Rice-specific DNA barcode design
Nucleotide diversity across all chloroplast genomes from allOryza species was quantified using DnaSP (Librado & Rozas, 2009) . The most hypervariable regions were selected as rice-specific barcodes. Primers were designed to amplify and sequence these regions.
To determine the origins of polyploid species, two highly variable and single-copy nuclear genes were selected from 142 candidate genes (Zou et al., 2008). Fragments were amplified using specific primers. The fragments of the same sample were mixed with the chloroplast fragments and sequenced together on an Illumina HiSeq X Ten platform. Reads were extracted using known references and assembled with Sequencher 5.4.