Millennial clonal persistence and transposable element-biased somatic mutations in an herbaceous plant (Typha latifolia).

Clonal reproduction represents a fundamental strategy in plant propagation, enabling the formation of extensive genetically identical populations through persistent asexual growth. Understanding the spatial-temporal dynamics of these clonal systems, particularly with regard to their age, size, and somatic mutation patterns, is crucial for unravelling the evolutionary ecology of long-lived plant species. While such investigations have been conducted in woody perennials, herbaceous clonal systems remain markedly understudied. We address this knowledge gap through an integrated genomic study (including de novo assembly of a gap-free reference genome and whole-genome resequencing of 72 spatially distributed samples) of Typha latifolia, a rhizomatous perennial inhabiting a 103.2 ha alpine wetland in Sichuan, China. We identify this population as a clonal population and estimated the clone's age to be ~1900 ( ± 100) years, with a species-level mutation rate and radiocarbon. Somatic mutations are significantly enriched in transposable elements (TEs), 71% occurring in TEs with one-third genomic coverage ( ~ 33% of callable sites and ~34% of total genome), and are significantly fixed in TEs in 50 out of 72 sampled ramets. This study provides insights into both clonal persistence and clonal expansion capacity and somatic mutation accumulation in herbaceous plants, advancing understanding of clonal plant survival and evolution.