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Abstract Cases of convergent adaptation, especially between close relatives within a lineage, provide insights into constraints underlying the mechanisms of evolution. We examined this in the carnivorous plant family Lentibulariaceae, with its highly divergent trap designs but shared need for prey digestion, by generating a chromosome-level genome assembly for Pinguicula gigantea, the giant butterwort. Our work confirms a history of whole-genome duplication in the genus and provides strong phylogenomic evidence for a sister-group relationship between Lentibulariaceae and Acanthaceae. The genome also reveals that a key digestive adaptation, the expansion of cysteine protease genes active in digestion, was achieved through independent tandem duplications in the butterwort (Pinguicula) and its close relative, the bladderwort (Utricularia). Most of these parallel expansions arose in non-homologous regions of the two genomes, with a smaller subset located on homologous blocks. This study provides clear genomic evidence for convergent evolution and illustrates how similar selective pressures can repeatedly shape genomes in analogous ways. 

Abstract Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods^1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome^3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins^5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.