Unraveling the Genome of Epidendrum Fulgens: Demographic History and Gene Family Dynamics in a Resilient Neotropical Orchid.

Epidendrum L. (Orchidaceae) is one of the largest plant genera in the neotropics, accounting for more than 1,500 species and a high variety of morphological, physiological, and ecological adaptations. However, addressing evolutionary and ecological questions in the genus is a challenge due to the lack of publicly available genomic resources. Here, we present the first chromosome-scale genome assembly from the orchid genus Epidendrum, E. fulgens (2n = 24, 2C = 2.4 pg), a perennial-terrestrial that occurs in coastal restingas and inland granitic rock outcrops along the Brazilian Atlantic Forest. The genome sequencing was performed using PacBio HiFi and Omni-C technologies, and the final assembly comprised 12 chromosome-scale scaffolds, representing the 12 pseudochromosomes expected for E. fulgens. The primary assembly pseudochromosomes captured 97.3% of BUSCO genes, with an N50 of 88.6 Mbp and L50 of 5; similar metrics were observed for both locally phased haplotypes. Approximately 77% of the genome consisted of transposable elements, and the annotation identified 30,830 protein-coding genes and 6,141 associated Gene Ontology (GO) terms. We also found two events of population expansion and retraction in E. fulgens demographic history, and many expanded and contracted gene families. GO enrichment analysis showed functional categorization for the expanded and contracted gene sets (cell cycle regulation, cell shape and morphology, osmoregulation, environmental plasticity, and stress response), evidencing the traits that are functionally important for this species' adaptation and persistence in nutrient-poor soils and extreme environments. With this study, we highlight the need to further explore the genomic space in the Orchidaceae family and in the Neotropical region, providing new resources for future studies aiming to investigate the origin and resilience of Neotropical flora.