Cellular senescence induction leads to progressive cell death via the INK4a-RB pathway in naked mole-rats.

Naked mole-rats (NMRs) have exceptional longevity and are resistant to age-related physiological decline and diseases. Given the role of cellular senescence in aging, we postulated that NMRs possess unidentified species-specific mechanisms to prevent senescent cell accumulation. Here, we show that upon induction of cellular senescence, NMR fibroblasts underwent delayed and progressive cell death that required activation of the INK4a-retinoblastoma protein (RB) pathway (termed "INK4a-RB cell death"), a phenomenon not observed in mouse fibroblasts. Naked mole-rat fibroblasts uniquely accumulated serotonin and were inherently vulnerable to hydrogen peroxide (H2 O2 ). After activation of the INK4a-RB pathway, NMR fibroblasts increased monoamine oxidase levels, leading to serotonin oxidization and H2 O2 production, which resulted in increased intracellular oxidative damage and cell death activation. In the NMR lung, induction of cellular senescence caused delayed, progressive cell death mediated by monoamine oxidase activation, thereby preventing senescent cell accumulation, consistent with in vitro results. The present findings indicate that INK4a-RB cell death likely functions as a natural senolytic mechanism in NMRs, providing an evolutionary rationale for senescent cell removal as a strategy to resist aging.

Transcriptome Analysis Reveals Enhancement of Cardiogenesis-Related Signaling Pathways by S-nitroso-N-pivaloyl-D-penicillamine (SNPiP): Implications for Improved Diastolic Function and Cardiac Performance.

We previously reported a novel compound called S-nitroso-N-pivaloyl-D-penicillamine (SNPiP), which was screened from a group of nitric oxide (NO) donor compounds with a basic chemical structure of S-nitroso-N-acetylpenicillamine (SNAP), to activate the non-neuronal acetylcholine (NNA) system. SNPiP-treated mice exhibited improved cardiac output and enhanced diastolic function, without an increase in heart rate. The NNA-activating effects included increased resilience to ischemia, modulation of energy metabolism preference, and activation of angiogenesis. Here, we performed transcriptome analysis of SNPiP-treated mice ventricles to elucidate how SNPiP exerts beneficial effects on cardiac function. A time-course study (24 and 48 h after SNPiP administration) revealed that SNPiP initially induced Wnt and cGMP-protein kinase G (PKG) signaling pathways, along with upregulation of genes involved in cardiac muscle tissue development and oxytocin signaling pathway. We also observed enrichment of glycolysis-related genes in response to SNPiP treatment, resulting in a metabolic shift from oxidative phosphorylation to glycolysis, which was suggested by reduced cardiac glucose contents while maintaining ATP levels. Additionally, SNPiP significantly upregulated atrial natriuretic peptide (ANP) and sarcolipin (SLN), which play crucial roles in calcium handling and cardiac performance. These findings suggest that SNPiP may have therapeutic potential based on the pleiotropic mechanisms elucidated in this study.

An extract from the frass of swallowtail butterfly (Papilio machaon) larvae inhibits HCT116 colon cancer cell proliferation but not other cancer cell types.

