, are unknown. Here we present a comprehensive stem-cell resolved genomic and transcriptomic study of the fresh-water cnidarian Hydra, an animal characterized by its high regenerative capacity, the ability to propagate clonally, and an apparent lack of aging. Using single-haplotype telomere-to-telomere genome assemblies of two recently diverged hydra strains, we show how the macro-evolutionary history of chromosomal elements is shaped by both old and recent transposable element (TE) expansions. Unique features of hydra biology allowed us to compare the individual genomes of hydras three stem cell lineages. We show that distinct TE families are active at both transcriptional and genomic levels via non-random insertions in the genomes of each of these lineages. In transcriptomes, over 14,000 transcripts were composed of nearly complete TE sequences, and further classification into families, subfamilies, and individual loci reveals cell type-specific TE expression. The active TEs include elements that differentially contribute to changes in the genome size as well as persistent structural variants around loci associated with cell proliferation. Our study reveals 14 active TE families that primarily act in this role and are predominantly composed of DNA elements. Evolutionary analysis revealed that these families constitute a highly conserved TE core in eukaryotic and metazoan genomes. Our results suggest an ancient role for these core TEs as self-renewing genomic components that persist beyond ancient chromosomal homologies.

genomics↗