The Telomere-to-Telomere Genome of Selaginella moellendorffii Provides Insights into Genome Evolution and Biflavone Biosynthesis

Abstract

Selaginella moellendorffii Hieron., a lycophyte of significant medicinal and evolutionary importance, is recognized as one of the earliest vascular plants. However, the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential, thereby limiting our understanding of its genomic structure and metabolic capabilities. In this study, we present the first chromosome-level, telomere-to-telomere (T2T) genome assembly of S. moellendorffii, constructed utilizing PacBio HiFi, Oxford Nanopore (ONT), and Hi-C technologies. The assembled genome, spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb, exhibited exceptional completeness (BUSCO score: 95.7 %) and accuracy (QV = 48.11). Comparative genomic analysis identified 3 515 gene families unique to S. moellendorffii, with significant enrichment in secondary metabolism pathways, including those related to flavonoid biosynthesis. Phylogenetic analysis revealed that S. moellendorffii diverged from Isoetes approximately 339.6 million years ago (MYA), representing a key evolutionary transition in early vascular plants. By integrating tissue-specific transcriptome and metabolome analyses, we uncovered the molecular basis of biflavone biosynthesis, identifying key enzymes and regulatory networks that govern the production of these bioactive compounds. We observed a correlation between the tissue-specific accumulation patterns of six major biflavones, including amentoflavone and ginkgetin, and the expression of their biosynthetic genes. This high-quality genome assembly, coupled with multi-omics analyses, offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.