Tŏnges, 2021

Tönges SM. 2021. Context-dependent DNA methylation variants in marbled crayfish (Procambarus virginalis). Doctoral dissertation, The Faculty of Bio Sciences, Ruperto Carola University Heidelberg, Germany. https://doi.org/10.11588/heidok.00029299

 

Abstract

The marbled crayfish is a recently discovered freshwater crayfish. It is the only known decapod crustacean that reproduces by obligate apomictic parthenogenesis resulting in a clonal, all-female population. All known marbled crayfish have a single origin, and the species is estimated to have an age of about 25-30 years. Furthermore, it has spread already into several countries globally and shows high adaptability to different environments in the absence of genetic adaptation. Epigenetic mechanisms were suggested to play a role in the rapid adaptation of this species. This thesis aims to identify context-dependent DNA methylation variants in marbled crayfish. Samples from two tissues and four distinct habitats were analyzed with a capture-based bisulfite sequencing approach to identify methylation variants. The results were validated by deep amplicon sequencing of tissue-specific and location-specific regions and with newly collected samples from the same tissues and locations as before. The location-specific methylation patterns suggest the existence of epigenetic ecotypes and allow the tracing of the origin of marbled crayfish populations by their DNA methylation fingerprint. In a laboratory trial, single rearing conditions were changed to see the influence of specific parameters on the methylation pattern. Within six months, methylation changes could be observed for the group kept at a lower temperature compared to the control group, indicating the adaptation of the methylation pattern caused by an environmental trigger. Furthermore, the laboratory population showed a different methylation pattern compared to the wild populations. Lastly, the potential of marbled crayfish as an aquaculture livestock was explored, and a framework for an environmentally safe aquaculture was established. Additionally, tracing the origin of marbled crayfish using location-specific methylation patterns was proposed for certifying sustainable and transparent aquaculture practices. These re-sults provide insight into the rapid adaptation in invasive species and provide a proof of concept for environmental origin tracing with DNA methylation fingerprinting.

Keywords: Epigenetics • ecology • aquaculture