miRNA-1-3p is an early embryonic male sex-determining factor in the Oriental fruit fly Bactrocera dorsalis

Integrated transcriptomic analysis reveals potential ceRNA network and hub genes involved in sex determination and differentiation of the Pacific oyster (Crassostrea gigas)

Non-coding RNA (ncRNA) and competing endogenous RNA (ceRNA) network play vital roles in gene expression regulation, but their involvement in sex determination and differentiation remains unclear in molluscs. In this study, a comprehensive transcriptomic analysis was performed to investigate ncRNAs and ceRNA network in female and male gonads of Crassostrea gigas. Differential expression analysis identified 3496 mRNAs, 582 lncRNAs, 184 miRNAs, and 644 circRNAs with sex-biased expression. Functional enrichment analyses highlighted key pathways such as the cell cycle, oocyte meiosis, energy metabolism, and lipid metabolism, underscoring their involvement in sex determination and differentiation. A ceRNA network was constructed involving 398 lncRNAs, 119 circRNAs, 140 miRNAs, and 720 mRNAs. Hub genes, such as Fem1c, Spef1, Dgkq, Ppp1ca, Nkd1, Morn3, Dpf2, and Gabarap were identified, with pronounced sex-biased expression and localization in specific gonadal cell types, as revealed by bulk and single-nucleus RNA-seq analysis. These genes are associated with critical processes, including follicle development, spermatogenesis, and hormonal regulation. Collectively, these findings provide novel insights into the ceRNA-mediated regulatory mechanisms underlying sex determination and differentiation in C. gigas, contributing to a deeper understanding of molluscan reproductive biology.

Increased expression of an isoform of the long non-coding RNA, lnc37707, is associated with malathion resistance in Bactrocera dorsalis

The oriental fruit fly, Bactrocera dorsalis (Hendel) is an invasive pest threatening global fruit industries. Field populations of B. dorsalis exhibit complex insecticide resistance, hindering pest control efforts and exacerbating damage. Long non-coding RNAs (lncRNAs) are critical regulators of multiple bioprocess in insects, including insecticide resistance, and have potentials as novel target for pest management. Here, the candidate lncRNAs associated with malathion resistance in B. dorsalis were identified through RNA-seq. One of the isoforms of lnc37707, designated as lnc37707.10, was significantly enriched in the detoxification tissues of malathion-resistant (MR) strain. A specific fragment of lnc37707.10 (sflnc37707) was strongly associated with malathion resistance, and silencing sflnc37707 increased the susceptibility, whereas overexpressing it decreased susceptibility to malathion. Silencing sflnc37707 resulted in the down-regulation of 248 genes, but none of them included the four adjacent genes as its potential target. Instead, pathway analysis revealed significant enrichment of down-regulated genes involved in drug and xenobiotics metabolism, including P450s and GSTs. Bioinformatic analysis suggested a potential regulatory role of miRNA in the function of lnc37707. Further combining silence or overexpression sflnc37707 with miRNA mimic treatment identified that BdGSTd10 (an important gene involved in malathion resistance) and miR-1000 was strongly linked to lnc37707.10. Finally, a ceRNA (competing endogenous RNA) regulatory axis was proposed, where lnc37707.10 might indirectly modulate BdGSTd10 by sponging miR-1000 to regulate the malathion resistance in B. dorsalis. These findings provide a new insight into insecticide resistance and a potential lncRNA target for the sustainable pest management.

miR-NPs-RVG promote spinal cord injury repair: implications from spinal cord-derived microvascular endothelial cells

BACKGROUND

Spinal cord injury (SCI) often leads to a loss of motor and sensory function. Axon regeneration and outgrowth are key events for functional recovery after spinal cord injury. Endogenous growth of axons is associated with a variety of factors. Inspired by the relationship between developing nerves and blood vessels, we believe spinal cord-derived microvascular endothelial cells (SCMECs) play an important role in axon growth.

RESULTS

We found SCMECs could promote axon growth when co-cultured with neurons in direct and indirect co-culture systems via downregulating the miR-323-5p expression of neurons. In rats with spinal cord injury, neuron-targeting nanoparticles were employed to regulate miR-323-5p expression in residual neurons and promote function recovery.

CONCLUSIONS

Our study suggests that SCMEC can promote axon outgrowth by downregulating miR-323-5p expression within neurons, and miR-323-5p could be selected as a potential target for spinal cord injury repair.

miR-34 negatively regulates the expression of Dmrt and related genes in the testis of mud crab Scylla paramamosain

The mud crab (Scylla paramamosain) is a commercially significant marine decapod crustacean. Due to its obvious sexual dimorphism, the mechanism of sex differentiation and gonadal development has attracted significant research interest. The Dmrt (double-sex and mab-3 related transcription factor) genes are vital in animal gonadal development and sex differentiation. In the present study, miR-34 was predicted to target the 3' end of Dmrt-1, idmrt-2, Dmrt-3, Dsx and Dmrt-like genes by prediction software, and the interactions between miR-34 and these Dmrt genes were validated by in vivo and in vitro experiments. Dual luciferase assay results indicated that miR-34 mimics/inhibitors co-transfected with plasmid vectors with 3' end of Dmrt-1, idmrt-2, Dmrt-3, Dsx and Dmrt-like, respectively, led to a significant decrease/increase of fluorescence activity in HEK293T cells. In vivo experiments showed that injection of agomir-34 significantly inhibited Dmrt-1, idmrt-2, Dsx and Dmrt-like expression, while injection of antagomir-34 caused the opposite result. However, Dmrt-3 expression was not affected by injection of miR-34 reagents. Meanwhile, the expression of spermatogenesis and testicular development-related molecular marker genes (IAG, foxl2 and vasa) in mud crabs was significantly changed after injecting the miR-34 reagent in vivo. Furthermore, the result of immunoblotting proved that the expression level of Dmrt-like protein can be regulated by miR-34. These results imply that miR-34 is indirectly involved in sex differentiation and testicular development of S. paramamosain by regulating Dmrt-1, idmrt-2, Dsx and Dmrt-like genes.

