Stage-specific transcription during development of Aedes aegypti

Full-length transcriptome-referenced analysis reveals developmental and olfactory regulatory genes in Dermestes frischii

Dermestes frischii Kugelann, 1792 is a storage pest worldwide, and is important for estimating the postmortem interval in forensic entomology. However, because of the lack of transcriptome and genome resources, population genetics and biological control studies on D. frischii have been hindered. Here, single-molecule real-time sequencing and next-generation sequencing were combined to generate the full-length transcriptome of the five developmental stages of D. frischii, namely egg, young larva, mature larva, pupa and adult. A total of 41,665 full-length non-chimeric sequences and 59,385 non-redundant transcripts were generated, of which 42,756 were annotated in public databases. Using the weighted gene co-expression network analysis, gene co-expression modules related to the five developmental stages were constructed and screened, and the genes in these modules were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The expression patterns of the differentially expressed genes (DEGs) related to olfaction and insect hormone biosynthesis were also explored. Transcription of most odorant binding proteins was up-regulated in the adult stage, suggesting they are important for foraging in adults. Many genes encoding for the ecdysone-inducible protein were up-regulated in the pupal stage, may be mainly responsible for the tissue remodelling of metamorphosis. The results of the quantitative real-time polymerase chain reaction (qRT-PCR) were consistent with the RNA-seq results. This is the first full-length transcriptome sequencing of dermestids, and the data obtained here are vital for understanding the stage-specific development and olfactory system of D. frischii, providing valuable resources for storage pest and forensic research.

Intrapuparial stage aging and PMI estimation based on the developmental transcriptomes of forensically important Aldrichina grahami (Diptera: Calliphoridae) gene expression

Background

The expression profiles of differentially expressed genes (DEGs) during pupal development have been demonstrated to be vital in age estimation of forensic entomological study. Here, using forensically important Aldrichina grahami (Diptera: Calliphoridae), we aimed to explore the potential of intrapuparial stage aging and postmortem interval (PMI) estimation based on characterization of successive developmental transcriptomes and gene expression patterns.

Methods

We collected A. grahami pupae at 11 successive intrapuparial stages at 20 °C and used the RNA-seq technique to build the transcriptome profiles of their intrapuparial stages. The DEGs were identified during the different intrapuparial stages using comparative transcriptome analysis. The selected marker DEGs were classified and clustered for intrapuparial stage aging and PMI estimation and then further verified for transcriptome data validation. Ultimately, we categorized the overall gene expression levels as the dependent variable and the age of intrapuparial A. grahami as the independent variable to conduct nonlinear regression analysis.

Results

We redefined the intrapuparial stages of A. grahami into five key successive substages (I, II, III, IV, and V), based on the overall gene expression patterns during pupal development. We screened 99 specific time-dependent expressed genes (stage-specific DEGs) to determine the different intrapuparial stages based on comparison of the gene expression levels during the 11 developmental intrapuparial stages of A. grahami. We observed that 55 DEGs showed persistent upregulation during the development of intrapuparial A. grahami. We then selected four DEGs (act79b, act88f, up and ninac) which presented consistent upregulation using RT-qPCR (quantitative real-time PCR) analysis, along with consideration of the maximum fold changes during the pupal development. We conducted nonlinear regression analysis to simulate the calculations of the relationships between the expression levels of the four selected DEGs and the developmental time of intrapuparial A. grahami and constructed fitting curves. The curves demonstrated that act79b and ninac showed continuous relatively increasing levels.

Conclusions

This study redefined the intrapuparial stages of A. grahami based on expression profiles of developmental transcriptomes for the first time. The stage-specific DEGs and those with consistent tendencies of expression were found to have potential in age estimation of intrapuparial A. grahami and could be supplementary to a more accurate prediction of PMI.

