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Transposable elements as catalysts of genome evolution in Drosophila virilis

ABSTRACT: Transposable elements as catalysts of genome evolution in Drosophila virilis

PROVIDER: PRJNA1327368 | ENA |

REPOSITORIES: ENA

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Transposable elements as catalysts of genome evolution in Drosophila virilis

Project description:Transposable elements (TEs) drive genomic innovation, but their dynamics in non-model species remain unclear. Herein, we integrated multiomics data to explore TE dynamics in Drosophila virilis, an important model for repetitive DNA research. By combining computational predictions with manual curation, we identified 100 TE families and delineated three temporal waves of TE mobilisation: recent activity, speciation-associated divergence, and ancient invasions. TEs in D. virilis dynamically colonise euchromatin and heterochromatin, contradicting the idea that heterochromatin is just a passive dump for degenerate repeats. Most TE families are prevalent across all analyzed D. virilis strains, while certain DNA transposons and retroelements exhibit strain-specific expansion, suggesting different TE activity and silencing across populations. Nonetheless, there is substantial evidence for extensive horizontal transfer of TEs among close relatives, demonstrating that the D. virilis species group function effectively as TE “ecosystem”. Epigenetic profiling revealed H3K9me3 spreading from TEs represses adjacent genes in a distance-dependent manner, influenced by insertion length and genomic context, affecting developmental and metabolic genes. We also discovered the first polymorphic inversion in D. virilis, likely linked to retrotransposons. Our findings illuminate TEs as catalysts of genomic innovation, influencing gene regulation and evolutionary trajectories, providing a framework for studying TE dynamics across species.

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Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy

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Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes

Project description:East African cichlid fishes have radiated in an explosive fashion. The (epi)genetic basis for the abundant phenotypic diversity of these fishes remains largely unknown. As transposable elements (TEs) contribute extensively to genome evolution, we reasoned that TEs may have fuelled cichlid radiations. While TE-derived genetic and epigenetic variability has been associated with phenotypic traits, TE expression and epigenetic silencing remain unexplored in cichlids. Here, we profiled TE expression in African cichlids, and describe dynamic expression patterns during embryogenesis and according to sex. Most TE silencing factors are conserved and expressed in cichlids. We describe an expansion of two truncated Piwil1 genes in Lake Malawi/Nyasa cichlids, encoding a Piwi domain with catalytic potential. To further dissect epigenetic silencing of TEs, we focused on small RNA-driven epigenetic silencing. We detect a small RNA population in gonads consistent with an active Piwi-interacting RNA (piRNA) pathway targeting TEs. We uncover fluid genomic origins of piRNAs in closely related cichlid species. This, along with signatures of positive selection in piRNA pathway factors, points towards fast co-evolution of TEs and the piRNA pathway. Our study is the first step to understand the contribution of ongoing TE-host arms races to the cichlid radiations in Africa.

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