The potential regulatory role of the non-coding RNAs in regulating the exogenous estrogen-induced feminization in Takifugu rubripes gonad

Estrogen plays a pivotal role in the early stage of sex differentiation in teleost. However, the underlying mechanisms of estrogen-induced feminization process are still needed for further clarification. Here, the comparative analysis of whole-transcriptome RNA sequencing was conducted between 17beta-Estradiol induced feminized XY (E-XY) gonads and control gonads (C) in Takifugu rubripes. A total of 57 miRNAs, 65 lncRNAs, and 4 circRNAs were found to be expressed at lower levels in control-XY (C-XY) than that in control-XX (C-XX), and were up-regulated in XY during E2-induced feminization process. The expression levels of 24 miRNAs, and 55 lncRNAs were higher in C-XY than that in C-XX, and were down-regulated in E2-treated XY. Furthermore, a correlation analysis was performed between miRNA-seq and mRNA-seq data. In C-XX/C-XY, 114 differential expression (DE) miRNAs were predicted to target to 904 differential expression genes (DEGs), while in C-XY/E-XY, 226 DEmiRNAs were predicted to target to 2,048 DEGs. In C-XX/C-XY, and C-XY/E-XY, KEGG pathway enrichment analysis showed that those targeted genes were mainly enriched in MAPK signaling, calcium signaling, steroid hormone biosynthesis and ovarian steroidogenesis pathway. Additionally, the competitive endogenous RNA (ceRNA) regulatory network was constructed by 24 miRNAs, 21 lncRNAs, 4 circRNAs and 5 key sex-related genes. These findings suggested that the expression of critical genes in sex differentiation were altered in E2-treated XY T. rubripes may via the lncRNA-miRNA-mRNA regulation network to facilitate the differentiation and maintenance of ovaries. Our results provide a new insight into the comprehensive understanding of the effects of estrogen signaling pathways on sex differentiation in teleost gonads.

Identification and functional verification of Y-chromosome-specific gene typo-gyf in Bactrocera dorsalis

Genes on the Y chromosome play important roles in male sex determination and development. The identification of Y-chromosome-specific genes not only provides a theoretical basis for the study of male reproductive development, but also offers genetic control targets for agricultural pests. However, Y-chromosome genes are rarely characterized due to their high repeatability and high heterochromatinization, especially in the oriental fruit fly. In this study, 1 011 Y-chromosome-specific candidate sequences were screened from 2 to 4 h Bactrocera dorsalis embryo datasets with the chromosome quotient method, 6 of which were identified as Y-chromosome-specific sequences by polymerase chain reaction, including typo-gyf, a 19 126-bp DNA sequence containing a 575-amino acid open reading frame. Testicular deformation and a significant reduction in sperm number were observed after typo-gyf knockdown with RNA interference in embryos. After typo-gyf knockout with clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR-associated protein 9 in the embryonic stage, the sex ratio of the emergent adults was unbalanced, with far more females than males. A genotype analysis of these females with the Y-chromosome gene MoY revealed no sex reversal. Typo-gyf knockout led to the death of XY individuals in the embryonic stage. We conclude that typo-gyf is an essential gene for male survival, and is also involved in testicular development and spermatogenesis. The identification of typo-gyf and its functional verification provide insight into the roles of Y-chromosome genes in male development.

Genome-wide analysis of Panonychus citri microRNAs with a focus on potential insecticidal activity of 4 microRNAs to eggs and nymphs

Panonychus citri McGregor (Acari: Tetranychidae), a destructive citrus pest, causes considerable annual economic losses due to its short lifespan and rapid resistance development. MicroRNA (miRNA)-induced RNA interference is a promising approach for pest control because of endogenous regulation of pest growth and development. To search for miRNAs with potential insecticidal activity in P. citri, genome-wide analysis of miRNAs at different developmental stages was conducted, resulting in the identification of 136 miRNAs, including 73 known and 63 novel miRNAs. A total of 17 isomiRNAs and 12 duplicated miRNAs were characterized. MiR-1 and miR-252-5p were identified as reference miRNAs for P. citri and Tetranychus urticae. Based on differential expression analysis, treatments with miR-let-7a and miR-315 mimics and the miR-let-7a antagomir significantly reduced the egg hatch rate and resulted in abnormal egg development. Overexpression or downregulation of miR-34-5p and miR-305-5p through feeding significantly decreased the adult eclosion rate and caused molting defects. The 4 miRNAs, miR-let-7a, miR-315, miR-34-5p, and miR-305-5p, had important regulatory functions and insecticidal properties in egg hatching and adult eclosion. In general, these data advance our understanding of miRNAs in mite biology, which can assist future studies on insect-specific miRNA-based green pest control technology.

microRNA-1 regulates sea urchin skeletogenesis by directly targeting skeletogenic genes and modulating components of signaling pathways

microRNAs are evolutionarily conserved non-coding RNAs that direct post-transcriptional regulation of target transcripts. In vertebrates, microRNA-1 (miR-1) is expressed in muscle and has been found to play critical regulatory roles in vertebrate angiogenesis, a process that has been proposed to be analogous to sea urchin skeletogenesis. Results indicate that both miR-1 inhibitor and miR-1 mimic-injected larvae have significantly less F-actin enriched circumpharyngeal muscle fibers and fewer gut contractions. In addition, miR-1 regulates the positioning of skeletogenic primary mesenchyme cells (PMCs) and skeletogenesis of the sea urchin embryo. Interestingly, the gain-of-function of miR-1 leads to more severe PMC patterning and skeletal branching defects than its loss-of-function. The results suggest that miR-1 directly suppresses Ets1/2, Tbr, and VegfR7 of the skeletogenic gene regulatory network, and Nodal, and Wnt1 signaling components. This study identifies potential targets of miR-1 that impacts skeletogenesis and muscle formation and contributes to a deeper understanding of miR-1's function during development.