BACKGROUND: The frass of several herbivorous insect species has been utilised as natural medicines in Asia; however, the metabolite makeup and pharmaceutical activities of insect frass have yet to be investigated. Oligophagous Papilionidae insects utilise specific kinds of plants, and it has been suggested that the biochemicals from the plants may be metabolised by cytochrome P450 (CYP) in Papilionidae insects. In this study, we extracted the components of the frass of Papilio machaon larvae reared on Angelica keiskei, Oenanthe javanica or Foeniculum vulgare and examined the biological activity of each component. Then, we explored the expression of CYP genes in the midgut of P. machaon larvae and predicted the characteristics of their metabolic system. RESULTS: The components that were extracted using hexane, chloroform or methanol were biochemically different between larval frass and the host plants on which the larvae had fed. Furthermore, a fraction obtained from the chloroform extract from frass of A. keiskei-fed larvae specifically inhibited the cell proliferation of the human colon cancer cell line HCT116, whereas fractions obtained from the chloroform extracts of O. javanica- or F. vulgare-fed larval frass did not affect HCT116 cell viability. The metabolites from the chloroform extract from frass of A. keiskei-fed larvae prevented cell proliferation and induced apoptosis in HCT116 cells. Next, we explored the metabolic enzyme candidates in A. keiskei-fed larvae by RNA-seq analysis. We found that the A. keiskei-fed larval midgut might have different characteristics from the O. javanica- or F. vulgare-fed larval metabolic systems, and we found that the CYP6B2 transcript was highly expressed in the A. keiskei-fed larval midgut. CONCLUSIONS: These findings indicate that P. machaon metabolites might be useful as pharmaceutical agents against human colon cancer subtypes. Importantly, our findings show that it might be possible to use insect metabolic enzymes for the chemical structural conversion of plant-derived compounds with complex structures.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor 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.

Meta-Analysis of Heat-Stressed Transcriptomes Using the Public Gene Expression Database from Human and Mouse Samples.

Climate change has significantly increased the frequency of our exposure to heat, adversely affecting human health and industries. Heat stress is an environmental stress defined as the exposure of organisms and cells to abnormally high temperatures. To comprehensively explain the mechanisms underlying an organism's response to heat stress, it is essential to investigate and analyze genes that have been under-represented or less well-known in previous studies. In this study, we analyzed heat stress-responsive genes using a meta-analysis of numerous gene expression datasets from the public database. We obtained 322 human and 242 mouse pairs as the heat exposure and control data. The meta-analysis of these data identified 76 upregulated and 37 downregulated genes common to both humans and mice. We performed enrichment, protein-protein interaction network, and transcription factor target gene analyses for these genes. Furthermore, we conducted an integrated analysis of these genes using publicly available chromatin immunoprecipitation sequencing (ChIP-seq) data for HSF1, HSF2, and PPARGC1A (PGC-1α) as well as gene2pubmed data from the existing literature. The results identified previously overlooked genes, such as ABHD3, ZFAND2A, and USPL1, as commonly upregulated genes. Further functional analysis of these genes can contribute to coping with climate change and potentially lead to technological advancements.

Activation of transcription factor HIF inhibits IL-1ß-induced NO production in primary cultured rat hepatocytes.

Roxadustat and other hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHIs) have recently been approved for the treatment of chronic renal anemia. In macrophages and monocytes, the activation of HIF-1 by pro-inflammatory cytokines induces iNOS expression and activity through the NF-κB pathway to produce nitric oxide (NO), which causes liver injury when excessively produced. Few studies have reported a relationship between HIF activity and iNOS induction in hepatocytes. We investigated the effect of drug- and hypoxia-induced HIF activations on NO production in primary cultured rat hepatocytes. Roxadustat treatment and hypoxic conditions activated HIF. Contrary to expectations, HIF-PHI treatment and hypoxia inhibited IL-1ß-induced NO production. RNA-Seq analysis of mRNA expression in rat hepatocytes showed that roxadustat treatment decreased the expression of genes related to inflammation, and genes in the NF-κB signaling pathway were induced by IL-1ß. Moreover, roxadustat suppressed IL-1ß-activated signaling pathways in an HIF-dependent manner. GalN/LPS-treated rats were used as in vivo models of hepatic injury, and roxadustat treatment showed a tendency to suppress the death of rats. Therefore, exogenous HIF-1 activation, including HIF-PHI and hypoxia exposures, suppressed IL-1ß-induced iNOS mRNA expression and subsequent NO production in hepatocytes, by suppressing the NF-κB signaling pathway. Roxadustat treatment suppresses the expression of pro-inflammatory genes by activating HIF, and thus may exhibit hepatoprotective effects.

