Pan-orchid transcriptomics sheds light on candidate regulators and the evolution of complex floral morphology and symmetry.

Complex floral traits contribute to reproductive fitness and are critical for diversification in many angiosperms; explicating their evolution and molecular basis is therefore crucial for a comprehensive understanding of this lineage. Orchidaceae species often have highly elaborated lips and specialized floral traits, providing excellent opportunities for the analysis of complex floral traits. Previous studies have made significant progress on the specification of orchid floral organ identities, including the roles of AP3 and AGL6 homologs in promoting the lip identity; however, few candidate genes have been reported for development and elaboration of the lip and other perianth organs at late floral stages. Here, we present an expanded orchid nuclear phylogeny with 709 species and use their phylogenetic relationships to facilitate investigations of the evolution of floral organs and related genes, including molecular phylogenetic analyses of 1,100 AP3 and ∼650 AGL6 homologs from hundreds of orchids and pan-orchid comparative transcriptomics for eight organs of opened flowers and the leaf from eight orchids in four subfamilies. These integrated analyses reveal high expression of the developmental regulators AP3-2 and AGL6-2 in the lips of eight orchids, supporting the functional conservation of specific AP3 and AGL6 paralogs in the orchid lip at the late stage of floral development. Our analyses also delineate the transcriptomic landscapes of organ-level gene activities, revealing similar expression patterns among different orchid lineages. Finally, we identify an ALOG gene, bZIP-family members, and HD-ZIP genes as candidate regulators of lip development and elaboration at the late floral stage in multiple orchid lineages. This study presents comprehensive molecular portraits of orchid floral organs, together with new insights into the development and evolution of complex angiosperm flowers.