Transposable Element Landscape in a Monotypic Species Barthea barthei (Hance) Krass (Melastomataceae) and Its Role in Ecological Adaptation

Background: Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation, yet their dynamics in non-model plant species remain poorly understood. Methods: Using a combination of genomic, transcriptomic and population genomics approaches, we analyzed the TE landscape in Barthea barthei, a unique member of Melastomataceae distributed across tropical and subtropical regions of South China. Results: Our analysis identified 64,866 TE copies comprising 16.76% of the compact genome (235 Mb), dominated by Ty3/Gypsy retrotransposons (8.82%) and DNA/Mutator elements (2.7%). Through genome-wide analysis, we discovered 13 TE islands enriched in genes related to photosynthesis, tryptophan metabolism, and stress response pathways. Moreover, we identified 3,859 high-confidence TE insertion polymorphisms (TIPs), including 29 fixed insertions between red and white flower ecotypes, affecting genes involved in cell wall modification, stress responses, and secondary metabolism. Transcriptome analysis of flower buds revealed 343 differentially expressed TEs between ecotypes, with 30 located near or within differentially expressed genes. The non-random distribution of TEs, predominantly within 5 kb of genes, and their association with adaptive traits suggest their significant role in B. barthei's successful colonization of diverse habitats. Conclusions: Our findings provide insights into how TEs contribute to plant genome evolution and ecological adaptation in tropical forest environments, particularly through their impact on regulatory networks governing stress response and developmental processes.