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution.

BACKGROUND: Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S rRNA gene analysis using the nanopore long-read sequencer MinION™. We compared it to the conventional short-read sequencing method in both a mock bacterial community and human fecal samples. RESULTS: We modified our existing protocol for full-length 16S rRNA gene amplicon sequencing by MinION™. A new strategy for library construction with an optimized primer set overcame PCR-associated bias and enabled taxonomic classification across a broad range of bacterial species. We compared the performance of full-length and short-read 16S rRNA gene amplicon sequencing for the characterization of human gut microbiota with a complex bacterial composition. The relative abundance of dominant bacterial genera was highly similar between full-length and short-read sequencing. At the species level, MinION™ long-read sequencing had better resolution for discriminating between members of particular taxa such as Bifidobacterium, allowing an accurate representation of the sample bacterial composition. CONCLUSIONS: Our present microbiome study, comparing the discriminatory power of full-length and short-read sequencing, clearly illustrated the analytical advantage of sequencing the full-length 16S rRNA gene.

GLIS1, a novel hypoxia-inducible transcription factor, promotes breast cancer cell motility via activation of WNT5A.

We previously demonstrated that expression of a Krüppel-like zinc finger transcription factor, GLIS1, dramatically increases under hypoxic conditions via a transcriptional mechanism induced by HIF-2α cooperating with AP-1 members. In this study, we focused on the functional roles of GLIS1 in breast cancer. To uncover its biological function, the effects of altered levels of GLIS1 in breast cancer cell lines on cellular growth, wound-healing and invasion capacities were assessed. Knockdown of GLIS1 using siRNA in BT-474 cells resulted in significant growth stimulation under normoxia, while attenuation was found in the cell invasion assay under hypoxic conditions. In MDA-MB-231 cells expressing exogenous 3xFLAG-tagged GLIS1, GLIS1 attenuated cell proliferation and enhanced cell mobility and invasion capacities under normoxia. In addition, breast cancer cells expressing GLIS1 acquired resistance to irradiation. Whole transcriptome analysis clearly demonstrated that downstream signals of GLIS1 are related to various cellular functions. Among the genes with increased expression, we focused on WNT5A. Knockdown of WNT5A indicated that enhancement of acquired cell motility in the MDA-MB-231 cells expressing GLIS1 was mediated, at least in part, by WNT5A. In an analysis of publicly available data, patients with estrogen receptor-negative breast cancer showing high levels of GLIS1 expression showed much worse prognosis than those with low levels. In summary, hypoxia-induced GLIS1 plays significant roles in breast cancer cells via regulation of gene expression related to cell migration and invasion capacities, resulting in poorer prognosis in patients with advanced breast cancer.

Apoptosis-mediated vasa down-regulation controls developmental transformation in Japanese Copidosoma floridanum female soldiers.

Copidosoma floridanum is a polyembryonic, caste-forming, wasp species. The ratio of investment in different castes changes with environmental stressors (e.g. multi-parasitism with competitors). The vasa gene was first identified in Drosophila melanogaster as a germ-cell-determining factor, and C. floridanum vasa (Cf-vas) gene positive cells have been known to develop into reproductive larvae. Cf-vas seems to control the ratio of investment in C. floridanum larval castes. In this study, we identified environmental factors that control Cf-vas mRNA expression in Japanese C. floridanum by examining Cf-vas mRNA expression under competitor (Meteorus pulchricornis) venom stress; we treated the male and female morulae with M. pulchricornis venom. We also assessed the effects of multi-parasitism of Japanese C. floridanum with M. pulchricornis and found an increasing number of female soldier larvae. The results showed that several amino acid sequences differ between the Japanese and US Cf-vas. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that Japanese Cf-vas mRNA is expressed in both male and female larvae and pupae, but mRNA expression decreases in adults. Cf-vas mRNA expression significantly decreased, while C. floridanum dronc (Cf-dronc) mRNA expression increased, in female morulae after M. pulchricornis venom treatment at 20 h and 0 h of the culture period, respectively. Females and males showed different Cf-vas or Cf-dronc mRNA expression after M. pulchricornis venom treatment. Therefore, M. pulchricornis venom could affect the ratio of investment in different female castes of Japanese C. floridanum by decreasing Cf-vas mRNA expression via apoptosis.

Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum.

BACKGROUND: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host insect; eventually, over 2000 individuals will arise from one egg. Previously, we reported that polyembryogenesis is enhanced when the juvenile hormone (JH) added to the culture medium in the embryo culture. Hence, in the present study, we performed RNA sequencing (RNA-Seq) analysis to investigate the molecular mechanisms controlling polyembryogenesis of C. floridanum. Functional annotation of genes is not fully available for C.floridanum; however, whole genome assembly has been archived. Hence, we constructed a pipeline for gene functional annotation in C. floridanum and performed molecular network analysis. We analyzed differentially expressed genes between control and JH-treated molura after 48 h of culture, then used the tblastx program to assign whole C. floridanum transcripts to human gene. RESULTS: We obtained 11,117 transcripts in the JH treatment group and identified 217 differentially expressed genes compared with the control group. As a result, 76% of C. floridanum transcripts were assigned to human genes. Gene enrichment analysis revealed genes associated with platelet degranulation, fatty acid biosynthesis, cell morphogenesis in the differentiation and integrin signaling pathways were fluctuated following JH treatment. Furthermore, Cytoscape analysis revealed a molecular interaction that was possibly associated with polyembryogenesis . CONCLUSIONS: We have constructed a pipeline for gene functional annotation of C. floridanum, and identified transcripts with high similarity to human genes during early embryo developmental. Additionally, this study reveals new molecular interactions associated with polyembryogenesis; these interactions could indicate the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis in human twins.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.

Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes.

BACKGROUND: Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. RESULTS: Enolase is an important glycolytic enzyme in all organisms. We used a combination of dry and wet bench processes to identify functional enolases in the silkworm Bombyx mori (BmEno). First, we detected five annotated enolases from public databases using a Hidden Markov Model (HMM) search, and then through cDNA cloning, Northern blotting, and RNA-seq analysis, we revealed three functional enolases in B. mori: BmEno1, BmEno2, and BmEnoC. BmEno1 contained a conserved key amino acid residue for metal binding and substrate binding in other species. However, BmEno2 and BmEnoC showed a change in this key amino acid. Phylogenetic analysis showed that BmEno2 and BmEnoC were distinct from BmEno1 and other enolases, and were distributed only in lepidopteran clusters. BmEno1 was expressed in all of the tissues used in our study. In contrast, BmEno2 was mainly expressed in the testis with some expression in the ovary and suboesophageal ganglion. BmEnoC was weakly expressed in the testis. Quantitative RT-PCR showed that the mRNA expression of BmEno2 and BmEnoC correlated with testis development; thus, BmEno2 and BmEnoC may be related to lepidopteran-specific spermiogenesis. CONCLUSIONS: We identified and characterized three functional enolases from public databases with a combination of dry and wet bench processes in the silkworm B. mori. In addition, we determined that BmEno2 and BmEnoC had species-specific functions. Our strategy could be helpful for the detection of minor genes and functional genes in non-model organisms from public databases.

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.

UNLABELLED: CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a ∼ 20 nt targeted sequence. The target sequence requirements are twofold. First, the 5'-NGG protospacer adjacent motif (PAM) sequence must be located adjacent to the target sequence. Second, the target sequence should be specific within the entire genome in order to avoid off-target editing. CRISPRdirect enables users to easily select rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. The server currently incorporates the genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. AVAILABILITY: Freely available at http://crispr.dbcls.jp/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.

