Phylogenetic and mutation sites analysis on chloroplast DNA sequences in Dendrobium Sw / 中草药

ABSTRACT

Objective To analyze the phylogenetic and mutation sites of IRa (trnV-GAC to trnR-ACG) sequence among 10 Dendrobium Sw. samples, to understand the similarities and differences of nine genes in this sequence, and to explore the system evolution and DNA barcode in species of Dendrobium Sw. Methods The improved kit method was used to extract total DNA and design primers, PCR method and T-vector cloning transformation were used to amplify the region of IRa and the sequences were obtained after the amplified fragment sequences were blasted in NCBI database and splicing. Genetic structures were drawn, and variable sites, genetic distance and phylogenetic relationship among 10 sequences were analyzed. Results The lengths of sequences were about 7 800 bp and 55 variable sites were found. The numbers of mutation points distributeed on trnV-GAC, rrn16, trnI-GAU, trnA-UGC, orf42, rrn23, and intergenic region were 1, 8, 12, 6, 1, 9, and 18, respectively. These 10 samples were clustered to four latitude-dependent groups based on IRa sequences. Conclusion A set of methods on sequence IRa is established. Phylogenetic and mutation point analysis indicate that there is a rich and relatively concentrated distribution variation loci among the research sequences. And it will provide a good theoretical basis on the further study of DNA barcodes, authentic assessment and identification of Dendrobium Sw. germplasm resources.