Complete Chloroplast Genome of the <i>Eria</i> Sensu Lato Complex (Orchidaceae): Comparative Analysis and Phylogenetic Relationship

The <i>Eria</i> sensu lato (<i>Eria</i> s.l.) complex represents a highly diverse yet taxonomically challenging orchid lineage. To comprehensively elucidate its evolutionary history, we sequenced 14 complete chloroplast genomes and assembled a robust 18-taxon dataset encompassing its major generic lineages. Comparative genomic analyses revealed that despite overall structural conservation with no rearrangements detected (genome sizes ranging from 150.9 to 159.7 kb), the complex exhibits a lineage-specific, stepwise degradation of the NAD(P)H dehydrogenase (NDH) complex. This progressive gene loss, coupled with the physical contraction of inverted repeat (IR) boundaries, directly drives plastome miniaturization in specific taxa (e.g., <i>Eria corneri</i> and <i>E. clausa</i>). To facilitate fine-scale species delimitation, we identified seven hypervariable mutational hotspots, which successfully resolved the majority of interspecific relationships with a topology highly congruent to the whole-plastome tree. Furthermore, selective pressure analysis via branch-site models detected strong episodic positive selection acting on the <i>ycf1</i> gene specifically within the <i>Pinalia</i> clade, highlighting potential eco-physiological adaptations to dynamic epiphytic environments. Finally, phylogenomic reconstructions and divergence dating unveiled a topological incongruence suggesting rapid evolutionary radiation. This concentrated period of early divergence (9.97-5.53 Ma) coincides with Late Miocene paleoclimatic shifts, particularly the intensification of the Asian summer monsoon. Ultimately, this study significantly enriches the plastomic resources for the taxonomically difficult <i>Eria</i> s.l. complex, laying a valuable foundation for future evolutionary studies and systematic revisions.