Comparative plastid genomics of Gastrochilus (Orchidaceae) with insights into molecular markers and phylogeny

Abstract Background Gastrochilus (Orchidaceae) is a genus of epiphytic orchids valued for horticultural and medicinal purposes. However, the structural and evolutionary features of its plastid genomes have not been systematically examined. Here, we characterize the complete plastid genomes of 23 Gastrochilus species, elucidating structural features and key variations to provide new insights into their evolutionary significance. Results The plastid genomes showed a typical quadripartite structure, ranging from 146,183 to 148,666 bp in length. Each genome encodes 120 genes, comprising 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A prominent feature was the recurrent pseudogenization or loss of ndh genes. We identified 1,200 simple sequence repeats and 905 dispersed repeats. Codon usage was highly conserved, with a consistent preference for A/U-ending codons and an overall weak codon usage bias. Expansion and contraction of the inverted repeat regions notably affected the position of ycf1 . Nucleotide diversity analysis revealed ten hypervariable regions and eight genes as potential molecular markers. Evidence of positive selection was detected in rps16 and ycf2 . Phylogenetic analysis divided the 23 Gastrochilus species into four well-supported clades. Conclusions The plastid genomes of Gastrochilus display highly conserved architecture. The recurrent loss or pseudogenization of ndh genes, along with positive selection in ycf2 , may reflect adaptations to low-light forest environments. The identified repeat sequences and hypervariable regions provide valuable molecular markers for phylogenetic studies and species identification. This phylogenetic framework, based on complete plastid genomes, offers the most comprehensive resolution for Gastrochilus to date. However, the adaptive significance of these genomic features requires further experimental validation to confirm their ecological relevance.