Biology subjects

Toga, K.

Publications and source records attributed to Toga, K..

9 recordsLinked to original sources

bioRxiv2026

Genome-wide Identification of Transcriptional Start Sites and Candidate Enhancers Regulating Worker Metamorphosis in Apis mellifera

Eusociality in bees represents a major evolutionary transition and understanding its molecular basis is fundamental for sociogenomic studies. Comparative genomics has revealed correlations between transcription factor binding site (TFBS) abundance and social complexity; however, when and where these TFBSs function in a eusocial context remains largely unclear. In this study, we performed cap analysis of gene expression (CAGE) during worker metamorphosis in the honeybee Apis mellifera to identify TFBSs within active enhancers and decipher the regulatory relationships between these enhancers and their target genes. We identified 17,349 transcription start sites (TSSs) and 842 candidate enhancers. Using CAGE, we identified five clusters based on expression patterns. Notably, genes associated with the canonical metamorphic regulators, Broad complex (Br-c) and E93, were found within specific clusters. By integrating the correlations between enhancer and TSS activities with motif enrichment analysis, we identified 15 transcription factor-enhancer-TSS regulatory relationships. Among these, tramtrack (ttk)-binding sites were identified in five enhancers associated with four target genes, including Br-c. The number of target genes regulated by ttk was the highest in our dataset. To examine whether this regulatory relationship is conserved across bee species with varying levels of sociality, we analyzed the sequence conservation of ttk-binding sites in Br-c enhancers and found that perfect sequence conservation of ttk-binding site was restricted to the Apis genus. The ttk-binding sites of other target genes exhibited the same Apis-specific conservation pattern. Our findings suggest that gene regulatory relationships during worker metamorphosis occur in a lineage-specific manner in the Apis genus. SignificanceHoneybees produce distinct castes--queens and workers--from genetically identical larvae via differences in gene regulation. Although enhancers have been computationally predicted, their actual activity during bee development has rarely been measured directly, and the CAGE technology has never been applied for this purpose. We identified active enhancers during worker metamorphosis and discovered that the transcription factor ttk may regulate Br-c, a key developmental gene. This study provides the first direct evidence of active enhancers and their regulatory roles in honeybee worker metamorphosis.

genomics↗

bioRxiv2025

Genome assembly and annotation of the naked mole rat Heterocephalus glaber reared in Japan

The naked mole rat (NMR, Heterocephalus glaber) is a eusocial rodent that is native to northeastern Africa. NMRs exhibit extraordinary traits such as longevity, resistance to age-related decline, and remarkable hypoxia tolerance. Although the reference genome of this species has been determined because of its unique characteristics, the significance or role of intraspecific genomic variations remains unknown. In this study, we used PacBio long-read sequencing to generate a genome assembly of NMR reared in Japan. The assembled genome is 2.56 Gb. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed high completeness (95.2%). BRAKER3 estimated 26,714 protein-coding genes, and we successfully added functional annotations for 26,232 protein-coding genes using the functional annotation workflow. We identified 417 gene models that were previously undetectable in the reference genome of this species. We also identified structural and amino acid sequence variations between our assembly and the reference genome, suggesting the presence of intraspecific genomic variations. This new genomic resource could help uncover the molecular mechanisms underlying the behavioral and physiological traits of NMR.

genomics↗

bioRxiv2025

Genes responsible for the formation of asymmetrical mandibular teeth in the giant mealworm beetle, Zophobas atratus

