Selection And Algorithms Of DNA Barcodes In The Genus Paris

DNA barcoding was a technique in which species identification and discovery were performed by using short and standard fragment of DNA sequences. Study on DNA barcodes in the genus Paris, classification and identification could be clarified further. In this study, eleven species of Paris, including seven varieties, were sampled. Five chloroplast sequences, psbA-trnH, rpoB, rpoCl, rbcL, matK, and one nuclear marker, the second internal transcribed spacer (ITS2) of ribosomal DNA, were amplified and sequenced. The PCR amplification and sequencing efficiency, intra-and interspecific divergence and barcoding gap were used to evaluate different loci, and the identification efficiency was assessed using BLAST1 and Nearest Distance methods. Good algorithms should be applicated in DNA barcoding as good sequences were selected. Using Liliopsida reference database, the identification efficiency of similarity methods, distance methods, HMM methods and diagnostic methods were studied.1. The ITS2 sequences in the studied samples of Paris were amplified and sequenced successfully using primers designed by our group, while matK showed low level in the amplification and psbA-trnH was difficult for sequencing because of over 800bp and poly (A) structure. Analysis of the intra-and interspecific divergence and barcoding gap showed ITS2 was superior to other loci. The ITS2 showed a much higher percentage of success (100%) in identification than other five loci, none of which indicated more than 50% except matK (52.9%). The 2-locus combination of rbcL+matK didn't improve ability of authentication. In addition, the rate of successful identification with ITS2 kept 100% when the samples were expanded to 67 samples of 29 species. In conclusion, ITS2 could be used to identify plant of Paris correctly, and it would be a potential DNA barcode for identifying plant of other taxa.2. In our study, BLAST, HMM, K2P Distance and DNA-BAR were used to distinguish the species of Liliopsida. According to the results, BLAST and HMM methods were superior to others because of high precision and accuracy, and approximately 80% samples could be differentiated perfectly. Based on BLAST and HMM methods, rapid and automatable identification for query was possibly. The identification efficiency was apparent in Liliopsida for ITS2, it would be a potential barcode in plant.3. Feature analysis of ITS2 sequences was necessary because of successful results in Paris, even Liliopsida. As the results, the sequences length was low variation, ranged from 214bp to 260bp, and GC contents were from 47% to 73% mainly. Using BLAST and HMM methods,67 samples of Paris could be distinguished successfully for ITS2 in Liliopsida. Lastly, Liliopsida ITS2 database was established for further study.