Identification of testis development-related genes by combining Iso-Seq and RNA-Seq in Zeugodacus tau

Introduction: Zeugodacus tau (Walker) is an invasive pest. An effective method to control this pest is the sterile insect technique (SIT). To better apply this technique, it is necessary to understand testis development progression. Methods: Differentially expressed genes (DEGs) during testis development were analyzed by PacBio Iso-Seq and RNA-seq. Results: RNA-Seq library of Z. tau testes on day 1, 6, and 11 post eclosion were constructed. We identified 755 and 865 differentially expressed genes in the comparisons of T6 (testes on day 6) vs. T1 and T11 vs. T1, respectively. The KEGG pathway analysis showed that the DEGs were significantly enriched in retinol metabolism, vitamin B6 metabolism, and ascorbate and aldarate metabolism pathways. Knockdown of retinol dehydrogenase 12-like (rdh12-like), pyridoxal kinase (pdxk) and regucalcin (rgn), the representative gene in each of the above 3 pathways, reduced the hatching rate of Z. tau offspring. In addition, we identified 107 Drosophila spermatogenesis-related orthologous genes in Z. tau, of which innexin 2 (inx2) exhibited significantly up-regulated expression throughout testis development, and the knockdown of this gene reduced offspring hatching rate. Discussion: Our data indicated that rdh12-like, pdxk, rgn, and inx2 genes were related to testis development, and they were conserved in tephritid species. These results suggested that this gene might have the same function in tephritid. The findings provide an insight into testis development and spermatogenesis in tephritid species.

Histomorphic analysis and expression of mRNA and miRNA in embryonic gonadal differentiation in Chinese soft-shelled turtle (Pelodiscus sinensis)

The Chinese soft-shelled turtle (Pelodiscus sinensis) is extensively cultured in Asia for its nutritional and medical value. Gonadal differentiation is fantastic in turtles, whereas morphologic, mRNA, and miRNA expressions were insufficient in the turtle. In this study, ovaries and testes histomorphology analysis of 14-23 stage embryos were performed, and mRNA and miRNA expression profiles were analyzed. Histomorphology analysis revealed that gonads were undifferentiated at embryonic stage 14. Ovarian morphological differentiation became evident from stage 15, which was characterized by the development of the cortical region and degeneration of the medullary region. Concurrently, testicular morphological differentiation was apparent from stage 15, marked by the development of the medullary region and degeneration of the cortical region. qRT-PCR results showed that Cyp19a1 and Foxl2 exhibited female-specific expression at stage 15 and the expression increased throughout most of the embryonic development. Dmrt1, Amh, and Sox9 displayed male-specific expression at stage 15 and tended to increase substantially at later developmental stages. The expression of miR-8356 and miR-3299 in ZZ gonads were significantly higher than that in ZW gonads at stage 15, 17 and 19, and they had the highest expression at stage 15. While the expression of miR-8085 and miR-7982 had the highest expression at stage 19. Furthermore, chromatin remodeler genes showed differential expression in female and male P. sinensis gonads. These results of master sex-differentiation genes and morphological characteristics would provide a reference for the research of sex differentiation and sex reversal in turtles. Additionally, the expression of chromatin remodeler genes indicated they might be involved in gonadal differentiation of P. sinensis.

Up-regulated lncRNA CYLD as a ceRNA of miR-2383 facilitates bovine viral diarrhea virus replication by promoting CYLD expression to counteract RIG-I-mediated type-I IFN production

Bovine viral diarrhea virus (BVDV) is one of the most important pathogens of cattle, causing numerous economic losses to the cattle industry. To date, many potential mechanisms of BVDV evading or subverting innate immunity are still unknown. In this study, an lnc-CYLD/miR-2383/CYLD axis involved in BVDV-host interactions was screened from RNA-seq-based co-expression networks analysis of long noncoding RNAs, microRNAs and mRNAs in BVDV-infected bovine cells, and underlying mechanisms of lnc-CYLD/miR-2383/CYLD axis regulating BVDV replication were explored. Results showed that BVDV-induced up-regulation of the lnc-CYLD competed for binding to the miR-2383, and then promoted CYLD expression, thereby inhibiting RIG-I-mediated type-I interferon (IFN) production, which was subsequently confirmed by treatment with lnc-CYLD overexpression and miR-2383 inhibitor. However, miR-2383 transfection and small interfering RNA-mediated lnc-CYLD knockdown inhibited CYLD expression and enhanced RIG-I-mediated type-I IFN production, inhibiting BVDV replication. In addition, interaction relationship between lnc-CYLD and miR-2383, and colocalization relationship of lnc-CYLD, miR-2383 and CYLD were confirmed by dual-luciferase assay and in situ hybridization assay. Conclusively, up-regulation of the lnc-CYLD as a competing endogenous RNA binds to the miR-2383 to reduce inhibitory effect of the miR-2383 on the CYLD expression, playing an important role in counteracting type-I IFN-dependent antiviral immunity to facilitate BVDV replication.

The identification and expression pattern of the sex determination genes and their sex-specific variants in the egg parasitoid Trichogramma dendrolimi Matsumura (Hymenoptera: Trichogrammatidae)

Introduction: Trichogramma wasps are egg parasitoids of agricultural lepidopteran pests. The sex of Trichogramma is determined by its ploidy as well as certain sex ratio distorters, such as the endosymbiotic bacteria Wolbachia spp. and the paternal sex ratio (PSR) chromosome. The sex determination systems of hymenopterans, such as Trichogramma spp., involve cascades of the genes transformer (tra), transformer-2 (tra2), and doublesex (dsx) and are associated with sex-specific tra and dsx splicing. First, these genes and their sex-specific variants must be identified to elucidate the interactions between the sex ratio disorders and the sex determination mechanism of Trichogramma. Methods: Here, we characterized the sex determination genes tra, tra2, and dsx in Trichogramma dendrolimi. Sex-specific tra and dsx variants were detected in cDNA samples obtained from both male and female Trichogramma wasps. They were observed in the early embryos (1-10 h), late embryos (12-20 h), larvae (32 h and 48 h), pre-pupae (96 h), and pupae (144 h, 168 h, 192 h, and 216 h) of both male and female T. dendrolimi offspring. Results: We detected female-specific tra variants throughout the entire early female offspring stage. The male-specific variant began to express at 9-10 h as the egg was not fertilized. However, we did not find any maternally derived, female-specific tra variant in the early male embryo. This observation suggests that the female-specific tra variant expressed in the female embryo at 1-9 h may not have originated from the maternal female wasp. Discussion: The present study might be the first to identify the sex determination genes and sex-specific gene splicing in Trichogramma wasps. The findings of this study lay the foundation for investigating the sex determination mechanisms of Trichogramma and other wasps. They also facilitate sex identification in immature T. dendrolimi and the application of this important egg parasitoid in biological insect pest control programs.

