Phylo-mobilome analysis provide insights into transposon dynamics, adaptation and impact on host genomes in Solanaceae

As essential components of eukaryotic genomes, transposable elements (TEs) play crucial roles in shaping genome architecture and driving evolution. To explore TE adaptation across diverse plant genera and understand their impact on genome diversity, we conducted comparative analyses of the mobilome, methylome and sRNAome using the Solanaceae family as a model. Our research indicates that TEs exhibit limited long-term conservation of individual families during diversification within Solanaceae, coupled with pronounced copy-number inequality among TE families. TEs contribute to the expansion of host genome size independently of whole-genome duplication. While under the repression of host gene silencing strategies, such as copy number- and context-specific DNA methylation, TEs coevolve with and adapt to the host genomes. Notably, TEs acquire silencing-related gene fragments from their hosts, thereby enhancing their adaptive capabilities. Furthermore, specific TE subfamilies trigger heterochromatin formation, while repeated insertions of TEs within centromeres result in the erosion of repetitive centromeric sequences. In summary, our phylo-mobilome analysis sheds light on TE dynamics and the intricate coevolution between TEs and their host genomes within the Solanaceae family.