Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum
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 Functional annotation of genes is not fully available for C.floridanum; however, whole genome assembly has been archived.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.
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 .
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.
KeywordsPolyembryony Xanthine dehydrogenase/oxidase Endoparasitoid Polyembryogenesis Copidosoma floridanum
Differentially expressed genes
Retinoid X receptor
Sensitive factor attachment protein receptor
Transcripts per kilobase million
The development of a single-cell egg into a multicellular organism begins with cell cleavage; however, polyembryogenesis—in which many embryos are produced from one egg—occurs in some species. Although identical twins are representative examples of human polyembryogenesis, the incidence of this situation is as low as 0.3% . Armadillos (Dasypus) are the only mammals to exhibit obligatory polyembryony, developing from one egg to four individuals through embryonic shield separation [2, 3]. Owing to the ethical limitations of experiments with animal, the phenomenon of polyembryogenesis remains poorly studied.
Furthermore, the occurrence of polyembryogenesis has been reported for insects such as the endoparasitic wasps Braconidae, Dryinidae, Platygasteridae, and Encyrtidae, and research on developmental patterns has progressed rapidly in recent years . The identification of molecules associated with polyembryogenesis could further our understanding of the mechanisms underlying the regulation of this process in animals.
Previously, we reported polyembryogenesis to be accelerated by exposure to juvenile hormone (JH) or the JH analog methoprene, under culture conditions . Although the molecular function of JH in the embryogenesis of C. floridanum remains unclear, we anticipated that either JH or methoprene would promote the progress of polyembryogenesis from the two-cell to polymorula stage. Functional annotation of genes is not fully available for C. floridanum; however, whole-genome sequence data is available. Thus, we were unable to analyze the molecular networks in C. floridanum as has been done for Drosophila melanogaster, a model insect. Accordingly, we constructed a pipeline for gene functional annotation of C. floridanum and performed molecular network analysis focusing on gene expression following polyembryony development in response to JH treatment in the two-cell developmental stage. We also performed RNA sequencing (RNA-Seq) analysis of C. floridanum as a model animal for polyembryogenesis to elucidate the molecular mechanisms underlying this process.
Juvenile hormone accelerates polyembryogenesis
Impact of polyembryogenesis by the juvenile hormone treatment to the early embryo of Copidosoma floridanum
Day of polymorula
Rate of polymorula (%)
4.88 ± 0.13
3.16 ± 0.23
Identification of differentially expressed genes and assignment of human homolog
Next, we assessed the number of C. floridanum genes by comparing our transcript dataset with the C. floridanum RefSeq datasets. Of the 11,117 transcripts in our C. floridanum RNA-Seq datasets, 9417 were present in the C. floridanum RefSeq datasets (84.7% coverage). We identified 6098 human homologs out of the 11,117 total transcripts of C. floridanum using tblastx with a cutoff E-value of 1e–10. Of the 217 DEGs that we identified, 88 corresponded to human genes (Additional file 1: Table S1).
Gene enrichment analysis of differentially expressed genes
For the gene enrichment analysis using Metascape, we needed to assign human gene IDs to C. floridanum genes IDs. Thus, we chose C.floridanum 88 genes, which have sequence similarity to human genes. Of 88 genes that were chosen to compare expression between the two groups, the expression of 42 genes was increased in the JH-treated group, whereas 46 were downregulated following JH treatment. We imported the list of DEGs and their expression levels into Metascape and converted to their human homologs for gene enrichment analysis. Metascape generated 12 genetic function groups for Gene Ontology (GO), indicating that upregulated genes in the JH-treated group were assigned to platelet degranulation (GO:0002576) and fatty acid biosynthetic process (GO:0006633) (Fig. 4b). Furthermore, Metascape indicated that downregulated genes in the JH-treated group were assigned to cell morphogenesis was involved in differentiation (GO: 0000904) and ST Integrin Signaling Pathway (M3270) (Fig. 4c).
Screening for related molecules using the molecular network analysis by Cytoscape
We investigated gene expression during polyembryogenesis of embryos of C. floridanum treated with JH in the two-cell stage. Additionally, we constructed a pipeline for functional gene annotation of C. floridanum and performed molecular network analysis.
Our previous study revealed that JH and methoprene accelerate polyembryogenesis; a phenomenon that was also observed when JH I or JH II were added to the culture medium . Methoprene had the strongest effect on promotion of polyembryogenesis, while farnesol, farnesyl acetate, and methyl caproate did not promote polyembryogenesis . Moreover, polyembryogenesis was not promoted by ecdysone (Additional file 2: Figure S1). Hence, only JH or methoprene promote polyembryogenesis in C. floridanum.
The insect hormone JH is unique in its structure; it has α-, and β-unsaturated methyl ester groups and epoxy groups at both ends of the terpenoid backbone . The importance of JH in processes such as regulation of molting, pheromone biosynthesis, maturation of gonads, egg development, homeostasis, maintenance of population, and body color change has been reported . Thus, JH is a critical element of insect physiology.