Intersex is required for female sexual development in Hermetia illucens

Sex-determination pathways are extremely diverse. Understanding the mechanism of sex determination in insects is important for genetic manipulation of the pest population and for breeding of economically valuable insects. Although sex determination has been well characterized in the model species Drosophila melanogaster, little is known about this pathway in Stratiomyidae. In the present study, we first identified the Drosophila intersex (ix) homolog in Hermetia illucens, also known as the black soldier fly, which belongs to the Stratiomyidae family and which is an important insect for the conversion of various organic wastes. Phylogenetic analyses and multiple sequence alignment revealed that Hiix is conserved compared with Drosophila. We showed that Hiix is highly expressed in internal genitalia. Disruption of the Hiix gene using CRISPR/Cas9 resulted in female-specific defects in external genitalia and abnormal and undersized ovaries. Taken together, our study furthers our understanding of sex determination in insects and could facilitate breeding of H. illucens.

Identification and Characterization of Development-Related microRNAs in the Red Flour Beetle, Tribolium castaneum

MicroRNAs (miRNAs) play important roles in insect growth and development, but they were poorly studied in insects. In this study, a total of 883 miRNAs were detected from the early embryo (EE), late larva (LL), early pupa (EP), late pupa (LP), and early adult (EA) of Tribolium castaneum by microarray assay. Further analysis identified 179 differentially expressed unique miRNAs (DEmiRNAs) during these developmental stages. Of the DEmiRNAs, 102 DEmiRNAs exhibited stage-specific expression patterns during development, including 53 specifically highly expressed miRNAs and 20 lowly expressed miRNAs in EE, 19 highly expressed miRNAs in LL, 5 weakly expressed miRNAs in EP, and 5 abundantly expressed miRNAs in EA. These miRNAs were predicted to target 747, 265, 472, 234, and 121 genes, respectively. GO enrichment analysis indicates that the targets were enriched by protein phosphorylation, calcium ion binding, sequence-specific DNA binding transcription factor activity, and cytoplasm. An RNA interference-mediated knockdown of the DEmiRNAs tca-miR-6-3p, tca-miR-9a-3p, tca-miR-9d-3p, tca-miR-11-3p, and tca-miR-13a-3p led to defects in metamorphosis and wing development of T. castaneum. This study has completed the identification and characterization of development-related miRNAs in T. castaneum, and will enable us to investigate their roles in the growth and development of insect.

Systematic Characterization and Regulatory Role of lncRNAs in Asian Honey Bees Responding to Microsporidian Infestation

Long noncoding RNAs (lncRNAs) are pivotal regulators in gene expression and diverse biological processes, such as immune defense and host-pathogen interactions. However, little is known about the roles of lncRNAs in the response of the Asian honey bee (Apis cerana) to microsporidian infestation. Based on our previously obtained high-quality transcriptome datasets from the midgut tissues of Apis cerana cerana workers at 7 days post inoculation (dpi) and 10 dpi with Nosema ceranae (AcT7 and AcT10 groups) and the corresponding un-inoculated midgut tissues (AcCK7 and AcCK10 groups), the transcriptome-wide identification and structural characterization of lncRNAs were conducted, and the differential expression pattern of lncRNAs was then analyzed, followed by investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in host response. Here, 2365, 2322, 2487, and 1986 lncRNAs were, respectively, identified in the AcCK7, AcT7, AcCK7, and AcT10 groups. After removing redundant ones, a total of 3496 A. c. cerana lncRNAs were identified, which shared similar structural characteristics with those discovered in other animals and plants, such as shorter exons and introns than mRNAs. Additionally, 79 and 73 DElncRNAs were screened from the workers' midguts at 7 dpi and 10 dpi, respectively, indicating the alteration of the overall expression pattern of lncRNAs in host midguts after N. ceranae infestation. These DElncRNAs could, respectively, regulate 87 and 73 upstream and downstream genes, involving a suite of functional terms and pathways, such as metabolic process and Hippo signaling pathway. Additionally, 235 and 209 genes co-expressed with DElncRNAs were found to enrich in 29 and 27 terms, as well as 112 and 123 pathways, such as ABC transporters and the cAMP signaling pathway. Further, it was detected that 79 (73) DElncRNAs in the host midguts at 7 (10) dpi could target 321 (313) DEmiRNAs and further target 3631 (3130) DEmRNAs. TCONS_00024312 and XR_001765805.1 were potential precursors for ame-miR-315 and ame-miR-927, while TCONS_00006120 was the putative precursor for both ame-miR-87-1 and ame-miR-87-2. These results together suggested that DElncRNAs are likely to play regulatory roles in the host response to N. ceranae infestation through the regulation of neighboring genes via a cis-acting effect, modulation of co-expressed mRNAs via trans-acting effect, and control of downstream target genes' expression via competing endogenous RNA networks. Our findings provide a basis for disclosing the mechanism underlying DElncRNA-mediated host N. ceranae response and a new perspective into the interaction between A. c. cerana and N. ceranae.

MiRNA Profiling and Its Potential Roles in Rapid Growth of Velvet Antler in Gansu Red Deer (Cervus elaphus kansuensis)

A significant variety of cell growth factors are involved in the regulation of antler growth, and the fast proliferation and differentiation of various tissue cells occur during the yearly regeneration of deer antlers. The unique development process of velvet antlers has potential application value in many fields of biomedical research. Among them, the nature of cartilage tissue and the rapid growth and development process make deer antler a model for studying cartilage tissue development or rapid repair of damage. However, the molecular mechanisms underlying the rapid growth of antlers are still not well studied. MicroRNAs are ubiquitous in animals and have a wide range of biological functions. In this study, we used high-throughput sequencing technology to analyze the miRNA expression patterns of antler growth centers at three distinct growth phases, 30, 60, and 90 days following the abscission of the antler base, in order to determine the regulatory function of miRNA on the rapid growth of antlers. Then, we identified the miRNAs that were differentially expressed at various growth stages and annotated the functions of their target genes. The results showed that 4319, 4640, and 4520 miRNAs were found in antler growth centers during the three growth periods. To further identify the essential miRNAs that could regulate fast antler development, five differentially expressed miRNAs (DEMs) were screened, and the functions of their target genes were annotated. The results of KEGG pathway annotation revealed that the target genes of the five DEMs were significantly annotated to the "Wnt signaling pathway", "PI3K-Akt signaling pathway", "MAPK signaling pathway", and "TGF-β signaling pathway", which were associated with the rapid growth of velvet antlers. Therefore, the five chosen miRNAs, particularly ppy-miR-1, mmu-miR-200b-3p, and novel miR-94, may play crucial roles in rapid antler growth in summer.

