Evolutionärer Wandel durch genomische Vermischung in einem Hybrid Fisch
Zusammenfassung der Projektergebnisse
This project aimed to explore alternative hypotheses explaining the previously observed accumulation of transposable elements (TEs) in the genome of a hybrid species of Cottus, as compared to its parental species C. rhenanus and C. perifretum. Sequencing efforts included PacBio HiFi and ultra-long sequencing, small-RNA sequencing and Hi-C sequencing in order to explore TE content and TE accumulation in highly repetitive sequence regions, signatures of disturbed TE silencing and structural variations in all three species. Because of unforeseen delays related to the coronavirus pandemic, fish sampling and technical sequencing issues, sequencing was not finalized before May 2024. The overall high quality of sequence data is suitable to investigate causes and consequences of TE accumulation. As an exception, the PacBio ultra-long sequencing produced very long reads mostly in the range of 50-100 kb (only few >200, max. 650kb), but suffered from a very high rate of sequencing errors and artifacts. Preliminary analyses show that only a minor fraction of the observed TE accumulation in hybrids could be explained by a disturbed small-RNA defense system. The possible roles of disturbed DNA methylation and expansion of repetitive sequence regions for increased TE content in hybrid genomes still need to be analyzed. Ongoing and future analyses will allow to better understand patterns of change in genomes following admixture, especially in large repetitive sequence regions that were not accessible before.