Krüppel homolog 1 (Kr-h1) is a JH-responsive gene . Kr-h1 was not affected by JH in this study (Additional file 3: Figure S2). Retinoid X receptor (RXR), a type of nuclear receptor that binds to 9-cis retinoic acid , may be able to bind to several chemicals that share the structure of retinoic acid . Reportedly, the JH analog methoprene and methoprene acid can bind to RXR , which also functions as a JH receptor in D. melanogaster . In this study, the expression of C. floridanum RXR-alpha-B tended to be increased following JH treatment (Additional file 3: Figure S2). Retinoic acid is involved in embryonic development and cell differentiation through its interaction with RXR . This suggests that JH could act in a similar manner to retinoic acid to affect embryonic development and participate in the retinoic acid signaling pathway in our model of polyembryony.
Additionally, C. floridanum RefSeq datasets were constructed by analyzing male and female adult C. floridanum transcriptome. A reference genome sequence of C. floridanum from male has been published (https://www.ncbi.nlm.nih.gov/assembly/GCF_000648655.2/). Overall, 17,038 of the estimated proteins have been registered in the NCBI Genome database (https://www.ncbi.nlm.nih.gov/genome/12734?genome_assembly_id=358239).
Previously, we identified human homologs of Bombyx mori and D. melanogaster through systematic BLAST analysis. We found B. mori and D. melanogaster to contain 58 and 63% of human homologs, respectively . In the present study, we found, C. floridanum exhibits 76% gene similarity with humans. The large number of human homologs that we observed in C. floridanum is therefore comparable with these model insects. In the present study, 88 C. floridanum genes that showed differential expression when comparing JH-treated and control groups corresponded to human genes, and we input these genes to gene enrichment and molecular network analyses.
Gene enrichment analysis revealed the expression of lipid metabolism-related (GO: 0006633) and platelet degranulation (GO: 0002576) related genes were upregulated in the JH-treated group. The characteristics of genes containing these GO terms have been shown to be involved with vesicle-associated V-soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) in cellular membrane adhesion . Additionally, genes encoding synaptosomal-associated protein (SNAP)25 and 29, (SNAPC) 3 and 4, SNARE-associated protein Snapin (SNAPIN), and syntaxin-binding protein (STXBP) were shown to be commonly expressed in both groups of the present study. Reportedly, these genes are involved in the membrane fusion of neurosecretory cells . Notably, STXBP interacts with these proteins to inactivate membrane fusion . Thus the decreased mRNA expression of STXBP that we observed following JH treatment may lead to activation of cellular membrane fusion. As the molura promotes fusion with the extraembryonic syncytium, it is possible that JH treatment could accelerate morula to polyembrogenesis.
The genes SNAP25 and SNAP29, SNAPC3 and SNAPC4, SNAPIN, and STXBP, which we observed to be expressed in C. floridanum morula embryos, also play a role for mediates membrane fusion during exocytosis in the neurosecretory cells of humans . Therefore, C. floridanum might employ similar molecular mechanisms for cellular membrane adhesion as human neurosecretory cells.
The morula comprises the outer extraembryonic syncytium and the inner embryonic cell; the extraembryonic syncytium separates by dividing the embryonic cell . Embryonic cells adhere to the extraembryonic syncytium via integrin in the morula. When integrin expression is decreased following exposure to JH, this adhesion may be loose, causing the extraembryonic syncytium to invaginate into the cell gap of embryonic cells. These cells might then divide, resulting in polyembryony. The actin filament crosslinking protein, FLNA, which is present in non-muscle cells  might be involved in the division of embryos interacting with SSH2 and ITGA4. Reportedly, SSH2 mediates actin dynamics , while ITGA4 belongs to the integrin family and plays a role in cell adhesion . These molecular interactions might contribute to the polyembryony.
Xanthine dehydrogenase/oxidase is the rate-limiting enzyme of purine metabolism, and a key component in uric acid synthesis. During egg development of B. mori the amount of uric acid gradually declines until blastokinesis, after which it increases until egg pigmentation . Remarkably, XHD knockdown has been shown to enhance cell mobility and invasion of HepG2 cells, although no effect on cell proliferation was observed . Furthermore, XDH converts retinoic acid to 9-cis retinal , and activity of the enzyme is essential in order for JH to induce bristle formation and cuticle production on the abdominal epidermis during pupal and adult development .
In this study, we constructed a pipeline for gene functional annotation of C. floridanum. We identified C. floridanum transcripts with high similarity with several human genes during early embryogenesis, and found that C. floridanum has many more human homologs than D. melanogaster. Additionally, we identified new molecular interactions associated with polyembryogenesis, which may enable the elucidatation of the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis for the investigation of polyembryogenesis of humans. In future studies, we intend to investigate the function of these molecules using RNAi in C. floridanum.
We obtained C. floridanum from parasitized T. intermixta larvae from burdock fields in Tokyo, Chiba, and Ibaraki Prefectures. Larvae were maintained with an artificial diet  at 25 °C with a 16- h light/8-h dark cycle. T. intermixta adults were fed a 10% sugar solution absorbed with cotton. C. floridanum adults were fed a 50% honey solution absorbed with cotton. We used T. intermixta eggs within 17 h post-oviposition for parasitism by C. floridanum. The parasitized hosts were kept in the same conditions as non-parasitized hosts.
