Is There a Key Primer for Amplification of Core Land Plant <scp>DNA</scp> Barcode Regions ( <scp> <i>rbcL</i> </scp> and <scp> <i>matK</i> </scp> )?

The DNA barcode is a technique for molecular identification of species. Two core genes, <i>matK</i> and <i>rbcL</i>, are widely used for land plants. In this technique, the selection of primers is a fundamental step for the success of amplification. Then, we aim to evaluate the primer amplification capability for the DNA barcode regions <i>rbcL</i> and <i>matK</i>. We extracted primer sequences from DNA barcode studies in the Web of Science and used chloroplast genome sequences from NCBI for <i>in silico</i> PCR tests using OpenprimeR. Physicochemical properties of <i>in silico</i> PCR were evaluated using OpenprimeR. Our literature review resulted in 366 and 489 different <i>rbcL</i> and <i>matK</i> primers. These were tested in 8665 sequences, 8463 species from 98 orders. Evaluating only the primer and sequence match, the primers with the highest number of sequences covered were 96.39% and 93.81% forward and reverse for <i>rbcL</i>, and 91.56% and 61.62% forward and reverse for <i>matK</i>. No universal primer for all land plants was found, but two <i>rbcL</i> primer pairs could amplify > 99% of the sequences. In contrast to the results obtained for the <i>matK</i> region, the 10 pairs optimized for the greatest coverage of sequences were not covered by > 85% of the sequences. Therefore, it is advisable to pay attention when selecting primers for the <i>matK</i> region and the need to develop new primers. Here, we recommend a set of primers to cover the largest number of sequences and orders.