miRNAs are small noncoding RNAs that have broad regulatory functions on gene expression. Several of the commonly used tools for identifying targets of various miRNAs perform poorly for non-model organisms (e.g., anything that is not a human, mouse, fly or worm). One of the methods that does seem to work well is TargetScan, which relies on both pairing of seed sequences (a subset of the 18-23 bp that make up a miRNA) and phylogenetic conservation of sites. Basically, if miRNA repression is evolutionarily important for a gene, we expect the miRNA binding sites to be shared across closely related species.
We will apply this approach to a non-model sparrow study system to answer questions about how hybridization can disrupt evolved miRNA-mRNA interactions, leading to insights about the formation of new species. The student will create a pipeline for identifying conserved miRNA binding sites across several sparrow species using TargetScan as a framework. The project will rely on published whole genome assemblies and gene annotations of various qualities. The student will be responsible for improving the annotations, especially for the untranslated regions that lie up and downstream of protein coding genes. Following TargetScan’s approach, students will evaluate conservation of miRNA binding sites across annotations. There may be scope for future work comparing miRNA expression in different tissues between hybrids and parental species.
Microbiome-mediated speciation
The microbiome is the community of bacteria and fungi that are associated with different environments, including the surface, digestive tract, or other organs of multicellular organisms. These microbes can have huge fitness consequences for their multicellular hosts. Recent studies even suggest that the microbiomes can buffer threatened populations from extinction. The role of the gut microbiome is especially critical for organisms with highly specialized diets, meaning they are dependent on only a few sources —or maybe even just one source— of food. In fact, it may be differences in the biology of the microbiome, not the host itself, that either allow or inhibit specialists feeding on new food sources.
We want to understand the role of the microbiome in the ongoing split between two specialized lineages of the peacock fly, Tephritis conura. Here in Scandinavia, adult flies lay eggs on, and larvae develop inside, the melancholy thistle, Cirsium heterophyllum. To the south, however, they have shifted their host use to the cabbage thistle, C. oleraceum. We have extensive whole genome and RNA sequencing data taken from whole samples of flies at three life stages: larva, pupa and adult. Because these flies are so small, we also extracted DNA and RNA of whatever organisms were living inside of sampled individuals. The goal for the student would be to use the tool Kraken2 to compare the microbiomes between these two host forms at various life stages. The student would further develop a metagenomics pipeline to compare abundance of different microbial symbionts between larvae feeding on their preferred and unpreferred host plant.
Selection on gene expression at different life stages
Changes in gene expression mediate growth and development in all living organisms. As they develop, the challenges faced by these organisms change. Strong selection pressures experienced during one stage of development may differ from those experienced in other stages, and with consequences for the underlying patterns of gene expression. For example, the peacock fly, Tephritis conura, has recently (ca. 10,000 years ago) split into two host forms: one that specializes on the melancholy thistle (Cirsium heterophyllum) and one that specializes on the cabbage thistle (C. oleraceum). When flies that are specialized on C. oleraceum lay eggs on C. heterophyllum, large proportions of the developing offspring die as larvae, rather than during the egg or pupal stages. This suggests that not only does feeding on the wrong host plant have large fitness costs for these flies, but the genes that are expressed during this life stage are under strong selection.
We want to understand differences in life stage-specific gene expression in the peacock fly and relate these patterns to signatures of selection across the genome. The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. This will include co-expression network analyses to identify groups of genes that are expressed similarly and might belong to the same or linked gene regulatory networks. The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection.
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