The Repeatome in the Mega-Genus Epidendrum L. (Epidendroideae, Orchidaceae): An In Silico Comparative Analysis

Background/Objectives: Variation in repeatome composition is a major determinant of genome architecture and an important substrate for evolutionary change in plants. Despite the availability of genomic sequence data, repeatome-wide assessments have not been performed for Epidendrum, the largest Neotropical genus of Orchidaceae. Here, we assessed repeatome profiles across 34 Epidendrum species using publicly available genomic datasets. Methods:Epidendrum repeatomes were characterized with the RepeatExplorer2 pipeline, and patterns of repeat composition were evaluated for phylogenetic structure using a species phylogeny. Results: Repeat composition showed no clear phylogenetic structure, with closely related species often displaying divergent satDNA and TE profiles. satDNA content varied widely among species (15.5–69% of the repeatome fraction). A total of 208 satDNA families were detected, which were used to build a custom database for comparative analyses. We detected 73 satDNA clusters shared among species, whereas only three were species-specific. Regarding TEs, Class I elements were the most abundant repeats, dominated by Ty3-Gypsy LTR retrotransposons. Only two Class II TIR superfamilies were detected (EnSpm/CACTA and hAT). Conclusions: This study provides the first comprehensive characterization of the Epidendrum repeatome and establishes a resource for future work on cytogenomic diversity within this megagenus. The heterogeneous distribution of repeats among closely related species is consistent with lineage-specific amplification and loss, highlighting rapid repeatome turnover in Epidendrum. Potential drivers, as hybridization and ecological differentiation, should be tested explicitly in future analyses integrating broader genome size sampling and trait data.