Genomic basis of adaptation to different habitats in the tube case making caddisfly (Trichoptera) family Limnephilidae

• Applicant: Jacqueline Heckenhauer, Ph.D.
• Subject Area: Evolution, Anthropology ; Evolutionary Cell and Developmental Biology (Zoology) ; Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 502865717

Limnephilidae is a diverse family within the insect order Trichoptera (or caddisflies) that uses silk to build tube cases at larval stages and open pupal cells with a permeable membrane at pupal stages. These evolutionary innovations are thought to have enabled the adaptation of members of this family to different habitats, i.e., from lotic (fast-moving water) to lentic (low oxygenated slow-moving and standing waters) or even terrestrial habitats. Moreover, expansions of transposable elements (TEs) and their influence on genome size and protein coding genes have previously been identified in Limnephilidae. The main objective of this project is to elucidate the genomic basis of the adaptation to different habitats in Limnephilidae on two different levels. First, comparative genomic and transcriptomic methods will be applied to identify gene families associated with adaptation to different habitats. These span respiratory, metabolic, olfactory, vision, thermal tolerance and other genes. It will be investigated whether these genes and gene families are under positive selection and/or have undergone gene family expansions, both of which can facilitate genome adaptation. Second, the project will aid in establishing Trichoptera as a model system in functional genomic studies by examining potential regulatory mechanisms for the evolution of innovations. In this context, building on previous findings about TE evolution in caddisflies, potential evolutionary and regulatory roles of TE activity and TE-gene associations will be examined. TEs might be involved in modification of chromatin folding and transcriptional activation that influence the expression of neighboring genes. Using genes involved in habitat shifts as a model for understanding TE-protein coding gene interactions, RNAseq will be applied to test whether genes are differentially expressed during larval stage and pupation in species occupying either fast current, slow current (streams), stagnant (lakes) and terrestrial environments and to investigate whether proximity to TE hubs affects gene expression. This also allows to evaluate the role of the pupal case for habitat shifts. At the pupal stage, silk characteristics of the pupal cell are likely linked with osmoregulation which potentially varies in species that pupate in different environments. Differential expression of genes associated with body fluid regulation may reflect adaptations to differences in osmotic pressure encountered during habitat transitions in Limnephilidae. To evaluate the chromatin availability of genic regions with high expression, chromatin accessibility profiling using ATAC-seq will be integrated. This data will be used to compare the regulatory landscapes, i.e., differences in open chromatin, between Limnephilidae species from different habitats. To get information on how genes of interest (genes expressed in a certain habitat) are regulated, open chromatin regions within the respective gene locus will be examined.

• DFG Programme: Priority Programmes
• Subproject of: SPP 2349: Genomic Basis of Evolutionary Innovations (GEvol)