The Complete Chloroplast Genome of Encyclia tampensis (Orchidaceae): Structural Variation and Heterogeneous...

The epiphytic orchids of the tribe Epidendreae represent a remarkably evolutionary radiation, yet their phylogenetic relationships and plastome evolutionary dynamics are still not fully resolved.

This study has sequenced, assembled, and annotated the complete chloroplast genome of Encyclia tampensis. Through comparative analyses of a curated dataset of 40 Epidendreae plastomes, we investigated codon usage bias, evolutionary selection pressures (Ka/Ks), and phylogenetic relationships.

The plastome of E. tampensis (160,650 bp) has a typical quadripartite structure, with a significant AT bias (62.09%), and contains 124 annotated genes. Comparative genomic analysis across 40 Epidendreae species revealed substantial plastome size variation (123,455 to 160,650 bp), pronounced small single copy (SSC) contraction in E. tampensis (608 bp), and atypical long simple sequence repeats (SSRs) accumulation. Natural selection dominated codon usage, with strongest purifying selection in rbcL (average Ka/Ks = 0.205). Phylogenetic analyses confirmed subtribal monophyly and detected evolutionary rate heterogeneity correlated with life history strategies.

These results establish that plastome evolution in Epidendreae has been principally driven by structural reorganization through SSC contraction and long SSR accumulation, selective constraints maintaining functional genes under purifying selection, and life history-strategy-mediated evolutionary rate diversification. These processes collectively account for the tribe's extensive genomic diversity and phylogenetic complexity, thereby providing a theoretical framework for understanding orchid plastome evolution and a molecular basis for the systematic classification and conservation of this economically significant plant group.