Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis

Despite the wealth of genomic and transcriptomic data of pivotal angiosperm species, the phylogenetic relationships of flowering plants are still not fully resolved. Microsynteny, or the conservation of relative gene order, has been recognized as a valuable and alternative phylogenetic character to sequence-based characters (nucleotides or amino acids). Here, we present a novel approach for phylogenetic tree reconstruction based on genome-wide synteny network data. We generated and analyzed synteny networks from 123 species from 52 families across 31 orders of flowering plants, including several lineages for which phylogenetic relationships are ambiguous. We obtained a stable and highly resolved phylogeny that is largely congruent with sequence-based phylogenies. However, our results unveiled several novel relationships for some key clades, such as magnoliids sister to monocots, Vitales as sister to core-eudicots, and Saxifragales sister to Santalales, in turn both sister to Caryophyllales. Our results highlight that phylogenies based on genome structure and organization are complementary to sequence-based phylogenies and provide alternative hypotheses of angiosperm relationships to be further tested.