Conventional DNA barcodes of rice
Three chloroplast regions (matK , psbA-trnH , andrbcL ) and one nuclear region (ITS) represent conventional DNA barcodes for higher plants (Hollingsworth et al., 2009; Kress et al., 2005). Chloroplast regions perform differently in different plant groups. Here, we extracted these regions and conducted phylogenetic analyses to evaluate their suitability for species resolution. Their performance was barely satisfactory in Oryza. Generally, thematK gene offers higher resolution than rbcL , but inOryza , it did not perform much better. Fewer than half of the 21 species were reliably (bootstrap values >75%) resolvable. Both barcodes failed to discriminate between species of the A ,B , and C genome types. Moreover, a combination ofmatK +rbcL did not improve the situation, because both barcodes resolved almost the same species without complementation. ThepsbA-trnH intergenic spacer, one of the most variable regions in chloroplast genomes, performed similarly poorly with only one identifiable species. This is probably due to the insertion ofrps19 , which replaced the spacer with rps19 sequences.
The nuclear ITS afforded similar resolution as conventional chloroplast regions. Although there are 10 allotetraploid species in Oryza , only one genome was detected in O. coarctata (KL ),O. ridleyi (HJ ), and O. schlechteri(HK ). However, two kinds of sequences were observed in O. longiglumis (HJ ), one of them was similar to that of O. ridleyi, and the other was similar to that of O. brachyantha , a phenomenon never reported previously. Similarly, only the Cgenome type was confirmed in O. alta and O. grandiglumis , whereas the B genome type defined O. malampuzhaensis . Both B and C genome types were detected in O. schweinfurthiana . The sequences deposited in GenBank include only one kind of sequence for species of the BC and CD genome types, which is probably because of concerted evolution of the ITS in relatively old tetraploids. Only newly formed tetraploids such asO. schweinfurthiana maintain both B and Cgenome types.