Total genomic DNA was extracted using a modified CTAB from silica-dried tissues of G. elata (Supplementary Table 42). The DNA was sheared to 500 bp, and sequencing libraries were generated using the NEBNext Ultra DNA Library Prep Kit (according to the manufacturer’s protocol) for sequencing on an Illumina Hiseq 2500 at the State Key Laboratory of Systematics and Evolutionary Botany, Chinese Academy of Sciences. The raw reads were filtered using NGSQCTOOLKIT v 2.3.3. The cleaned reads were mapped to Calanthe triplicata in GENEIOUS 9.0 (Biomatters, Inc., Auckland, New Zealand; http://www.geneious.com). Used reads were exported and assembled using SOAPDENOVO2. The plastid sequences were extracted from the total contigs using BLASTN 2.2.29+ and the C. triplicata plastome (GenBank ID: NC_024544) as subject sequence. The finished plastome scaffolds were reoriented according to the C. triplicata reference plastome. The boundaries of IRs were determined by BLAST, and finished manually. The plastomes of G. elata were determined using DOGMA with an e-value of 5, a 60% cut-off for protein-coding genes and 80% cut-off for tRNAs; the GENEIOUS annotation tool was used to determine the plastomes of C. triplicata and Oncidium Gower Ramsey (GenBank ID: NC_014056.1) as references. Linear plastome maps were drawn using OGDRAW.