Boraginales phylogenomics
• Background and Aims Boraginales, a subcosmopolitan order with ~2,700 species in currently 11 families, has seen fluctuating classification at family and genus levels. Gynoecium and fruit morphology have been pivotal in morphological classifications, but a systematic evaluation based on anatomical and ontogenetic data has not been attempted. • Methods We revisited the phylogenetic relationships in Boraginales by analysing 162 newly sequenced samples using the Angiosperms353 probe set, together with existing data from 88 samples. Our sampling covers >80% of the genera and all currently and previously recognized families. A morphological assessment of taxonomically important gynoecial and fruit characters was done to guide our proposed family-level classification. • Key Results The phylogenies are largely consistent with previous phylogenetic studies, with overall better resolution and support from both data sets (exons, supercontigs) and all analyses implemented (coalescence, ASTRAL-Pro3, concatenation). Novel findings include Hydrophyllaceae nested within Namaceae. The parasitic Lennoaceae is as expected nested within Ehretiaceae. The placement of Codonaceae remains ambiguous: retrieved within the Boraginales I, as sister to the clade comprising Wellstediaceae and Boraginaceae based on exons, and as sister branch to all remaining Boraginales II based on supercontigs. We propose the recognition of a total of nine families in Boraginales. Tribal relationships in Boraginaceae subfam. Cynoglossoideae are fully resolved for the first time. Our data show that shifts in placentation and ovule number are instrumental for the arisal of complex internal ovary architectures. • Conclusions The results highlight the effectiveness of the Angiosperms353 probe set for understanding the evolutionary history of Boraginales and pave the way for resolving remaining unresolved nodes and taxonomic issues. Complex modifications of the bicarpellate ovaries lead to an extreme and lineage-specific diversification of fruits that likely played a crucial role in Boraginales macroevolution. Combining this highly resolved phylogeny with critical morphological analyses in the future promises a deep understanding of evolutionary trajectories in Boraginales.