Gene coexpression network during ontogeny in the yellow fever mosquito, Aedes aegypti

BACKGROUND

The behaviors and ontogeny of Aedes aegypti are closely related to the spread of diseases caused by dengue (DENV), chikungunya (CHIKV), Zika (ZIKV), and yellow fever (YFV) viruses. During the life cycle, Ae. aegypti undergoes drastic morphological, metabolic, and functional changes triggered by gene regulation and other molecular mechanisms. Some essential regulatory factors that regulate insect ontogeny have been revealed in other species, but their roles are still poorly investigated in the mosquito.

RESULTS

Our study identified 6 gene modules and their intramodular hub genes that were highly associated with the ontogeny of Ae. aegypti in the constructed network. Those modules were found to be enriched in functional roles related to cuticle development, ATP generation, digestion, immunity, pupation control, lectins, and spermatogenesis. Additionally, digestion-related pathways were activated in the larvae and adult females but suppressed in the pupae. The integrated protein‒protein network also identified cilium-related genes. In addition, we verified that the 6 intramodular hub genes encoding proteins such as EcKinase regulating larval molt were only expressed in the larval stage. Quantitative RT‒PCR of the intramodular hub genes gave similar results as the RNA-Seq expression profile, and most hub genes were ontogeny-specifically expressed.

CONCLUSIONS

The constructed gene coexpression network provides a useful resource for network-based data mining to identify candidate genes for functional studies. Ultimately, these findings will be key in identifying potential molecular targets for disease control.

Dynamics of maternal gene expression in Rhodnius prolixus

The study of developmental processes in Rhodnius prolixus has recently advanced with the sequencing of the genome. In this work, we analyze the maternal gene expression driving oogenesis and early embryogenesis in R. prolixus. We examined the transcriptional profile of mRNAs to establish the genes expressed across the ovary, unfertilized eggs and different embryonic stages of R. prolixus until the formation of the germ band anlage (0, 12, 24, and 48 h post egg laying). We identified 81 putative maternal and ovary-related genes and validated their expression by qRT-PCR. We validate the function of the ortholog gene Bicaudal-D (Rp-BicD) by in situ hybridization and parental RNAi. Consistent with a role in oogenesis and early development of R. prolixus, we show that lack of Rp-BicD does not significantly affect oogenesis but impairs the formation of the blastoderm. Based on our findings, we propose three times of action for maternal genes during oogenesis and embryogenesis in R. prolixus.

Development of the transcriptome for a sediment ecotoxicological model species, Chironomus dilutus

Chironomus dilutus is a prominent model species in conventional sediment toxicity testing and sediment contamination diagnosis. However, lack of genomic data significantly limited its application in identifying toxicological mode of action (MOA) and molecular biomarkers of toxicants. Here the transcriptome of C. dilutus in full life span and both sexes (1st, 2nd, 3rd and 4th instar larvae, pupae, and adults) were developed and temporal gene expression across adjacent life stages were investigated to understand the regulation of development. Furthermore, transcriptional response of Midges (the 4th instar larvae) exposed to chemicals of different MOAs (CdCl₂, nonylphenol and triclosan) were profiled based on the reference transcriptome. Consequently, a complete transcriptome of 31132 unigenes with N50 of 3117bp, covering 98.8% of the arthropod single-copy orthologs were assembled. While 364 genes were differentially expressed among adjacent larval stages, 7142 and 2127 of transcripts were significantly changed for the transition of larvae-pupae and pupae-adults, respectively. Finally, chemical-specific gene expression profile were identified in the midges, showed its potential in classifying distinct contaminants. Overall, the comprehensive transcriptome of C. dilutus developed here could not only facilitate the mechanistic understanding of environmental toxicants during critical life stage of aquatic insects, but also provide molecular diagnostic tools in sediment ecotoxicology.

