Figure 3 - available via license: Creative Commons Attribution 4.0 International
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Representation of active modules identified at day 1. On the networks, the nodes correspond to genes, and the edges correspond to interactions reported in the String database with an evidence score ≥0.7. The number associated with each module corresponds to the module ID specified in Table S6. Each module is annotated with a representative enrichment. The complete lists of the enrichments of all the modules are shown in Table S9. The node colors represent the log 2 FC values of the corresponding gene on a scale varying from blue (for the most underexpressed genes) to red (for the most overexpressed genes). The diamond-shaped nodes represent genes that are considered differentially expressed based on the DESeq2 method.
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In this study, we reanalyzed available datasets of gene expression changes in female Drosophila head induced by mating. Mated females present metabolic phenotypic changes and display behavioral characteristics that are not observed in virgin females, such as repulsion to male sexual aggressiveness, fidelity to food spots selected for oviposition, a...
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... day 4, we retrieved a large module (module 1 of Fig 4) containing overexpressed genes linked to rRNA processing and On the networks, the nodes correspond to genes, and the edges correspond to interactions reported in the String database with an evidence score ≥0.7. The number associated with each module corresponds to the module ID specified in Table S7. ...
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... biogenesis. We found 37 other active modules enriched in genes with implied functions investigated in other studies, such as changes in the immune response ( Kapelnikov et al, 2008aKapelnikov et al, , 2008b modules 6 and 13), lowering the expression of genes implied in the perception of smell ( Lebreton et al, 2014 -module 14), midgut development (White et al, 2021 -module 29), and other processes that have been uncovered (Fig 4 and Table S10). At 20 d, the transcriptomes of virgin and mated females were quite similar because only four active modules were highlighted. ...
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... found a cluster of 22 genes implied in this process, ClustEx2 highlighted a cluster of 100 genes, JActiveModules detected three overlapping modules representing a total of 37 genes, and GiGA found a cluster of 19 genes. Fig S4A shows the overlap between the modules associated with "chitinbased cuticle development" for the four different methods. Differential expression analysis reveals 625 genes with a log 2 FC greater than 0.32 or less than −0.32. ...
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... again emphasizes that searching for groups of genes working together can pick out important genes that move very little during the experiment. The overlap between differentially expressed genes and modules associated with "chitin-based cuticle development" for AMINE, ClustEx2, JActiveModules, and GiGA is shown in Fig S4B. This illustrates that only using methods that combine both the differential expression of genes and their interactions can relate the process under study to particular genes that vary only slightly. ...
Citations
... Hemolymph serves as a vital circulatory fluid throughout the honey bee's body, playing a central role in transporting hormones and small-molecule regulatory factors that are crucial for regulating honey bee development [13,14]. In this study, metabolomics was employed to investigate differences in the composition of hemolymph metabolites in larvae of worker bees (Apis mellifera) across three physiological developmental stages. ...
Metabolites present in the hemolymph of honey bees play a crucial role in modulating the metamorphic process within the species. However, the precise alterations in metabolite composition, along with the associated variances and regulatory pathways implicated during the larvae-to-pupae metamorphosis of honey bees, remain incompletely elucidated. In this investigation, we gathered hemolymph samples from honey bee larvae at three distinct physiological stages-feeding, prepupal, and pupae and subjected them to metabolite analysis utilizing the liquid chromatography-mass spectrometry (LC-MS) technique. Employing principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), we identified significant differential metabolites and conducted a metabolic pathway analysis on those differentially up-regulated during the prepupal and pupae stages. Notably, metabolites up-regulated in the hemolymph of prepupal stage larvae primarily governed glucose metabolism and fat digestion and absorption, while those in pupae stage larvae were involved in regulating chitin and lipopolysaccharide precursor formation, as well as the biosynthesis of phenylalanine, tyrosine, and tryptophan. These findings bear significant implications for advancing our comprehension of the metamorphic processes in honey bees.
... The networks we generate, with the parameters presented in this article, are closer to a real interaction network than the networks used by some competing methods. In addition to the results reported in this article, several studies utilizing AMINE to analyze various types of data have already been published (Feliz Morel et al, 2022;Pasquier & Robichon, 2022a;2022b), which also emphasizes the relevance of the results obtained by the method. ...
