Project description:Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries. Sequencing of Tribolium small RNAs from adults and embryos.
Project description:Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle Four biological replicates for male and female beetles with 20 individuals per replicate. Two technical replicates, one replicate per sex. 16,434 genes/expressed non-coding regions represented twice on each array. Three 60 mer probes for most exons/expressed non-coding regions. 167,538 unique genomic probes replicated twice per array.
Project description:Evolution of cis-properties (such as enhancers) often plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods to study enhancers in species outside of established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum. To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium via FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)-sequencing. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and stage. Second, we established the first reporter assay system that works in both Drosophila and Tribolium, using nubbin in the wing and hunchback in the embryo as case studies. Together, these advances will be useful to study the evolution of cis-language and morphological diversity in Tribolium and other insects.
Project description:Epigenetic mechanisms, such as CpG DNA methylation enable phenotypic plasticity and rapid adaptation to changing environments. CpG DNA methylation is established by DNA methyltransferases (DNMTs), which are well conserved across vertebrates and invertebrates. There are insects with functional DNA methylation despite lacking a complete set of Dnmts. But at least one of the enzymes, DNMT1, appears to be required to maintain an active DNA methylation system. The red flour beetle, Tribolium castaneum, lacks Dnmt3 but possesses Dnmt1 and it has been controversial whether it has a functional DNA methylation system. Using whole genome bisulfite sequencing, we did not find any defined patterns of CpG DNA methylation in embryos. Nevertheless, we found Dnmt1 expressed throughout the entire life cycle of the beetle, with mRNA transcripts significantly more abundant in eggs and ovaries. A maternal knockdown of Dnmt1 caused a developmental arrest in offspring embryos. We show that Dnmt1 plays an essential role in T. castaneum embryos and that its downregulation leads to an early developmental arrest. This function appears to be unrelated to DNA methylation, since we did not find any evidence for this modification. This strongly suggests an alternative role of this protein.
Project description:The presence of DNA methylation in beetles (Coleoptera) has only been investigated with bisulfite sequencing of Tribolium castaneum, which produced no evidence of DNA methylation. Here, we used whole genome bisulfite sequencing to assay if DNA methylation was present in another beetle, Nicrophorus vespilloides. We used T. castaneum as a negative control.
Project description:Virulence is a key trait under selection during host-parasite coevolution. In order to obtain increased fitness, parasites are predicted to increase their ability to circumvent and overcome host immunity. A particular challenge for pathogens are external immune systems, found among various invertebrates. Such external immune systems are chemical defence systems comprised of highly potent antimicrobial compounds released by prospective hosts into the environment. We carried out a coevolution experiment with the entomopathogenic fungus, Beauveria bassiana, and the red flour beetle, Tribolium castaneum, which has a well-documented external immune system. Surprisingly, after just seven transfers of experimental evolution we saw a significant increase in virulence in all B. bassiana. This increase in virulence was mainly the result of the B. bassiana isolates evolving resistance to the external immune defences of the T. castaneum beetles, but not obviously through the increased production of toxins or other harmful substances. Furthermore, transcriptomic analyses of B. bassiana RNA-seq data implicates up-regulation of genes responsible for resistance to oxidative stress underlying the observed resistance. We conclude that external immunity acts as a powerful selective force for virulence evolution, with an increase in virulence being achieved apparently entirely by overcoming these defences, most likely due to elevated oxidative stress resistance.