We dissected the two-cell stage of the embryo from T. intermixta eggs within 2-h post-oviposition and, then, cultured it with the modified MGM medium . We dissolved JH III (J2000; Sigma-Aldrich Co. Ltd., Munich, Germany) in ethanol to prepare a stock solution (10 mg/mL); then, 1 μL of this stock solution was added to the modified MGM medium as the final concentration was 1 μg/mL. In the control group, an equivalent volume of ethanol alone was added to the culture medium. We used two-cell stage embryos produced from T. intermixta eggs within 2 h of oviposition for the control group (experimental 1, n = 10; experimental 2, n = 25; experimental 3, n = 21) and the JH group (experimental 1, n = 10; experimental 2, n = 24, experimental 3, n = 23).
We isolated total RNA from morulae cultured for 2 days in control (experimental 1, n = 24; experimental 2, n = 16; experimental 3, n = 11), and JH conditions (experimental 1, n = 17; experimental 2, n = 28; experimental 3, n = 23) using a combination of TRIzol® LS Reagent and the PureLink® RNA Extraction Kit (Thermo Fisher Scientific Inc., Valencia, CA) per the manufacturer’s instructions. Then, we used an Agilent TapeStation 2200 (Agilent Technologies, Santa Clara, CA) to assess the RNA quality. Additionally, single-end sequencing cDNA libraries were constructed with 100 ng of total RNA from these samples (control group: n = 3; JH group: n = 3) with a TruSeq® Stranded mRNA Sample Preparation Kit (Illumina Inc., San Diego, CA) per the manufacturer’s instructions. Next, libraries were sequenced (75 bp, single-end) on the Illumina NextSeq500 platform, and FASTQ files were assessed by Trim Galore! v0.4.5 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Sequencing of the JH group of experimental 3 was not possible as the creation of a library for RNA-Seq failed. Thus, we omitted the data of this group. Finally, we analyzed gene expression using three biological replicates in the control group and two biological replicates in the JH group. Notably, the C. floridanum genome (GCF_000648655.2) sequence is available in the NCBI Genome database (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Copidosoma_floridanum/101/). The obtained FASTQ sequence files were aligned to the genomic reference sequence by HISAT2 v2.1.0 with default parameters . Next, SAM files were converted to BAM files by Samtools v1.8 . Using StringTie v1.3.4, we estimated the transcript abundance, and the count data were extracted by Subread v1.6.0 [34, 35]. All statistical analyses were performed using R software version 3.4.3 (https://www.r-project.org). To normalize the data and compare the control and JH-treated groups, we used the TCC and DEseq2 packages . We generated a scatter plot using TIBCO Spotfire Desktop v7.6.0 with the “Better World” program license (TIBCO Spot re, Inc., Palo Alto, CA; http://spotfire.tibco.com/better-world-donation-program/). Furthermore, the sequence data (FASTQ files) were deposited to the DDBJ Sequence Read Archive (accession numbers DRR138914-DRR138918).
C. floridanum gene functional annotation pipeline for molecular network analysis
The transcripts were extracted from the C. floridanum genome using gffread software (https://github.com/gpertea/gffread). To annotate C. floridanum gene, we identified genes homologous to those of human by conducting a systematic BLAST search (tblastx) with a cutoff E-value of significant similarity at 1e–10 (query: C. floridanum cDNA sequence; database: whole human cDNA sequence set from Ensembl database). Using the generated assignment table, we reconstructed conserved pathways common to C. floridanum and humans by projecting C. floridanum genes onto the human pathway.
Gene enrichment analysis and pathway analysis
We performed the gene enrichment analysis using Metascape (http://metascape.org/); a gene list for Metascape analysis was generated from the TCC output. Then, we performed the molecular network analysis using IntAct Molecular Interaction Database (https://www.ebi.ac.uk/intact/) and Cytoscape v3.6.1 (http://www.cytoscape.org). We converted the gene IDs from the C. floridanum RNA-Seq data to human Ensembl IDs, using the assignment table described above and, then, input the list of genes obtained from the RNA-Seq data into Cytoscape to obtain the significant molecular interactions with corresponding E values.
We thank to Dr. Madoka Nakai, Tokyo University of Agriculture and Technology for helpful discussion.
Conceived and designed the experiments: TS, HT, and KI. Performed the experiments: TS and MN. Contributed reagents/materials/analysis tools: JY, KI, and HT. Analyzed the data: TS, HB, TN and HT. Contributed to the writing of the paper under draft version: TS and HT. All authors discussed the data and helped with manuscript preparation. KI and HT supervised the project. All authors read and approved the final manuscript.
This work was supported by JSPS KAKENHI grant number JP15H02483 to KiI, JY and HT, 15H04420 to JY, 26257405 to JY, 18H02212 to HT.
The funders declare that they have no role for the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.
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The authors declare that they have no competing interests.
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