RNA sequencing identifies an ovary-enriched microRNA, miR-311-3p, involved in ovarian development and fecundity by targeting Endophilin B1 in Bactrocera dorsalis

BACKGROUND

The oriental fruit fly, Bactrocera dorsalis, is a highly invasive pest in East Asia and the Pacific. With the development of pesticides resistance, environment-friendly pesticides are urgently needed. MicroRNAs (miRNAs) are critical regulators of numerous biological processes, including reproduction. Thus, it is significant to identify reproductive-related miRNAs in this notorious pest to facilitate its control, such as RNAi-based biopesticides targeting essential miRNAs.

RESULTS

A high-throughput sequencing was carried out to identify miRNAs involved in reproduction from the ovary and fat body at four developmental stages [1 day (d), 5, 9, and 13 days post-eclosion] in female B. dorsalis. Results showed that 98 and 74 miRNAs were differentially expressed in ovary and fat body, respectively, during sexual maturation. Gene ontology analysis showed that target genes involved in oogenesis and lipid particle accounted for 33% and 15% of the total targets, respectively. Among these differentially expressed miRNAs, we found by qPCR that miR-311-3p was enriched in the ovary and down-regulated during sexual maturation. Injection of agomir-miR-311-3p resulted in arrested ovarian development, reduced egg deposition and progeny viability. Endophilin B1 was confirmed to be the target of miR-311-3p, via dual-luciferase assay and expression profiling. Knockdown of Endophilin B1 resulted in reproductive defects similar to those caused by injection of miR-311-3p agomir. Thus, miR-311-3p might play a critical role in female reproduction by targeting Endophilin B1.

CONCLUSION

Our data not only provides knowledge on the abundance of reproductive-related miRNAs and target genes, but also promotes new control strategies for this pest. © 2022 Society of Chemical Industry.

miR-275/305 cluster is essential for maintaining energy metabolic homeostasis by the insulin signaling pathway in Bactrocera dorsalis

Increasing evidence indicates that miRNAs play crucial regulatory roles in various physiological processes of insects, including systemic metabolism. However, the molecular mechanisms of how specific miRNAs regulate energy metabolic homeostasis remain largely unknown. In the present study, we found that an evolutionarily conserved miR-275/305 cluster was essential for maintaining energy metabolic homeostasis in response to dietary yeast stimulation in Bactrocera dorsalis. Depletion of miR-275 and miR-305 by the CRISPR/Cas9 system significantly reduced triglyceride and glycogen contents, elevated total sugar levels, and impaired flight capacity. Combined in vivo and in vitro experiments, we demonstrated that miR-275 and miR-305 can bind to the 3'UTR regions of SLC2A1 and GLIS2 to repress their expression, respectively. RNAi-mediated knockdown of these two genes partially rescued metabolic phenotypes caused by inhibiting miR-275 and miR-305. Furthermore, we further illustrated that the miR-275/305 cluster acting as a regulator of the metabolic axis was controlled by the insulin signaling pathway. In conclusion, our work combined genetic and physiological approaches to clarify the molecular mechanism of metabolic homeostasis in response to different dietary stimulations and provided a reference for deciphering the potential targets of physiologically important miRNAs in a non-model organism.

Two Short Repeats in the 5′ Untranslated Region of Insulin-like Androgenic Gland Factor in Procambarus clarkii (PcIAG) That Regulate PcIAG Expression

Insulin-like androgenic gland factor (IAG) plays an important role in sex manipulation in decapods. Understanding the molecular regulation mechanism of IAG in Procambarus clarkii (PcIAG) is important for realizing its sex control. In this study, the promoter and gene structure of PcIAG, mRNA, and miRNA expression profiles after interfering with two siRNAs synthesized according to the two short repeats in the 5′ untranslated regions (5′UTR) of PcIAG were analyzed, and miRNAs of exosomes were investigated to explore the role of repeated sequences with tandem two short repeats located in the 5′UTR of PcIAG isolated from the androgenic gland (AG) in the regulation of IAG expression. The results showed that the repeated sequences of 5′UTR only occurred completely in the cDNA from AG, and the function of the two repeats was different in regulating the expression of PcIAG, in which the Wnt signaling pathway may be involved. Furthermore, we found that six miRNAs including miR-133, miR-193, miR-34, miR-1, miR-100, and let-7 might be involved in the regulation of the expression of PcIAG, wherein miR-133 might directly be related with the repeated sequences of 5′UTR.

Transcriptome analysis and screening of putative sex-determining genes in the invasive pest, Frankliniella occidentalis (Thysanoptera: Thripidae)

The invasive insect pest, Frankliniella occidentalis, is a well-known vector that transmits a variety of ornamental and vegetable viruses. The mechanistic basis of sex determination in F. occidentalis is not well understood, and this hinders our ability to deploy sterile insect technology as an integrated pest management strategy. In this study, six cDNA libraries from female and male adults of F. occidentalis (three biological replicates each) were constructed and transcriptomes were sequenced. A total of 6000 differentially-expressed genes were identified in the two sexes including 2355 up- and 3645 down-regulated genes. A total of 149 sex-related genes were identified based on GO enrichment data and included transformer-2 (tra2), fruitless (fru), male-specific lethal (msl) and sex lethal (sxl); several of these exhibited sex-specific and/or sex-biased expression in F. occidentalis. This study contributes to our understanding of the sex-determined cascade in F. occidentalis and other members of the Thysanoptera.

ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation

Competing endogenous RNAs (ceRNAs) are vital regulators of gene networks in mammals. The involvement of noncoding RNAs (ncRNAs) as ceRNA in genotypic sex determination (GSD) and environmental sex determination (ESD) in fish is unknown. The Chinese tongue sole, which has both GSD and ESD mechanisms, was used to map the dynamic expression pattern of ncRNAs and mRNA in gonads during sex determination and differentiation. Transcript expression patterns shift during the sex differentiation phase, and ceRNA modulation occurs through crosstalk of differentially expressed long ncRNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), and sex-related genes in fish. Of note was the significant up-regulation of a circRNA from the sex-determining gene dmrt1 (circular RNA dmrt1) and a lncRNA, called AMSDT (which stands for associated with male sex differentiation of tongue sole) in Chinese tongue sole testis. These two ncRNAs both share the same miRNA response elements with gsdf, which has an up-regulated expression when they bind to miRNA cse-miR-196 and concurrent down-regulated female sex-related genes to facilitate testis differentiation. This is the first demonstration in fish that ceRNA crosstalk mediated by ncRNAs modulates sexual development and unveils a novel regulatory mechanism for sex determination and differentiation.