... Several studies utilizing AMINE to analyze various types of data have already been published (Feliz Morel et al, 2022;Pasquier & Robichon 2022a;2022b). ...
The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical methods of differential expression analysis, designed to assess individual gene variations, have trouble highlighting modules of small varying genes whose interaction is essential to characterize phenotypic changes. To identify these highly informative gene modules, several methods have been proposed in recent years, but they have many limitations that make them of little use to biologists. Here, we propose an efficient method for identifying these active modules that operates on a data embedding combining gene expressions and interaction data. Applications carried out on real datasets show that our method can identify new groups of genes of high interest corresponding to functions not revealed by traditional approaches. Software is available at https://github.com/claudepasquier/amine.
... Temporal aspects are clearly important in the female's response to mating. Gene expression in mated females changes over time (38)(39)(40)(41)(42)(43)(44), and distinct aspects of mating, such as seminal fluid proteins, sperm, or pheromones, exert their effects within different time windows after mating (45)(46)(47)(48)(49). Related to how SP alters regulatory networks, we do not know whether gene networks that are regulated by SP act independently of each other, or whether they are under the control of a shared molecular regulator that exerts pleiotropic effects downstream of SP. Fine-scale temporal transcriptomics analysis provides a powerful tool to investigate the genetic architecture of a response, as it can distinguish primary from secondary (and later) responses, pinpoint potential regulators and coregulated targets, and can be used to construct gene interaction networks (50)(51)(52). ...
Sex peptide (SP), a seminal fluid protein of Drosophila melanogaster males, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses including increased egg laying, activity, and food intake and a decreased remating rate. While it is known that SP achieves this, at least in part, by altering neuronal signaling in females, the genetic architecture and temporal dynamics of the female’s response to SP remain elusive. We used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 h after mating to learn about the genetic architecture, at the gene and exon levels, of the female’s response to SP. We find that SP is not essential to trigger early aspects of a virgin-to-mated transcriptional switch, which includes changes in a metabolic gene regulatory network. However, SP is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that SP alters rhythmic gene expression in females and suggests that SP’s disruption of the female’s circadian rhythm might be key to its widespread effects.
RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.
Drosophila melanogaster has one of the best characterized antiviral immune responses among invertebrates. However, relatively few easily transmitted natural virus isolates are available, and so many Drosophila experiments have been performed using artificial infection routes and artificial host–virus combinations. These may not reflect natural infections, especially for subtle phenotypes such as gene expression. Here, to explore the laboratory virus community and to better understand how natural virus infections induce changes in gene expression, we have analysed seven publicly available D. melanogaster transcriptomic sequencing datasets that were originally sequenced for projects unrelated to virus infection. We have found ten known viruses—including five that have not been experimentally isolated—but no previously unknown viruses. Our analysis of host gene expression revealed that numerous genes were differentially expressed in flies that were naturally infected with a virus. For example, flies infected with nora virus showed patterns of gene expression consistent with intestinal vacuolization and possible host repair via the upd3 JAK/STAT pathway. We also found marked sex differences in virus-induced differential gene expression. Our results show that natural virus infection in laboratory Drosophila does indeed induce detectable changes in gene expression, suggesting that this may form an important background condition for experimental studies in the laboratory.
Sex Peptide, a seminal fluid protein of D. melanogaster males, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses, including increased egg laying, activity and food intake and a decreased re-mating rate. While it is known that Sex Peptide achieves this, at least in part, by altering neuronal signaling in females, the identity of key molecular regulators that act downstream of Sex Peptide is not known. Here, we used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 hours after mating to investigate the genetic architecture, at the gene- and exon-level, of the female’s response to Sex Peptide. We find that Sex Peptide is not essential to trigger a virgin-to-mated transcriptional switch, which involves changes in a metabolic gene regulatory network. However, Sex Peptide is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that Sex Peptide might interact with the female’s circadian clock to orchestrate transcriptional changes across different regulatory networks. That a male seminal fluid protein can alter a female’s rhythmic gene expression has implications for our understanding of both reproductive and circadian behaviors.
