Phylogenomics and comparative genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)

Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (2,172 species) and Peperomia (1,347 species). To address this gap, we used genome skimming to assemble a >5kbp nuclear ribosomal DNA region and whole plastomes (152-161kbp) from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study the evolution of plastomes and investigate the role of hybridization in this group. Resulting plastome phylogenies were well resolved and highly supported, wit...