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

<b>Background/Objectives:</b> 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 <i>Epidendrum</i>, the largest Neotropical genus of Orchidaceae. Here, we assessed repeatome profiles across 34 <i>Epidendrum</i> species using publicly available genomic datasets. <b>Methods:</b><i>Epidendrum</i> repeatomes were characterized with the RepeatExplorer2 pipeline, and patterns of repeat composition were evaluated for phylogenetic structure using a species phylogeny. <b>Results:</b> 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). <b>Conclusions:</b> This study provides the first comprehensive characterization of the <i>Epidendrum</i> 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 <i>Epidendrum</i>. Potential drivers, as hybridization and ecological differentiation, should be tested explicitly in future analyses integrating broader genome size sampling and trait data.