The Coelogyne s.l. is one of the emblematic genera of the Asian orchids, with high horticultural and medicinal values. However, the phylogenetic relationships of the genus inferred from previous studies based on a limited number of DNA markers remain ambiguous. In this study, we newly sequenced and assembled the complete plastomes of seven Coelogyne species: C. bulleyia, C. fimbriata, C. flaccida, C. prolifera, C. tricallosa, C. uncata, and an unknown taxa, Coelogyne sp. The plastomes of Coelogyne exhibited a typical quadripartite structure, varying in length between 157,476 bp and 160,096 bp, accompanied by a GC content spanning from 37.3% to 37.5%. A total of 132 genes were annotated for each plastome, including 86 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Among these, 19 genes underwent duplication within the inverted repeat (IR) regions, and 18 genes exhibited the presence of introns. Additionally, we detected 54 to 69 simple sequence repeats (SSRs) and 30 to 49 long repeats. In terms of codon usage frequency, leucine (Leu) emerged with the highest frequency, while cysteine (Cys) exhibited the lowest occurrence. Furthermore, eight hypervariable regions (atpB-rbcL, psbK-psbI, rps8-rpl14, rps16-trnQ^UUG, psaC-ndhE, ndhF-rpl32, psbB-psbT, and ycf1) were identified. Phylogenetic analyses using complete plastomes and protein-coding genes indicated that Coelogyne s.l. was monophyletic. Moreover, the results robustly supported the division of Coelogyne s.l. into five clades. This study provides a comprehensive analysis of the structural variation and phylogenetic analysis of the Coelogyne s.l. based on plastome data. The findings offer significant insights into the plastid genomic characteristics and the phylogenetic relationships of Coelogyne s.l., contributing to a deeper understanding of its evolutionary history.

Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In this study, we sequenced and analyzed the complete plastome sequences of A. gracile and E. japonica for the first time, aiming to elucidate their plastome characteristics and phylogenetic relationships. Both plastomes exhibited a conserved quadripartite structure, with 158,358 bp in A. gracile and 152,432 bp in E. japonica, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: E. japonica lacked seven ndh genes (ndhC/D/F/G/H/I/K), whereas A. gracile retained a complete ndh gene set. Repetitive sequence analysis identified an abundance of simple sequence repeats (68 and 77), tandem repeats (43 and 30), and long repeats (35 and 40). Codon usage displayed a bias toward the A/U termination, with leucine and isoleucine being the most frequent. Selection pressure analysis indicated that 68 protein-coding genes underwent purifying selection (Ka/Ks < 1), suggesting evolutionary conservation of plastome protein-coding genes. Nucleotide diversity analysis highlighted six hypervariable regions (rps8-rpl14, rps16-trnQ^UUG, psbB-psbT, trnT^UGU-trnL^UAA, trnF^GAA-ndhJ, and ycf1), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. A. gracile formed a sister relationship with Mengzia foliosa and E. japonica, whereas Arundina graminifolia exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae.