Transposable elements as catalysts of genome evolution in Drosophila virilis
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PROVIDER: PRJNA1327368 | ENA |
REPOSITORIES: ENA
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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.
2025-09-16 | GSE307819 | GEO
Project description:Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
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Project description:Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution [RNA-seq]
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Project description:Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution [ChIP-seq]
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Project description:Transposable elements drive the evolution of metazoan zinc finger genes
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Project description:A major challenge in biology is to determine how evolutionarily novel characters originate, however, mechanistic explanations for the origin of novelties are almost completely unknown. The evolution of mammalianM-BM- pregnancy is an excellent system in which to study the origin of novelties because extant mammals preserve major stages in the transition from egg-laying to live-birth. To determine the molecular bases of this transition we characterized the pregnant/gravid uterine transcriptome from tetrapods, including species in the three major mammalian lineages, and used ancestral transcriptome reconstruction to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved endometrial expression during the origins of mammalian pregnancy, including numerous genes that mediate maternal-fetal communication and immunotolerance.Furthermore we show that thousands of regulatory elements active inM-BM- decidualized human endometrial stromal cellsM-BM- are derived from ancient mammalian transposable elements which provided binding sites for transcription factors that mediate decidualization and endometrial cell-type identity.M-BM- Our results indicate that one of the defining mammalian novelties evolved via domestication of ancient mammalian transposable elements into hormone-responsive regulatory elements throughout the genome. Examination of histone modification and DNAse hypersensitivity in decidualized dESC
2015-01-30 | E-GEOD-61793 | biostudies-arrayexpress
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.
2024-04-02 | PXD047439 | Pride
Project description:Gene annoation and determination of gene expression levels in Drosophila virilis and Drosophila yakuba by deep sequencing.
2015-01-29 | GSE61222 | GEO
Project description:Piwi interacting (pi)RNAs repress diverse transposable elements in the germ cells of metazoans and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two Drosophila virilis strains that show differential ability to generate piRNAs from several genomic regions. We found that active piRNA biogenesis correlates with high levels of histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Furthermore, piRNA biogenesis in the progeny requires the trans-generational inheritance of an epigenetic signal, presumably in form of homologous piRNAs that are generated in the maternal germline and deposited into the oocyte. The inherited piRNAs enhance piRNA biogenesis by installment of H3K9me3 mark on piRNA clusters and by promoting ping-pong processing of homologous transcripts into mature piRNAs. We submitted the resequencing data together with the functional genomic datasets because it was generated with the sole purpose of supporting those. The SRA accession numbers are SRR1536176 and SRR1536175. ChIP-seq against H3K9me3 and Pol2, Total RNA-seq, in Drosophila virilis Strain9 and Strain160 as well as crosses between them
2014-09-01 | E-GEOD-59965 | biostudies-arrayexpress