The microRNAs in the antennae of Apolygus lucorum (Hemiptera: Miridae): Expression properties and targets prediction

MicroRNAs (miRNAs) regulate gene expression and contribute to numerous physiological processes. However, little is known about the functions of miRNAs in insect chemosensation. In this study, nine small RNA libraries were constructed and sequenced from the antennae of nymphs, adult males, and adult females of Apolygus lucorum. In total, 399 (275 known and 124 novel) miRNAs were identified. miR-7-5p_1 was the most abundant miRNA. Altogether, 69,708 target genes related to biogenesis, membrane, and binding activities were predicted. In particular, 15 miRNAs targeted 16 olfactory genes. Comparing the antennae of nymphs and adult males and females, 94 miRNAs were differentially expressed. Alternatively, a subset of differentially expressed miRNAs was verified by qPCR, supporting the reliability of the sequencing results. This study provides a global miRNA transcriptome for the antennae of A. lucorum and valuable information for further investigations of the functions of miRNAs in the regulation of chemosensation.

Early embryonic transcriptomes of Zeugodacus tau provide insight into sex determination and differentiation genes

Zeugodacus tau (Walker) is an invasive pest. The sterile insect technique is an environment-friendly method for pest control. Understanding the mechanism of sex determination will contribute to improving efficiency of this technique. In this study, we identified the transformer (tra) gene in Z. tau. One female-specific and two male-specific isoforms of tra were found in Z. tau, and the male-specific splicing pattern of tra was found to occur 5 h after egg laying. We performed transcriptome sequencing at 1 h (E1), 5 h (E5), and 9 h (E9) after egg laying and obtained high-quality transcriptome libraries of early embryo development. We identified 13 297 and 11 713 differentially expressed genes (DEGs) from E5 versus E1 and E9 versus E1 comparisons, respectively. To explore the potential functions of the DEGs during embryonic development, Gene Ontology, Clusters of Orthologous Groups of proteins, and Kyoto Encyclopedia of Genes and Genomes analyses were performed. Twenty-six genes potentially involved in sex determination or differentiation, including Maleness-on-the-Y (MoY), were identified in Z. tau. To verify the transcriptome results, 15 genes were selected for quantitative real-time PCR validation. The results were consistent with the transcriptome sequencing results. Moreover, U2 small nuclear riboprotein auxiliary factor (U2AF-50), female lethal d (fl(2)d), and virilizer (vir) were highly expressed at E5, indicating that they may be related to the sex-specific splicing of tra. Further functional analysis is needed to confirm this speculation. Our data provide an insight into the mechanism underlying sex determination and differentiation in tephritid species.

Identification and Characterization of MicroRNAs Involving in Initial Sex Differentiation of Chlamys farreri Gonads

Simple Summary

Sex formation of gonads encompasses two ancient and highly conserved biological processes, sex determination and sex differentiation. The processes are strictly regulated by a complex of gene networks. There is increasing evidence that miRNAs play key roles in many biological processes. however, information is limited in their contribution to sex differentiation in animals. In the present study, we identified the novel miRNAs involved in sex-related genes regulation and explored the miRNA–mRNA networks underlying the posttranscriptional regulation during the initial sex differentiation in Zhikong scallop, Chlamys farreri. Our findings provide an important basis for studying the sex differentiation mechanisms, as well as developing sex control techniques in bivalves.

Abstract

Research on expressional regulation of genes at the initial sex differentiation of gonads will help to elucidate the mechanisms of sex determination and differentiation in animals. However, information on initial sex differentiation of gonads is limited in bivalves. MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that can regulate the target gene expression at the posttranscription level by degrading the mRNA or repressing the mRNA translation. In the present study, we investigated the small RNAs transcriptome using the testes and ovaries of Zhikong scallop Chlamys farreri juveniles with a shell height of 5.0 mm, a critical stage of initial sex differentiation of gonads. A total of 75 known mature miRNAs and 103 novel miRNAs were identified. By comparing the expression of miRNAs between the ovary and testis, 11 miRNAs were determined to be differentially expressed. GO annotations and KEGG analyses indicated that many putative target genes that matched to these differentially expressed miRNAs participated in the regulation of sex differentiation. Furthermore, two selected miRNAs, cfa-novel_miR65 and cfa-miR-87a-3p_1, were confirmed to downregulate expressions of Foxl2 (a female-critical gene) and Klf4 (a male-critical gene), respectively, using a dual-luciferase reporter analysis. Our findings provided new insights into the initial sex differentiation of gonads regulated by miRNAs in bivalves.

Regulatory roles of three miRNAs on allergen mRNA expression in Tyrophagus putrescentiae

BACKGROUND

Tyrophagus putresecentiae is an important mite species in rural and urban environments, causing sensitization and allergic disease. While evidence suggests that microRNAs (miRNAs) may regulate the expression of allergen-encoding genes, no study has directly investigated this possibility. Here, this gap was addressed by profiling miRNAs and elucidating their target allergen messenger RNAs (mRNAs) in this mite species.

METHODS

Small RNA and transcriptome libraries were constructed for eggs, larvae, nymphs, and adults. After deep miRNA and whole-transcriptome sequencing were performed, the miRNA and allergen-encoding mRNA regulatory networks were explored.

RESULTS

A total of 540 miRNAs were identified, including 155 with expression levels differing significantly across the four mite developmental stages (p < .01), 59 of which were novel. The mRNA expression for allergens was higher for Tyr p 1 in adults than in other developmental stages; Tyr p 2-5, 7, 10, 13, 33, and 34 in immature stages; and Tyr p 28, 35, and 36 in eggs and adults. A combined miRNA and transcriptome bioinformatics analysis showed that allergen Tyr p 3 was regulated by miRNA PC-5p-5698441_1, Tyr p 4 was regulated by PC-5p-7050653_1, and Tyr p 34 was regulated by PC-5p-5534223_1 and PC-5p-5698441_1. These three allergen mRNA and three miRNAs were identified using qRT-PCR, and their regulatory roles were confirmed by double-fluorescent reporter gene system and site-directed mutagenesis technology.

