Chloroplast DNA sequencing protocol

After the cpDNA isolation with modified high salt method, approximately 5–10 µg of DNA was sheared, followed by adapter ligation and library amplification, subjecting to Illumina Sample Preparation Instructions. The fragmented cpDNAs were sequenced at both single-read using the Illumina Genome Analyzer IIx platform at the in-house facility at The Germplasm Bank of Wild Species in Southwestern China. The obtained paired-end reads (2×100 bp read lengths) were assembled to the reference genome sequence to roughly estimate the genome coverage and cpDNA purity (the reads aligned to the reference genome sequence were served as cpDNA sequence) using the software program Geneious version 4.7 [20] . The reference chloroplast genome sequence of O. nivara (NC_005973) and P. persica (NC_014697) were downloaded from GenBank.