Bioinformatics for Molecular Authentication of Chinese Medicinal Materials

Abstract

Correctly identified medicinal materials are the premise of research and applications on Chinese medicine. DNA authentication is an accurate method for routine identification of medicinal herbs. The molecular authentication procedure involving DNA sequencing takes five steps: (a) to extract DNA from the sample, (b) to amplify a specific region of the genome by polymerase chain reaction; (c) to sequence the PCR product; (d) to find the available DNA sequences in a nucleotide database; and (e) to compare the unknown sequence with the available reference sequences. Molecular authentication can also be done by DNA fingerprinting that assess the whole or specific region of genome. In the process, informatics assists in: (a) providing a means for storing, sorting, retrieving, and analyzing of experimental data; (b) providing computer programs for identifying the unknown sample by matching with the reference sequences; and (c) aiding the design of appropriate testing procedures and identification tools. This chapter introduces several public databases for the search of taxonomic and nucleotide information, such as Flora of China, NCBI Nucleotide database, Barcode of Life Data Systems (BOLD), and Medicinal Materials DNA Barcode Database (MMDBD). The procedures of mass retrieving and sorting of sequences from databases will be demonstrated. The pros and cons of various DNA sequence formats like FASTA, Abstract Syntax Notation 1 (ASN1), eXtensible Markup Language (XML) will be discussed. Finally, the precautions of using software packages for performing sequence alignment, matching species in databases, and constructing phylogenetic trees will be described.