The Gongora gibba genome assembly provides new insights into the evolution of floral scent in male euglossine bee-pollinated orchids

Orchidaceae is one of the most prominent flowering plant families, with many species exhibiting highly specialized reproductive and ecological adaptations. An estimated 10% of orchid species in the American tropics are pollinated by scent-collecting male euglossine bees; however, to date, there are no published genomes of species within this pollination syndrome. In this study, we present the first draft genome of an epiphytic orchid from the genus Gongora, a representative of the male euglossine bee-pollinated subtribe Stanhopeinae. The 1.83-Gb de novo genome with a scaffold N50 of 1.7 Mb was assembled using short- and long-read sequencing and chromosome capture (Hi-C) information. Over 17,000 genes were annotated, and 82.95% of the genome was identified as repetitive content. Furthermore, we identified and manually annotated 26 terpene synthase genes linked to floral scent biosynthesis and performed a phylogenetic analysis with other published orchid terpene synthase genes. The Gongora gibba genome assembly will serve as the foundation for future research to understand the genetic basis of floral scent biosynthesis and diversification in orchids.