In recent years, biological web resources such as databases and tools have become more complex because of the enormous amounts of data generated in the field of life sciences. Traditional methods of distributing tutorials include publishing textbooks and posting web documents, but these static contents cannot adequately describe recent dynamic web services. Due to improvements in computer technology, it is now possible to create dynamic content such as video with minimal effort and low cost on most modern computers. The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability.

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant RefSeq transcripts. A typical search takes just a few seconds, which dramatically enhances the usability of routine searching. In particular, GGRNA can search sequences as short as 10 nt or 4 amino acids, which cannot be handled easily by popular sequence analysis tools. Nucleotide sequences can be searched allowing up to three mismatches, or the query sequences may contain degenerate nucleotide codes (e.g. N, R, Y, S). Furthermore, Gene Ontology annotations, Enzyme Commission numbers and probe sequences of catalog microarrays are also incorporated into GGRNA, which may help users to conduct searches by various types of keywords. GGRNA web server will provide a simple and powerful interface for finding genes and transcripts for a wide range of users. All services at GGRNA are provided free of charge to all users.

Meta-analysis of public RNA sequencing data of abscisic acid-related abiotic stresses in Arabidopsis thaliana.

Abiotic stresses such as drought, salinity, and cold negatively affect plant growth and crop productivity. Understanding the molecular mechanisms underlying plant responses to these stressors is essential for stress tolerance in crops. The plant hormone abscisic acid (ABA) is significantly increased upon abiotic stressors, inducing physiological responses to adapt to stress and regulate gene expression. Although many studies have examined the components of established stress signaling pathways, few have explored other unknown elements. This study aimed to identify novel stress-responsive genes in plants by performing a meta-analysis of public RNA sequencing (RNA-Seq) data in Arabidopsis thaliana, focusing on five ABA-related stress conditions (ABA, Salt, Dehydration, Osmotic, and Cold). The meta-analysis of 216 paired datasets from five stress conditions was conducted, and differentially expressed genes were identified by introducing a new metric, called TN [stress-treated (T) and non-treated (N)] score. We revealed that 14 genes were commonly upregulated and 8 genes were commonly downregulated across all five treatments, including some that were not previously associated with these stress responses. On the other hand, some genes regulated by salt, dehydration, and osmotic treatments were not regulated by exogenous ABA or cold stress, suggesting that they may be involved in the plant response to dehydration independent of ABA. Our meta-analysis revealed a list of candidate genes with unknown molecular mechanisms in ABA-dependent and ABA-independent stress responses. These genes could be valuable resources for selecting genome editing targets and potentially contribute to the discovery of novel stress tolerance mechanisms and pathways in plants.

High expression of serine protease, Brachyurin in the posterior midgut of black soldier fly (Hermetia illucens) during horse dropping processing.

OBJECTIVE: Livestock droppings cause some environmental problems, but they have the potential to be used as effective biomass resources. The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is suitable for efficiently processing such resources. By using BSF larvae for the disposal of livestock droppings, we can obtain two valuable products: protein resources and organic fertilizer. However, there is insufficient research on the digestive enzymes suitable for processing this waste. Here, we aimed to construct an efficient BSF processing system using livestock droppings, and we explored the digestive enzymes involved in this process. RESULTS: First, we investigated the characteristics of transcripts expressed in the midgut of BSF larvae and found that immune response-related genes were expressed in the midgut. Then, we investigated digestive enzymes and identified a novel serine protease, HiBrachyurin, whose mRNA was highly expressed in the posterior midgut when BSF larvae fed on horse droppings. Despite the low protein content of horse droppings, larvae that fed on horse droppings accumulated more protein than those in the other groups. Therefore, HiBrachyurin may contribute to digestibility in the early stage of protein degradation in BSF larvae fed on horse droppings.

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 over two thousands of genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior are differed between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute our understanding of the molecular bases underlying progression of polyembryony. However, only the genome sequence of the US strain from generating by short-read assembly 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.