BR-C Z4 and FoxJ interact to regulate expression of a chitin synthase gene CHSA-2b in the pupal wing discs of the silkworm, Bombyx mori

Elaborate regulation of tissue- and stage-specific expression of genes is prerequisite for insect development. The hormone 20-hydroxyecdysone (20E) initiates metamorphosis by regulating the expression of a series of genes. However, how 20E orderly regulates the pupa-specific expression of genes remains unclear. In this study, we report a regulatory mechanism for the pupa-specific expression of chitin synthase A 2b (CHSA-2b) in Bombyx mori. We found that Broad-Complex Z4 (BR-C Z4) was up-regulated by 20E just before pupation, while transcription factor FoxJ and CHSA-2b were up-regulated during the pupal stage. There is a Fox cis-regulatory element in the CHSA-2b promoter region, and FoxJ protein bound to this element, enhancing the CHSA-2b transcription during the pupal stage. In addition to CHSA-2b, FoxJ also up-regulated the expression of 16 out of 19 pupa-specific genes tested. However, at the prepupal stage, 20E-induced BR-C Z4 inhibited the FoxJ transcription, indirectly inhibiting the CHSA-2b transcription. These data suggest that at the pre-pupation stage, 20E-induced BR-C Z4 inhibited the expression of pupa-stage genes like CHSA-2b by inhibiting the expression of FoxJ; by the pupal stage, the expression of BR-C Z4 decreased, releasing its inhibition on FoxJ, which then up-regulated the expression of the pupa-specific genes. This study explains the elaborate regulation of the pupa-specific gene expression during metamorphosis in B. mori.

Biochemical and Functional Characterization of Glycoside Hydrolase Family 16 Genes in Aedes aegypti Larvae: Identification of the Major Digestive β-1,3-Glucanase

Insect β-1,3-glucanases belong to Glycoside Hydrolase Family 16 (GHF16) and are involved in digestion of detritus and plant hemicellulose. In this work, we investigated the role of GHF16 genes in Aedes aegypti larvae, due to their detritivore diet. Aedes aegypti genome has six genes belonging to GHF16 (Aae GH16.1 – Aae GH16.6), containing two to six exons. Sequence analysis suggests that five of these GHF16 sequences (Aae GH16.1, 2, 3, 5, and 6) contain the conserved catalytic residues of this family and correspond to glucanases. All genomes of Nematocera analyzed showed putative gene duplications corresponding to these sequences. Aae GH16.4 has no conserved catalytic residues and is probably a β-1,3-glucan binding protein involved in the activation of innate immune responses. Additionally, Ae. aegypti larvae contain significant β-1,3-glucanase activities in the head, gut and rest of body. These activities have optimum pH about 5–6 and molecular masses between 41 and 150 kDa. All GHF16 genes above showed different levels of expression in the larval head, gut or rest of the body. Knock-down of AeGH16.5 resulted in survival and pupation rates lower than controls (dsGFP and water treated). However, under stress conditions, severe mortalities were observed in AeGH16.1 and AeGH16.6 knocked-down larvae. Enzymatic assays of β-1,3-glucanase in AeGH16.5 silenced larvae exhibited lower activity in the gut and no change in the rest of the body. Chromatographic activity profiles from gut samples after GH16.5 silencing showed suppression of enzymatic activity, suggesting that this gene codes for the digestive larval β-1,3-glucanase of Ae. aegypti. This gene and enzyme are attractive targets for new control strategies, based on the impairment of normal gut physiology.

Genome-Wide Transcriptome Profiling Reveals Genes Associated with Meiotic Drive System of Aedes aegypti

Aedes aegypti is an important mosquito vector of several arboviruses, including dengue, yellow fever, Zika, and Chikungunya, which cause significant human morbidity and mortality globally. In certain populations of this mosquito, a native meiotic drive system causes abnormal spermatogenesis that results in highly male-biased progenies from some matings. Although the basic genetics and cytogenetics of the drive mechanism were elucidated, very little is known on a transcriptome level about how the meiotic drive phenotype is expressed in individual males. To address this question, we conducted a whole-genome microarray expression study of testes from a meiotic-drive-carrying strain (T37) in comparison with testes from a non-drive-carrying strain (RED). Based on bioinformatics analyses of the microarray data, we identified 209 genes associated with the meiotic drive phenotype that were significantly differentially expressed between the two strains. K-means cluster analysis revealed nine clusters, in which genes upregulated in T37 testes were assigned to five clusters and genes downregulated in T37 testes were assigned to four clusters. Our data further revealed that genes related to protein translation, phosphorylation, and binding, as well as to G-protein-coupled receptor (GPCR) and peptidase activities, are differentially upregulated in testes from males with the meiotic drive genotype. Based on pathway analysis of these differentially expressed genes, it was observed that the glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway may play a role in the meiotic drive system. Overall, this investigation enhances our understanding of whole-genome gene expression associated with the meiotic drive system in Ae. aegypti.

