ArticleGenetica2026
Repeatome divergence and recent LTR retrotransposon dynamics in phylogenetically diverse medicinal plant genomes.
Article in Genetica, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Transposable elements drive plant genome size variation and structural diversification, but their recent dynamics remain poorly characterized in medicinal plants. We analyzed 95 medicinal plant genomes to evaluate repeatome divergence, recent transposable element composition and long terminal repeat retrotransposon dynamics. Genome-wide transposable element proportion varied substantially among species and was strongly positively associated with genome size, indicating that repeat accumulation is a major axis of genome-size divergence. Recent transposable element fractions, operationally defined by sequence identity ≥ 85%, were dominated by long terminal repeat retrotransposons in most genomes. Higher recent transposable element fractions were negatively associated with Shannon diversity and Pielou's evenness, suggesting compositional concentration rather than balanced expansion across major classes. Phylogenetically informed Bayesian models revealed class-specific differences in the magnitude and uncertainty of estimated recent transposable element proportions across taxonomic orders. Insertion-time analyses showed heterogeneous recent accumulation patterns, whereas phylogenetic reconstruction of intact long terminal repeat retrotransposons with paired long terminal repeat identity ≥ 95% revealed contrasting lineage composition between Copia and Gypsy. Copia elements were concentrated mainly in two dominant lineages, whereas Gypsy elements were distributed across a broader set of lineages. An exploratory 2-kb gene-centered analysis of predicted biosynthetic gene clusters showed that 62.5% of 31,162 unique genes had at least one proximal long terminal repeat retrotransposon annotation, usually together with other transposable element classes. These results indicate that medicinal plant repeatome evolution is associated with genome-wide transposable element burden, recent compositional concentration and lineage-level long terminal repeat retrotransposon dynamics.
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