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).