High functional conservation of takeout family members in a courtship model system

takeout (to) is one of the male-specific genes expressed in the fat body that regulate male courtship behavior, and has been shown to act as a secreted protein in conjunction with courtship circuits. There are 23 takeout family members in Drosophila melanogaster, and homologues of this family are distributed across insect species. Sequence conservation among family members is low. Here we test the functional conservation of takeout family members by examining whether they can rescue the takeout courtship defect. We find that despite their sequence divergence takeout members from Aedes aegypti and Epiphas postvittana, as well as family members from D. melanogaster can substitute for takeout in courtship, demonstrating their functional conservation. Making use of the known E. postvittana Takeout structure, we used homology modeling and amphipathic helix analysis and found high overall structural conservation, including high conservation of the structure and amphipathic lining of an internal cavity that has been shown to accommodate hydrophobic ligands. Together these data suggest a high degree of structural conservation that likely underlies functional conservation in courtship. In addition, we have identified a role for a conserved exposed protein motif important for the protein’s role in courtship.

De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts

Burying beetles (Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages. RNA-Seq reads were obtained by next-generation sequencing and the transcriptome was assembled using the Trinity assembler. Validation of the assembly was performed by functional characterization using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differential expression analysis highlights developmental stage-specific expression patterns, and immunity-related transcripts are discussed. The data presented provides a valuable molecular resource to aid further investigation into immunocompetence throughout this organism's sexual development.

Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti

The mosquito Aedes aegypti is the primary vector of human arboviral diseases caused by dengue, chikungunya and Zika viruses. Many studies have shown the potential roles of small RNA molecules such as microRNA, small interfering RNA and PIWI-interacting RNA in vector mosquitoes. The function of tRNA fragments (tRF), the newly discovered class of small RNAs, in mosquitoes is not known. In this study, we show that specific tRFs are expressed in significantly differential manner between males and females of Ae. aegypti strains. Specific tRFs also show differential response during developmental transition from larvae to adults, as well as after blood feeding of adult females. The expression pattern of tRFs upon blood feeding varied depending upon if the blood contained dengue virus, and also if the females were treated with antibiotic prior to feeding to cleanse of the gut bacteria. Our findings show that a single tRF derived from the precursor sequences of a tRNA-Gly was differentially expressed between males and females, developmental transitions and also upon blood feeding by females of two laboratory strains that vary in midgut susceptibility to dengue virus infection. The multifaceted functional implications of this specific tRF suggest that biogenesis of small regulatory molecules from a tRNA can have wide ranging effects on key aspects of Ae. aegypti vector biology.

The mosquito Aedes aegypti is a major vector of arboviral diseases in subtropics and tropics. The confounding effects of immature development and adult microbiome on the ability of Ae. aegypti to transmit diseases (vector competence) have gained renewed attention in the recent years. However, the molecular nature of these links/ effects remains unknown. This is major gap in knowledge regarding how vector competence is regulated at molecular level, and how that regulation may be variable among different strains of this mosquito. In this study, we investigated expression of newly discovered class of small RNAs, called tRNA fragments (tRF) in Ae. aegypti strains. Based on small RNA sequencing and bioinformatics analyses, we show that tRFs are expressed in Ae. aegypti, and they are associated with significant changes in expression between males and females, during development stages, and post blood feeding responses. A single tRF showed association with sex-biased expression, developmental regulation and in response to blood meals between Moyo-S and Moyo-R strains that differ in midgut susceptibility to dengue virus. The findings of this study are expected to guide future research efforts directed toward examining detailed regulatory mechanisms of tRFs in vector competence of Ae. aegypti to disease transmission.

