Comparative plastid genome analysis of four different variants of Gastrodia elata and development of molecular markers based on plastid DNA sequences

BACKGROUND: Gastrodia elata is an important medicinal plant, generally considered to have five distinct variants. These variants differ in quality and medicinal value. However, accurately identifying them has remained a significant challenge in both production and research due to their confusingly similar morphology. RESULTS: This study describes the morphological characteristics of both the underground tubers and the aerial parts of plants from four variants of G. elata collected from major producing areas in China. Subsequently, we performed plastid genome sequencing on 11 of these samples, assembling and annotating their complete plastid genomes. The 11 plastid genomes range in size from 35,275 to 35,328 base pairs, and all encode 20 protein-coding genes, 3 rRNA genes, and 5 tRNA genes, demonstrating highly conserved genome size and gene content. Phylogenetic analysis revealed that the four G. elata variants can be classified into three clades: G. elata f. elata and G. elata f. glauca, each formed distinct monophyletic clade, while G. elata f. flavida and G. elata f. viridis clustered together. Based on comparative analysis of the plastid genomes, we identified two insertion-deletion (InDel) loci and successfully developed the corresponding InDel markers, designated as GEpt11 and GEpt13. These markers were validated via PCR amplification experiments on 22 samples. CONCLUSIONS: Here, we report the first complete plastome of Gastrodia elata f. flavida; and development of practical InDel markers GEpt11 and GEpt13 distinguishing G. elata variants. These results providing molecular tools for germplasm identification, breeding, and quality control of G. elata.