Biology subjects

Bono, H.

Publications and source records attributed to Bono, H..

At least 37 records · Page 2Linked to original sources

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↗

bioRxiv2024

Meta-analysis of public RNA-sequencing data of drought and salt stresses in different phenotypes of Oryza sativa

Environmental stresses, such as drought and salt, adversely affect plant growth and crop productivity. While many studies have focused on established components of stress signaling pathways, research on unknown elements remains limited. In this study, we collected RNA sequencing (RNA-Seq) data from Oryza sativa registered in public databases and conducted a meta-analysis integrating multiple studies. We analyzed 105 paired RNA-Seq datasets from resistant or susceptible Oryza sativa cultivars under salt and drought conditions to identify novel stress-responsive genes with common expression changes across these datasets. A meta-analysis identified 10 genes specifically upregulated in resistant cultivars and 12 specifically upregulated in susceptible cultivars under both drought and salt conditions. Furthermore, by comparing previously identified stress-responsive genes in Arabidopsis thaliana, we explored genes potentially involved in stress response mechanisms that are conserved across plant species. The genes identified in this data-driven study may serve as targets for future research and genome editing.

plant biology↗

bioRxiv2024

Transcriptional Signatures of Domestication Revealed by Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data

Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as "upregulated," "downregulated," or "unchanged" based on their DW-ratio, and DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications. Simple SummaryDomesticated animals, such as pigs and chickens, have undergone significant genetic changes compared to their wild ancestors. We collected gene expression data from pigs, chickens, wild boars, and red junglefowl, and performed a comprehensive analysis. We identified differentially expressed genes by comparing the gene expression patterns of domesticated animals and their wild counterparts. These genes are involved in various biological processes, including immune response, metabolism, and stress response. Notably, domesticated animals exhibited higher expression of genes related to viral resistance and bone weakness, whereas their wild ancestors showed higher expression of genes associated with stress response and energy metabolism. Identifying these differentially expressed genes provides valuable insights into the genetic changes that occurred during the domestication process. Furthermore, these findings have highlighted potential candidate genes that could be targeted in breeding programs to improve the health and productivity of domesticated animals, ultimately contributing to the development of sustainable livestock production and addressing the growing global food demand.

zoology↗

bioRxiv2024

PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing

BackgroundTracking of Insertions and DEletions (TIDE) analysis, which computationally deconvolves capillary sequencing data derived from the DNA of bulk or clonal cell populations to estimate the efficiency of targeted mutagenesis by programmable nucleases, has played a significant role in the field of genome editing. However, the detection range covered by conventional TIDE analysis is limited. Range extension for deconvolution is required to detect larger deletions and insertions (indels) derived from genome editing in TIDE analysis. However, extending the deconvolution range introduces uncertainty into the deconvolution process. Moreover, the accuracy and sensitivity of TIDE analysis tools for large deletions (>50 bp) remain poorly understood. ResultsIn this study, we introduced a new software called PtWAVE that can detect a wide range of indel sizes, up to 200 bp. PtWAVE also offers options for variable selection and fitting algorithms to prevent uncertainties in the model. We evaluated the performance of PtWAVE by using in vitro capillary sequencing data that mimicked DNA sequencing, including large deletions. Furthermore, we confirmed that PtWAVE can stably analyze trace sequencing data derived from actual genome-edited samples. ConclusionsPtWAVE demonstrated superior accuracy and sensitivity compared to the existing TIDE analysis tools for DNA samples, including large deletions. PtWAVE can accelerate genome editing applications in organisms and cell types in which large deletions often occur when programmable nucleases are applied.

molecular biology↗

bioRxiv2024

A systematic exploration of unexploited genes for oxidative stress in Parkinson's disease

Human disease-associated gene data are accessible through databases, including the Open Targets Platform, DisGeNET, miRTex, RNADisease, and PubChem. However, missing data entries in such databases are anticipated because of factors, such as errors/biases by curators and text mining failures. Additionally, the extensive research on human diseases has resulted in challenges to register comprehensive data. The lack of essential data in databases hinders knowledge sharing and should be addressed. Therefore, we propose an analysis pipeline to explore missing entries of unexploited genes in the human disease-associated gene databases. To demonstrate this, we used the pipeline for genes in Parkinsons disease with oxidative stress, which revealed two unexploited genes: nuclear protein 1 (NUPR1) and ubiquitin-like with PHD and ring finger domains 2 (UHRF2). The proposed methodology and findings facilitate the identification of disease-associated genes that are not completely represented in existing databases, thereby facilitating easier access to the potential human disease-related functional genes.