ABSTRUCTThe mandibles of coleopteran insects are typical examples of external morphological asymmetry in animals. The developmental molecular mechanisms underlying the external morphological asymmetry remain to be elucidated compared to those of the internal asymmetric organ. In the tenebrionid beetle, Zophobas atratus, the inner teeth of adult mandibles are asymmetric, while the pupal mandibles are nearly symmetric. The asymmetric morphogenesis is assumed to be caused by the left-right regulatory differences of inner teeth formation, but even the developmental mechanisms involved in the inner teeth per se remains unknown. In this study, we investigated the morphogenetic process involved in the formation of inner teeth and searched for genes responsible for this process. Morphological observation showed that the inner teeth of adults formed during 0-5 days after pupal molting. Left mandibles possessed the characteristic second inner teeth, whereas the right mandibles exhibited invaginations between apical and second inner teeth. We performed RNAi for candidate genes and successfully identified four genes (paired, alistaless, Lim1, and mlpt) involved in the formation of inner teeth. Among them, mlpt RNAi had a strong effect on the morphology of the right mandibles, suggesting its involvement in the asymmetrical formation of mandibles.

developmental biology↗

bioRxiv2024

Genome-wide Search for Gene Mutations likely Conferring Insecticide Resistance in the Common Bed Bug, Cimex lectularius

Insecticide resistance in the bedbug Cimex lectularius is poorly understood due to the lack of genome sequences for resistant strains. In Japan, we identified a resistant strain of C. lectularius that exhibits a higher pyrethroid resistance ratio compared to many previously discovered strains. We sequenced genomes of the pyrethroid resistant and susceptible strains using long-read sequencing, resulting in the construction of highly contiguous genomes (N50 of resistant strain: 2.1Mb and N50 of susceptible strain: 1.5 Mb). Gene prediction was performed by BRAKER3 and Functional annotation was performed by Fanflow4insects workflow. Next, we compared their amino acid sequences to identify gene mutations, identifying 729 mutated transcripts that were specific to the resistant strain. Among them, those defined previously as resistance genes were included. Additionally, enrichment analysis implicated DNA damage response, cell cycle regulation, insulin metabolism, and lysosomes in the development of pyrethroid resistance. Genome editing of these genes can provide insights into the evolution and mechanisms of insecticide resistance. This study expanded the target genes to monitor allele distribution and frequency changes, which will likely contribute to the assessment of resistance levels. These findings highlight the potential of genome-wide approaches to understand insecticide resistance in bed bugs. Simple SummaryBedbugs have expanded globally over the past two decades, causing several health risks. Mutations in their genes allow bed bugs to develop insecticide resistance. However, the extent to which gene mutations exist in the bug genome remains largely unknown because the genomes of resistant strains have not been determined. We accurately sequenced the genomes of both susceptible and resistant strains and compared the gene sequences between the two strains. Several genes with resistance-specific mutations have been identified. These mutations can alter gene function and lead to insecticide resistance.

genomics↗

bioRxiv2023

Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae)

Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which thousands of genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae, and their developmental patterns differ between the US and Japanese C. floridanum strains. Genome sequencing can accelerate our understanding of the molecular bases underlying polyembryony, including the production of soldier castes. However, only the genome sequence of the US strain has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structure from those in the US strain. This was accomplished through the functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected to amino acid sequences of vasa that plays a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detail genomic regions responsible for the ecological and physiological characters of C. floridanum.

genomics↗

bioRxiv2022

Meta-analysis of public RNA sequencing data of queens and workers in social Hymenoptera and termites

Eusociality in insects has evolved independently many times. One of the most notable characteristics of eusociality is the reproductive division of labor. In social insects, the reproductive division of labor is accomplished by queens and workers. Transcriptome analyses of queens and workers have been conducted for various eusocial species. However, the genes that regulate the reproductive division of labor across all or multiple eusocial species have not yet been fully elucidated. Therefore, we conducted a meta-analysis using publicly available RNA-sequencing data from four major groups of social insects. In this meta-analysis, we collected 258 pairs (queen vs. worker) of RNA-sequencing data from 34 eusocial species. The meta-analysis identified a total of 20 genes that were differentially expressed in queens or workers. Out of these, 12 genes have not previously been reported to be involved in the reproductive division of labor. Functional annotation of these 20 genes in other organisms revealed that they could be regulators of behaviors and physiological states related to the reproductive division of labor. These 20 genes, revealed using massive datasets of numerous eusocial insects, may be key regulators of the reproductive division of labor.