CONCLUSIONS

For the first time, allergen mRNA expression and miRNAs were profiled throughout the life cycle for an allergen-producing mite, and the results showed that miRNAs bind to target allergen mRNAs to regulate their expression.

Identification and characterization of microRNAs in the immature stage of the beneficial predatory bug Arma chinensis Fallou (Hemiptera: Pentatomidae)

MicroRNAs (miRNAs) are a type of small noncoding RNAs that regulate gene expression at the posttranscriptional level and can influence significant biological processes. Arma chinensis (Hemiptera: Pentatomidae) is a predaceous insect species that preys upon a wide variety of insect pests. It is important to explore and understand the molecular mechanisms involving miRNAs in regulating developmental and other gene expression for beneficial insects. However, examination of miRNAs associated with Hemiptera, especially predatory bugs, has been absent or scarce. This study represents the first comprehensive analysis of predatory bug A. chinensis encoded miRNAs through high throughput sequencing and predicts genes and biological processes regulated by the newly identified miRNAs through analyzing their differential expression in and across five nymphal instars. A total of 64 A. chinensis miRNAs, including 46 conserved miRNAs and 18 novel miRNAs, were identified by analysis of high throughput sequence reads mapped to the genome. A total of 2913 potential gene targets for these 64 miRNAs were predicted by comprehensive analyses utilizing miRanda, PITA, and RNAhybrid. Gene Ontology annotation of predicted target genes of A. chinensis suggested the key processes regulated by miRNAs involved biological processes, regulation of cellular processes, and transporter activity. Kyoto Encyclopedia of Genes and Genomes pathway predictions included the Toll and Imd signaling pathway, Valine, leucine and isoleucine degradation, Steroid biosynthesis, the AGE-RAGE signaling pathway in diabetic complications, and Alanine, aspartate and glutamate metabolism. This newly identified miRNAs through analyzing their differential expression, assessment of their predicted functions forms a foundation for further investigation of specific miRNAs.

Introduction of a cold sensitivity-conferring mutation into the RTA-Bddsx hybrid system of Bactrocera dorsalis for establishment of a thermally controllable homozygous line

BACKGROUND

For efficient control of the economically important fruit pest Bactrocera dorsalis, a hybrid system combining ricin toxicity and sex-related alternative splicing of the doublesex gene has been developed. This system exhibits the expected female-specific lethal effect; however, the transgenic females do not survive, making it difficult to raise stable homozygous lines. Since modification of ricin toxin A chain (RTA) through a single-residue change (Gly²¹² > Arg²¹² ) leads to cold-sensitive posttranslational repression of its toxicity, we utilized this unique property to obtain RTA-Bddsx females that survive at low temperature for line maintenance.

RESULTS

In transient expression experiments using embryonic injection, two groups treated with RTAcs-derived DNA (LERQcs and RTAcs) exhibited temperature-dependent effects. The toxicity was higher at 29 °C than at 18 °C. The proportion of males was close to 50% at 18 °C in all the tested groups except LERQcs-treated flies, which exhibited a high proportion of males (over 70%) at 29 °C. The results indicate the cold-sensitive responses of RTA and further suggest a female-specific lethal effect. Subsequently, 14 putative RTAcs-Bddsx transgenic Ds-Red⁺ G₁ males were identified, and female-specific lethal effects were observed in Ds-Red⁺ G₂ and G₃ lines under cultivation at 29 °C but not at 18 °C. The male ratio can be increased to up to 95% in G₃ line 001, indicating that RTAcs functions well in B. dorsalis.

CONCLUSION

The improved RTAcs-Bddsx system with conditional toxicity represents a novel and promising step toward the practical control of B. dorsalis. © 2021 Society of Chemical Industry.

Regulatory roles of microRNAs in insect pests: prospective targets for insect pest control

At the post-transcriptional level, microRNAs (miRNAs) play an important role in the regulation of gene expression, thereby influencing the outcome of many biological processes in insects, such as development, reproduction, metamorphosis, immunity, and insecticide resistance. The alteration of miRNA expression by mimic/agomir or inhibitor/antagomir via injection/feeding can lead to pest developmental abnormalities, death, or reduced pesticide resistance, indicating that miRNAs are potential targets for pest control. This review provides an overview of recent advances in understanding the regulatory roles of miRNA in agricultural and public health insect pest, and further highlights the potential of miRNAs as prospective targets in pest control.

Evolution of sexual development and sexual dimorphism in insects

Most animal species consist of two distinct sexes. At the morphological, physiological, and behavioral levels the differences between males and females are numerous and dramatic, yet at the genomic level they are often slight or absent. This disconnect is overcome because simple genetic differences or environmental signals are able to direct the sex-specific expression of a shared genome. A canonical picture of how this process works in insects emerged from decades of work on Drosophila. But recent years have seen an explosion of molecular-genetic and developmental work on a broad range of insects. Drawing these studies together, we describe the evolution of sexual dimorphism from a comparative perspective and argue that insect sex determination and differentiation systems are composites of rapidly evolving and highly conserved elements.

Ultrasensitive multiplexed detection of miRNA targets of interest based on encoding probe extension in improved cDNA library

MicroRNAs (miRNAs) are a class of regulatory small RNA molecules that play critical roles in a wide variety of biological processes. Abnormally expressed miRNAs have been increasingly utilized as biomarkers for cancer diagnosis. Generally, a specific cancer is associated with expression alterations of several species of miRNAs and different types of cancers are related to different miRNA species. Therefore, a universal method for multiplexed detection of miRNA targets of interest is now desirable for cancer diagnosis. In this paper, by adding an enzymatic digestion step to reduce the nonspecific adaptor dimers, we firstly improved the method to construct cDNA library of all miRNAs, which greatly increased the cDNA yield. By specifically designing DNA probes to hybridize with the cDNAs at key positions and doubly encoding DNA probes with different lengths and different fluorophores during single-base extension, each miRNA could produce a unique product, which could be separated and detected by capillary electrophoresis. Thus, miRNA targets of interest could be simultaneously detected with great specificity at single-base resolution. By using seventeen randomly selected miRNAs as the model, as low as 1.0 fM of each miRNA target could be simultaneously determined. Furthermore, we had achieved accurate analysis of multiple miRNAs in real biological RNA samples and found that several miRNAs expressed differently between cancer cells and normal cells, indicating that the proposed method had the ability to pick out aberrant expression miRNAs in real biological samples. Compared with high-throughput sequencing methods, the proposed method is simpler and specific, and very suitable for the detection of specific miRNAs associated with a disease, which shows great potential for cancer diagnosis.