bioinformatics↗

bioRxiv2024

Time-course transcriptome data of silk glands in day 0-7 last-instar larvae of Bombyx mori (w1 pnd strain)

Time-course transcriptome expression data were constructed for four parts of the silk gland (anterior, middle, and posterior parts of the middle silk gland, along with the posterior silk gland) in the domestic silkworm, Bombyx mori, from days 0 to 7 of the last-instar larvae. For sample preparation, silk glands were extracted from one female and one male larva every 24 hours accurately after the fourth ecdysis. The reliability of these transcriptome data was confirmed by comparing the transcripts per million (TPM) values of the silk gene and quantitative reverse transcription PCR results. Hierarchical cluster analysis results supported the reliability of transcriptome data. These data are likely to contribute to the progress in molecular biology and genetic research using B. mori, such as elucidating the mechanism underlying the massive production of silk proteins, conducting entomological research using a meta-analysis as a model for lepidopteran insect species, and exploring medical research using B. mori as a model for disease species by utilising transcriptome data.

molecular biology↗

bioRxiv2024

Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework

Plants produce structurally diverse triterpenes (triterpenoids and steroids). Their biosynthesis occurs from a common precursor, namely 2,3-oxidosqualene, followed by cyclization catalyzed by oxidosqualene cyclases (OSCs) to yield various triterpene skeletons. Steroids, which are biosynthesized from cycloartenol or lanosterol, are essential primary metabolites in most plant species, along with lineage-specific steroids, such as steroidal glycoalkaloids found in the Solanum species. Other diverse triterpene skeletons are converted into triterpenoids, often classified as specialized compounds that are biosynthesized only in a limited number of plant species with tissue-or cell-type-specific accumulation in plants. Recent studies have identified various tailoring enzymes involved in the structural diversification of triterpenes as well as transcription factors that regulate the expression of these enzymes. However, the coverage of these proteins is scarce in publicly available databases for curated proteins or enzymes, which complicates the functional annotation of newly assembled genomes or transcriptome sequences. Here, we created the Triterpene RDF, a manually curated database of enzymes and transcription factors involved in plant triterpene biosynthesis. The database (https://github.com/ktamura2021/triterpene_rdf/) contains 526 proteins, with links to the UniProt Knowledgebase or NCBI protein database, and it enables direct download of a set of protein sequences filtered by protein type or taxonomy. Triterpene RDF will enhance the functional annotation of enzymes and regulatory elements for triterpene biosynthesis, in a current expansion of availability of genomic information on various plant species.

plant biology↗

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↗

bioRxiv2023

Genome assembly reconstruction of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae), using homology-based assembly and nanopore long-reads

Honey bees are important for agriculture (e.g., pollination and honey production). Additionally, honey bees are an important insect model species, especially as model social insects. The Japanese honey bee, Apis cerana japonica (a subspecies of the Asian honey bee, Apis cerana), is a Japanese domestic honey bee, which has several subspecies-specific traits. We previously constructed the draft genome sequence data of A. cerana japonica, but it needed to be improved considering the use of the genome sequence data for genome structural analysis and repetitive region analysis, as well as the availability of chromosome-level genome data of A. mellifera and A. cerana. In this study, we constructed the improved A. cerana japonica genome data and new gene set data with functional annotations. The constructed genome data, including 16 pseudochromosomes, was found to be highly contiguous and complete, and the gene set data covered most of the core genes in the BUSCO database. Thus, the constructed genome and gene set data have become more suitable as the reference data of A. cerana japonica.

genomics↗

bioRxiv2023

Meta-analysis of gonadal transcriptomes in protogynous fishes provides novel perspective into sex change machinery

Protogyny, being capable of changing from female to male during their lifetime, is prevalent in 20 families of teleosts but is believed to have evolved within specific evolutionary lineages. Therefore, shared regulatory factors governing the sex change process are expected to be conserved across protogynous fishes. However, a comprehensive understanding of this mechanism remains elusive. To identify these factors, we conducted a meta-analysis using gonadal transcriptome data from seven species. We curated data pairs of ovarian tissue and transitional gonad, and employed ratios of expression level as a unified criterion for differential expression, enabling a meta-analysis across species. Our approach revealed that classical sex change-related genes exhibited differential expression levels between the ovary and transitional gonads, consistent with previous reports. These results validate our methodologys robustness. Additionally, we identified novel genes not previously linked to gonadal sex change in fish. Notably, changes in the expression levels of acetoacetyl-CoA synthetase and apolipoprotein Eb, which are involved in cholesterol synthesis and transport, respectively, suggest that the levels of cholesterol, a precursor of steroid hormones crucial for sex change, are decreased upon sex change onset in the gonads. This implies a potential universal influence of cholesterol dynamics on gonadal transformation in protogyny.

