Application of rbcL in DNA barcoding of Phaleria macrocarpa (Scheff.) Boerl. and its processed commercial products

Abstract

DNA barcoding is a molecular-based identification method which utilizes specific short DNA fragment known as DNA barcode. It can be used to assist species identification of specimens already lacking its original morphological traits such as processed herbal products. Phaleria macrocarpa (Scheff.) Boerl. is a plant species that originated from Malaysia and Indonesia and is locally known as God’s crown or Mahkota dewa in Malaysia. It is frequently used in Malaysian and Indonesian traditional medicines. Its fruits for example are used to treat flu, rheumatism, cancer, diabetes mellitus and hypertension. Due to its restorative properties, this plant is now commercially grown in Malaysia where its fruit is usually processed into various types of herbal products such as capsules, tea and coffee. However, due to the increasing popularity of this plant, it is important to have an effective method that can determine the authenticity of P. macrocarpa based products. In this study, the plastid rbcL barcoding gene was used to verify the authenticity of two local processed products claimed to have been made using the fruit of P. macrocarpa. The amplification of the partial rbcL gene was done via Polymerase Chain Reaction (PCR) using KAPA3G Plant PCR Kit. The DNA sequencing results were trimmed using ChromasPro before being aligned using ClustalW which was included in MEGA5. Species verification using the BLASTn search tool revealed that the species contained in both products were found to be P. macrocarpa. Phylogenetic reconstruction via Neighbour-Joining tree using partial rbcL gene amplified from the two tested products and fresh Mahkota dewa plant also revealed high similarity, supporting the BLASTn analysis. In conclusion, this study has shown that the rbcL barcode is suitable to be used to determine the authenticity of processed commercial products of P. macrocarpa. Furthermore, we believe that there is currently no DNA barcoding study that focuses solely on P. macrocarpa and its commercial products. To the extent of our abilities, we believe that there is currently no DNA barcoding study that focuses solely on P. macrocarpa and its commercial products, using the KAPA3G Plant PCR kit. We propose that to determine the authenticity of any P. macrcarpa based products; the rbcL barcode can be used with the KAPA3G Plant PCR kit, especially in laboratories that do not have access to liquid nitrogen.