Downregulation of miR-3934 in Peripheral Blood Mononuclear Cells of Asthmatic Patients and Its Potential Diagnostic Value

Background

The present study focused on the potential clinical significance of miR-3934 in the occurrence and development of asthma.

Methods

80 asthma and 80 healthy controls were recruited in this study. The peripheral blood mononuclear cells (PBMCs) and serum samples of the asthma patients as well as the healthy controls were isolated, and the expression levels of miR-3934 in PBMCs were examined by RT-qPCR methods. Furthermore, the relationship between the level of miR-3934 in PBMCs and the disease severity has been analyzed, and the potential diagnostic value of miR-3934 was evaluated by the receiver operating characteristics (ROC) curve. Finally, the expression level of IL-6, IL-8, and IL-33 have been detected using the ELISA kits, and Pearson's correlation analysis was performed to investigate the relationship between the level of miR-3934 in PBMCs and the serum expression of those inflammatory cytokines in asthma patients.

Results

miR-3934 was dramatically decreased in PBMCs of the asthma patients, and miR-3934 was markedly reduced in PBMCs of patients with severe asthma vs. mild asthma. Furthermore, ROC analysis showed that levels of miR-3934 in PBMCs can distinguish asthma patient, especially the severe asthma patients from the controls. Finally, the levels of miR-3934 in PBMCs were negatively correlated with the serum levels of IL-6, IL-8, and IL-33 in asthma patients, respectively.

Conclusions

miR-3934 was downregulated in PBMCs of asthmatic patients and may function as a potential diagnosis biomarker.

Identification and profiling of Bactrocera dorsalis microRNAs and their potential roles in regulating the developmental transitions of egg hatching, molting, pupation and adult eclosion

MicroRNAs (miRNAs) are endogenous small noncoding RNAs (18-25 nt) that are involved in many physiological processes including development, cancer, immunity, apoptosis and host-microbe interactions through post-transcriptional regulation of gene expression. In this study, we measured the profile of small RNAs over the developmental transitions of the oriental fruit fly Bactrocera dorsalis from egg hatching, molting, and pupation to adult eclosion. We identified 250 miRNAs, including 83 known and 167 novel miRNAs, and 47 isomiRNAs. In addition, we identified the miRNAs differentially expressed over the developmental transitions. Interestingly, the miR-309 cluster, the miR-2 cluster/family and the let-7 cluster were among these differentially expressed miRNAs, suggesting a role in the regulation of egg hatching, molting and pupation/adult eclosion, respectively. Moreover, a detailed analysis of the temporal expression patterns of 14 highly expressed miRNAs in the pupal stage revealed three types of expression profiles. Furthermore, injection of a miR-100 mimic in the 3rd instar larvae resulted in a significant decrease in pupation and adult eclosion rates, whereas injection of a miR-317 antagomir resulted in a significant decrease in the pupation rate and a decrease in the pupation time, indicating that miR-100 and miR-317 are involved in the process of pupation. Finally, injection of a miR-100/miR-285 mimic or antagomir in pupae resulted in a significant decrease in the eclosion rate and a significant increase in the prevalence of a partial eclosion phenotype, implying the involvement of miR-100 and miR-285 in the process of adult eclosion. This study identified critical miRNAs involved in the transitions of this important holometabolic model and pest insect B. dorsalis from egg hatching to adult eclosion, thus providing a useful resource for exploring the regulatory role of miRNAs during insect post-embryonic development.

miR-1: A comprehensive review of its role in normal development and diverse disorders

MicroRNA-1 (miR-1) is a conserved miRNA with high expression in the muscle tissues. In humans, two discrete genes, MIRN1-1 and MIRN1-2 residing on a genomic region on 18q11.2 produce a single mature miRNA which has 21 nucleotides. miR-1 has a regulatory role on a number of genes including heat shock protein 60 (HSP60), Kruppel-like factor 4 (KLF4) and Heart And Neural Crest Derivatives Expressed 2 (HAND2). miR-1 has critical roles in the physiological processes in the smooth and skeletal muscles as well as other tissues, thus being involved in the pathogenesis of a wide range of disorders. Moreover, dysregulation of miR-1 has been noted in diverse types of cancers including gastric, colorectal, breast, prostate and lung cancer. In the current review, we provide the summary of the data regarding the role of this miRNA in the normal development and the pathogenic processes.

The transformer-2 and fruitless characterisation with developmental expression profiles of sex-determining genes in Bactrocera dorsalis and B. correcta

Sex determination in tephritid fruit flies involves a signaling cascade of alternatively spliced genes. The Transformer (TRA) and Transformer-2 (TRA-2) complex establishes an autoregulatory loop switching sex-specific splicing of tra pre-mRNA in females. The TRA/TRA-2 complex also regulates the sex-specific splicing of downstream effector genes, doublesex (dsx) and fruitless (fru). In Ceratitis capitata, a Maleness-on the-Y (MoY) gene modulates sex-specifically spliced Cctra pre-mRNA and results in the breakdown of the Cctra autoregulatory loop in males. In this study, the tra-2 and fru genes were characterised in two key pests, Bactrocera dorsalis and B. correcta. The tra-2 genes showed high degrees of conservation among tephritids. The complex gene organisation for each of Bdfru and Bcfru were identified. There are sex-specific and non sex-specific transcripts generated by alternative promoters as found in Drosophila melanogaster and other insects. RNAi knockdown of Bdtra transcripts showed that BdTRA controls the sex-specific splicing of Bddsx and Bdfru pre-mRNAs. Developmental expression analysis shows that multiple splice variants of Bdtra and Bctra RNAs are present before and during cellular blastoderm formation and that the mature sex-specific variants become fixed later in embryogenesis. Furthermore, the Bddsx^M splice variants are found in early embryos at the beginning of gastulation, but Bdfru^M does not appear until the larval stage. We proposed that the zygotic tra loop is initiated in both female and male embryos before becoming automatised or abolished by MoY, respectively.