Evidences of the Low Implication of Mosquitoes in the Transmission of Mycobacterium ulcerans, the Causative Agent of Buruli Ulcer

Background

Buruli ulcer (BU) continues to be a serious public health threat in wet tropical regions and the mode of transmission of its etiological agent, Mycobacterium ulcerans (MU), remains poorly understood. In this study, mosquito species collected in endemic villages in Benin were screened for the presence of MU. In addition, the ability of mosquitoes larvae to pick up MU from their environment and remain colonized through the larval developmental stages to the adult stage was investigated.

Methods

7,218 adults and larvae mosquitoes were sampled from endemic and nonendemic villages and screened for MU DNA targets (IS2404, IS2606, and KR-B) using qPCR. Results. MU was not detected in any of the field collected samples. Additional studies of artificially infected larvae of Anopheles kisumu with MU strains revealed that mosquitoes larvae are able to ingest and host MU during L1, L2, L3, and L4 developmental stages. However, we noticed an absence of these bacteria at both pupae and adult stages, certainly revealing the low ability of infected or colonized mosquitoes to vertically transmit MU to their offspring.

Conclusion

The overall findings highlight the low implication of mosquitoes as biological vectors in the transmission cycle of MU from the risk environments to humans.

Transcriptional Profile for Detoxification Enzymes AeaGGT1 and AaeGGT2 From Aedes aegypti (Diptera: Culicidae) in Response to Larvicides

Aedes aegypti (L.) is the vector responsible for transmitting dengue, chikungunya, yellow fever, and Zika viruses, as well as other pathogens. Microbial larvicides based on Bacillus thuringiensis Berliner israelensis (Bti) and Saccharopolyspora spinosa Mertz and Yao, such as VectoBac 12AS and Natular 2EC, have been shown to be effective in reducing larval populations of Ae. aegypti. We examined the gene expression of two detoxification enzymes, glucosyl and glucuronosyl transferases (AaeGGT1 and AaeGGT2), through developmental stages and a time course study in response to larvicide exposure using qualitative real-time polymerase chain reaction (qPCR). AaeGGT1 and AaeGGT2 gene expressions were differentially regulated during development of the immature stages. We also found that male adults had higher expression than female adults after controlling for age effects. AaeGGT1 and AaeGGT2 gene expression were both upregulated in response to VectoBac 12AS and Natular 2EC treatments with the maximum level of expression occurring 24 h after treatment applications. This information sheds light on larvicide-induced changes in the physiology of Ae. aegypti with implications for development of mosquito control strategies.

Evolutionary origin and function of NOX4-art, an arthropod specific NADPH oxidase

BACKGROUND

NADPH oxidases (NOX) are ROS producing enzymes that perform essential roles in cell physiology, including cell signaling and antimicrobial defense. This gene family is present in most eukaryotes, suggesting a common ancestor. To date, only a limited number of phylogenetic studies of metazoan NOXes have been performed, with few arthropod genes. In arthropods, only NOX5 and DUOX genes have been found and a gene called NOXm was found in mosquitoes but its origin and function has not been examined. In this study, we analyzed the evolution of this gene family in arthropods. A thorough search of genomes and transcriptomes was performed enabling us to browse most branches of arthropod phylogeny.

RESULTS

We have found that the subfamilies NOX5 and DUOX are present in all arthropod groups. We also show that a NOX gene, closely related to NOX4 and previously found only in mosquitoes (NOXm), can also be found in other taxonomic groups, leading us to rename it as NOX4-art. Although the accessory protein p22-phox, essential for NOX1-4 activation, was not found in any of the arthropods studied, NOX4-art of Aedes aegypti encodes an active protein that produces H₂O₂. Although NOX4-art has been lost in a number of arthropod lineages, it has all the domains and many signature residues and motifs necessary for ROS production and, when silenced, H₂O₂ production is considerably diminished in A. aegypti cells.