zoology↗

bioRxiv2023

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 SNPiP-treated samples, indicating a metabolic shift from oxidative phosphorylation to glycolysis following SNPiP administration in the hearts. 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.

molecular biology↗

bioRxiv2023

Meta-analysis of heat-stressed transcriptomes using the public gene expression database from human and mouse samples

BackgroundClimate change has significantly increased the frequency of exposure to heat, adversely affecting human health and various industrial sectors. Heat stress is an environmental stress defined as the exposure of organisms and cells to abnormally high temperatures. Heat-stress research has predominantly focused on response systems involving heat shock factors acting as transcription factors and heat shock proteins functioning as molecular chaperones. However, to comprehensively elucidate the mechanisms underlying an organisms response to heat stress, it is essential to investigate and analyze genes that have been underrepresented, less well-known, or overlooked in previous studies. In this study, we analyzed heat stress-responsive genes using a meta-analysis of numerous gene expression datasets. ResultsFirst, we collected paired heat exposure and control data from public databases. Gene expression data were obtained for 322 human and 242 mouse pairs. The expression ratios (HN-ratios) of the collected pairs were calculated, and the identification of upregulated and downregulated expression profiles was determined according to defined thresholds. The number of upregulated and downregulated genes was calculated as the heat stress - non-treatment score (HN-score), which is the value of: [number of upregulated genes] - [number of downregulated genes] for each gene and was used as the index of analysis. The HN-score comprehensively evaluated gene expression variation, and 76 upregulated and 37 downregulated genes common to human and mouse were identified. We performed enrichment, protein-protein interaction network, and transcription factor target gene analyses. Furthermore, we evaluated the extracted genes through integrated analysis using publicly available ChIP-seq data for HSF1, HSF2, and PPARGC1A (PGC1-), and gene2pubmed data, which were sourced from previous literature. The results identified previously overlooked genes, such as ABHD3, ZFAND2A, and USPL1, as commonly upregulated genes. ConclusionsBased on the findings of this study, further functional analysis of the extracted genes using genome editing and other technologies has the potential to contribute to coping with climate change and potentially lead to new knowledge and technological advances.

molecular biology↗

bioRxiv2023

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 on 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.

plant biology↗

bioRxiv2023

DANGER analysis: Risk-averse on/off-target assessment for CRISPR editing without a reference genome

The CRISPR-Cas9 system has successfully achieved site-specific gene editing in organisms ranging from humans to bacteria. The technology efficiently generates mutants, allowing for phenotypic analysis of the on-target gene. However, some conventional studies did not investigate whether deleterious off-target effects partially affect the phenotype. Herein, we present a novel phenotypic assessment of CRISPR-mediated gene editing: Deleterious and ANticipatable Guides Evaluated by RNA-sequencing (DANGER) analysis. Using RNA-seq data, this bioinformatics pipeline can elucidate genomic on/off-target sites on mRNA-transcribed regions related to expression changes and then quantify phenotypic risk at the gene ontology (GO) term level. We demonstrated the risk-averse on/off-target assessment in RNA-seq data from gene-edited samples of human cells and zebrafish brains. Our DANGER analysis successfully detected off-target sites, and it quantitatively evaluated the potential contribution of deleterious off-targets to the transcriptome phenotypes of the edited mutants. Notably, DANGER analysis harnessed de novo transcriptome assembly to perform risk-averse on/off-target assessments without a reference genome. Thus, our resources would help assess genome editing in non-model organisms, individual human genomes, and atypical genomes from diseases and viruses. In conclusion, DANGER analysis facilitates the safer design of genome editing in all organisms with a transcriptome.

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

Reference genome sequences of Mythimna separata (Lepidoptera: Noctuidae)

