Rice-specific DNA barcodes
The hypervariable regions in the chloroplast genomes were identified by the sliding window method of DnaSP, and 36 regions (Table S2) were picked based on nucleotide diversity. Further evaluation of these 36 regions was carried out using the tree building method, and six high-resolution regions (psaJ -rpl33 , rpoB -trnC ,rps16 -trnQ , rps19 -rpl22 ,trnK -matK , and trnV -ndhC , Table 2) were finally chosen as rice-specific chloroplast DNA barcodes. While the above markers displayed higher nucleotide diversity and more variable sites than rbcL ; overall, these two parameters were much higher in nuclear markers (Table 2).