Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides new insights into its evolution and polysaccharide biosynthesis

Abstract Phragmites australis , widely distributed worldwide, has a vast biomass and a strong ability to adapt to the environment. Its rhizome (known as "Lugen" in Chinese medicine) has been used as a traditional Chinese medicine for over 2,000 years. In this study, we assembled a chromosome-level reference genome of Phragmites australis containing one B chromosome. An explosion of LTR-RTs, centered on the Copia family, occurred during the late Pleistocene, driving the expansion of reeds genome size and subgenomic differentiation. Comparative genomic analysis showed that P. australis underwent two whole gene duplication events, was segregated from Cleistogenes songorica at 34.6 Mya, and that 41.26% of the gene families underwent expansion. Based on multi-tissue transcriptomic data, we identified structural genes in the biosynthetic pathway of pharmacologically active Phragmites polysaccharides that have important roles in rhizome development. The assembly of the P. australis genome contributes to our understanding of Arundiaceae evolution and polysaccharide biosynthesis in phragmitis rhizoma .