Lepidopteran insects are an important group of animals, among which some are used as biochemical and physiological model species in the insect and silk industries, whereas others are major agricultural pests. Therefore, genome sequences of several lepidopteran insects have been reported thus far. The oriental armyworm, Mythimna separata, is an agricultural pest commonly used to study insect immune reactions and interactions with parasitoid wasps as hosts. To improve our understanding of these research topics, reference genome sequences were constructed in the present study. Using long-read and short-read sequence data, de novo assembly and polishing were performed, and haplotigs were purged. Subsequently, gene predictions and functional annotations were performed. To search for orthologs of the Toll and immune deficiency (IMD) pathways and C-type lectins, annotation data analysis, BLASTp, and Hummer scans were performed. The M. separata genome is 682 Mbp; its contig N50 was 2.7 Mbp with 21,970 genes and 24,452 coding sites predicted. All orthologs of the core components of the Toll and IMD pathways and 105 C-type lectins were identified. These results suggest that the genome data were of sufficient quality as reference genome data and could contribute to promoting M. separata and lepidopteran research at the molecular and genome levels. Simple SummaryThe oriental armyworm, Mythimna separata, an agricultural pest, is commonly used to study insect immune reactions and interactions with parasitoid wasps. To promote such studies, a reference genome was constructed. The M. separata genome is 682Mbp long--a size comparable to that of other lepidopteran insects. The contig N50 value of the genome is 2.7 Mb, which indicates sufficient quality to be used as reference genome data. Gene set data were constructed using genome and RNA-sequencing data; a total of 21,970 genes and 24,452 coding sites were predicted. Functional gene annotation was performed using the predicted amino acid sequences and reference gene set data of the model organism and other insect species as well as Unigene and Pfam datasets. Consequently, 45-80% of the amino acid sequences were annotated using these data sets. Using these data, most of the orthologs of core components in the Toll and immune deficiency (IMD) pathways were identified, suggesting the presence of these two pathways in M. separata. Additionally, 105 C-type lectins were identified in the M. separata genome, which were more numerous than those in other insect species, suggesting that these genes may be duplicated.

bioinformatics↗

bioRxiv2022

A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan

Perilla frutescens (Lamiaceae) is an important herbal plant with hundreds of bioactive chemicals, among which perillaldehyde and rosmarinic acid are the two major bioactive compounds in the plant. The leaves of red perilla are used as traditional Kampo medicine or food ingredients. However, the medicinal and nutritional uses of this plant could be improved by enhancing the production of valuable metabolites through the manipulation of key enzymes or regulatory genes using genome editing technology. Here, we generated a high-quality genome assembly of red perilla domesticated in Japan. A near-complete chromosome level assembly of P. frutescens was generated contigs with N50 of 41.5 Mb from PacBio HiFi reads. 99.2% of the assembly was anchored into 20 pseudochromosomes, among which seven pseudochromosomes consisted of one contig, while the rest consisted of less than six contigs. Gene annotation and prediction of the sequences successfully predicted 86,258 gene models, including 76,825 protein-coding genes. Further analysis showed that potential targets of genome editing for the engineering of anthocyanin pathways in P. frutescens are located on the late-stage pathways. Overall, our genome assembly could serve as a valuable reference for selecting target genes for genome editing of P. frutescens.

plant biology↗

bioRxiv2022

Meta-analysis of the public RNA-Seq data of the Western honeybee Apis mellifera to construct reference transcriptome data

The Western honeybee (Apis mellifera) is valuable in biological research and agriculture. Its genome sequence was published before those for other insect species. RNA-Seq data for A. mellifera have been applied in several recently published studies. Nevertheless, these data have not been prepared for use in subsequent meta-analyses. To promote A. mellifera transcriptome analysis, we constructed reference transcriptome data using the reference genome sequence and RNA-Seq data curated from about 1,000 runs of public databases. The new reference transcriptome data construct comprised 149,685 transcripts, and 194,174 protein sequences were predicted. About 50-60% of the predicted protein sequences were functionally annotated using the protein sequence data for several model and insect species. Novel candidate immune-related transcripts were searched by meta-analysis using immune response-related RNA-Seq and reference transcriptome data. Three to 20 candidate transcripts including autophagy related protein 3 were upregulated or downregulated in response to both viral and bacterial infections. The constructed reference transcriptome data may facilitate future transcriptome analyses of A. mellifera. Simple SummaryThe honeybee is an economically and ecologically essential insect species and a critical social behavior model. It is vital to honey production and pollinates. Therefore, it has been studied extensively in entomological research. The Western honeybee (Apis mellifera) is a representative species of honeybees. The reference transcriptome data are required to perform the meta-analyses using public RNA-Seq data and transcriptome analysis using newly sequenced RNA-Seq data. The reference transcriptome sequences was constructed, which consisted of 149,685 transcripts, and 194,174 predicted amino acid sequences. Half the predicted protein sequences were functionally annotated using protein sequence datasets for several model and insect species. We performed meta-analysis to search for novel immune response-related transcripts. We identified 3-20 transcripts that were upregulated or downregulated in response to both viral and bacterial infections. However, the immune-related transcripts were not included among them. Autophagy related protein 3 was downregulated by viral infections. The results suggested that autophagy was implicated in the viral immune responses, and autophagy was not regulated by the canonical immune pathways in A. mellifera. The results of the meta-analysis suggested that the reference transcriptome data could be used for transcriptome analysis in A. mellifera.

bioinformatics↗