ecology↗

bioRxiv2022

Meta-analysis of transcriptomes in insects showing density-dependent polyphenism

With increasing public data, a statistical analysis approach called meta-analysis, which combines transcriptome results obtained from multiple studies, has succeeded in providing novel insights into targeted biological processes. Locusts and aphids are representative of insect groups that exhibit density-dependent plasticity. Although the physiological mechanisms underlying density-dependent polyphenism have been identified in aphids and locusts, the underlying molecular mechanisms remain largely unknown. In this study, we performed a meta-analysis of public transcriptomes to gain additional insights into the molecular underpinning of density-dependent plasticity. We collected RNA sequencing data of aphids and locusts from public databases and detected differentially expressed genes (DEGs) between crowded and isolated conditions. Gene set enrichment analysis was performed to reveal the characteristics of the DEGs. DNA replication (GO:0006260), DNA metabolic processes (GO:0006259), and mitotic cell cycle (GO:0000278) were enriched in response to crowded conditions. To date, these processes have scarcely been the focus of research. The importance of the oxidative stress response and neurological system modifications under isolated conditions has been highlighted. These biological processes, clarified by meta-analysis, are thought to play key roles in the regulation of density-dependent plasticity. Simple SummaryPopulation density can be an environmental cue to induce modification of insect morphology, physiology, and behavior. This phenomenon is called density-dependent plasticity. Aphids and locusts exhibit textbook examples of density-dependent plasticity but there is a lack of integrative understanding for insect density-dependent plasticity. To address this problem, we combined public gene expression data obtained from multiple studies and re-analyzed them (this process is called meta-analysis). The present study provides additional insight into the regulatory mechanisms of density-dependent plasticity, demonstrating the effectiveness of meta-analyses of public transcriptomes.

bioinformatics↗

bioRxiv2022

The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

genomics↗

bioRxiv2021

Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: gene duplication facilitates social evolution

Termites are model social organisms characterized by a polyphenic caste system. Subterranean termites (Rhinotermitidae) are ecologically and economically important species, including acting as destructive pests. Rhinotermitidae occupies an important evolutionary position within the clade representing an intermediate taxon between the higher (Termitidae) and lower (other families) termites. Here, we report the genome, transcriptome and methylome of the Japanese subterranean termite Reticulitermes speratus. The analyses highlight the significance of gene duplication in social evolution in this termite. Gene duplication associated with caste-biased gene expression is prevalent in the R. speratus genome. Such duplicated genes encompass diverse categories related to social functions, including lipocalins (chemical communication), cellulases (wood digestion and social interaction), lysozymes (social immunity), geranylgeranyl diphosphate synthase (social defense) and a novel class of termite lineage-specific genes with unknown functions. Paralogous genes were often observed in tandem in the genome, but the expression patterns were highly variable, exhibiting caste biases. Some duplicated genes assayed were expressed in caste-specific organs, such as the accessory glands of the queen ovary and frontal glands in soldier heads. We propose that gene duplication facilitates social evolution through regulatory diversification leading to caste-biased expression and subfunctionalization and/or neofunctionalization that confers caste-specialized functions. Significance StatementTermites are model social organisms characterized by a sophisticated caste system, where distinct castes arise from the same genome. Our genomics data of Japanese subterranean termite provides insights into the evolution of the social system, highlighting the significance of gene duplication. Gene duplication associated with caste-biased gene expression is prevalent in the termite genome. Many of the duplicated genes were related to social functions, such as chemical communication, social immunity and defense, and they often expressed in caste-specific organs. We propose that gene duplication facilitates social evolution through regulatory diversification leading to caste-biased expression and functional specialization. In addition, since subterranean termites are ecologically and economically important species including destructive pests in the world, our genomics data serves as a foundation for these studies.

genomics↗