CONCLUSIONS

Combining all bioinformatic analyses and laboratory work we have reached interesting conclusions regarding arthropod NOX gene family evolution. NOX5 and DUOX are present in all arthropod lineages but it seems that a NOX2-like gene was lost in the ancestral lineage leading to Ecdysozoa. The NOX4-art gene originated from a NOX4-like ancestor and is functional. Although no p22-phox was observed in arthropods, there was no evidence of neo-functionalization and this gene probably produces H₂O₂ as in other metazoan NOX4 genes. Although functional and present in the genomes of many species, NOX4-art was lost in a number of arthropod lineages.

Comparative analysis of zygotic developmental genes in Rhodnius prolixus genome shows conserved features on the tracheal developmental pathway

Most of the in-depth studies on insect developmental genetic have been carried out in the fruit fly Drosophila melanogaster, an holometabolous insect, so much more still remains to be studied in hemimetabolous insects. Having Rhodnius prolixus sequenced genome available, we search for orthologue genes of zygotic signaling pathways, segmentation, and tracheogenesis in the R. prolixus genome and in three species of Triatoma genus transcriptomes, concluding that there is a high level of gene conservation. We also study the function of two genes required for tracheal system development in D. melanogaster - R. prolixus orthologues: trachealess (Rp-trh) and empty spiracles (Rp-ems). From that we see that Rp-trh is required for early tracheal development since Rp-trh RNAi shows that the primary tracheal branches fail to form. On the other hand, Rp-ems is implied in the proper formation of the posterior tracheal branches, in a similar way to D. melanogaster. These results represent the initial characterization of the genes involved in the tracheal development of an hemimetabolous insect building a bridge between the current genomic era and V. Wigglesworth's classical studies on insects' respiratory system physiology.

Dynamic expression of miRNAs across immature and adult stages of the malaria mosquito Anopheles stephensi

Background

MicroRNAs are small non-coding RNAs that are involved in various biological processes including insect development. Anopheles stephensi serves as primary vector of malaria parasite in Asia and exhibits holometabolous life cycle that involves four different stages of development. Regulation and role of mosquito miRNAs during various stages of mosquito development remain largely unknown.

Methods

High throughput small RNA sequencing was employed for identification and profiling of miRNAs across immature and adult stages of malaria vector, which were further validated using Northern hybridization and real time PCR. Target prediction and pathway analysis was carried out to understand the role of regulated miRNAs in insect development. Degradome sequencing was employed to identify cleaved targets of some regulated miRNAs. Loss of function strategy was employed for miR-989 to understand its probable role in female reproductive process.

Results

Small RNA sequencing and data analysis revealed 111 and 14 known and novel miRNAs respectively across all stages of Anopheles stephensi. Nine miRNAs showed gender specific regulation across different stages of mosquito development. Analysis of miRNAs revealed regulation of 24 and 26 miRNAs across different stages of male and female mosquito development respectively. mRNA targets and significant pathways targeted by regulated miRNAs were identified for each stage of mosquito development. Degradome sequencing revealed twenty nine cleaved targets of insect miRNAs. MicroRNA-989 showed significant up-regulation in the adult female as compared to adult male mosquito. Knockdown of miR-989 expression in adult female using miRNA specific antagomir affected targets playing roles in protein binding, proteolysis and nucleic acid binding in ovary tissue of female mosquito post blood feeding.

Conclusions

This is the first comprehensive effort to understand regulation of Anopheles stephensi miRNAs across developmental stages of male and female mosquito. Preliminary role of regulated miRNAs in mosquito development was revealed by target prediction and pathway analysis. MicroRNA-989 emerged to have important roles in adult female mosquitoes showing significant up-regulation which was further studied using miR-989 specific antagomir. This study provides insights into mosquito development and reproductive process and has implications for effective control of mosquito population required for reducing spread of mosquito-borne infectious diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-0772-y) contains supplementary material, which is available to authorized users.