Assessment Of Candidate DNA Sequences For Barcoding Plants From Rubiaceae And Verbenaceae Family

Objective:To screen out suitable DNA barcodes for identifying plant in Verbenaceae family and Rubiaceae family, we evaluate hotspot candidate sequence of DNA barcodes in the international, psbA-trnH, rbcL, matK and ITS2/ITS, discussed the status of this sequences in Verbenaceae family and Rubiaceae family.Methods:Using universal primers, three chloroplast sequences, psbA-trnH, rbcL, matK and two nuclear ribosomal DNA ITS2, ITS were amplified and sequenced. PCR amplification and sequencing efficiency, intra-and inter-specific variation, barcoding gap and identification efficiency (with BLAST1and Nearest Distance methods), phylogenetic tree were used to evaluate these DNA barcodes.Result:The rate of successful amplification using matK was too low to further analysis, and the rate of successful amplification and sequencing using psbA-trnH, ITS, ITS2and rbcL sequence was83.6%(46)、83.6%(46)、96.4%(53) and98.2%(54) seperately. The rate of successful identification using psbA-trnH, ITS, and ITS2was100%at the species level except that rbcL was77.8%(BLAST1) and75.9%(Nearest Distance) for55samples belonging to32species in Verbenaceae family, but ITS2did better in intra-and inter-specific variation, barcoding gap than the other loci. The rate of successful identification of ITS2was89.5%(BLAST1) and87.6%(Nearest Distance) even when joining the date of163samples from GenBank, while was100%in the level of genus of all.The rate of successful amplification and sequencing using ITS, ITS2,psbA-trnH and rbcL sequence was96.0%(24).96.0%(24).100%(25) and100%(25) seperately for clerodendreae briq. The intra-and inter-specific variation and rate of successful identification using psbA-trnH and ITS2had no significant differences.In Rubiaceae family, the rate of successful amplification and sequencing using psbA-trnH, ITS2and rbcL sequence was96.5%(82)、72.9%(62) and88.2%(75) seperately. The rate of successful identification using psbA-trnH, ITS2was100%at the species level except that rbcL was76.0%and73.3%for85samples belonging to53species in Rubiaceae family. The rate of successful identification of ITS2for929samples was83.5%(BLAST1) and80.4%(Nearest Distance) even when joining the date of samples from GenBank in species level,96.7%(BLAST1) and96.4%(Nearest Distance) in genus level.Conclusion:It proposes that the ITS2was candidate DNA barcodes for identifying plant in Verbenaceae family and Rubiaceae family, psbA-trnH can be added because of higher PCR amplification and sequencing efficiency. The combination of ITS2and psbA-trnH senquence is suitable for the identification of the species in Verbenaceae family and Rubiaceae family, and psbA-trnH was main sequence in clerodendreae briq (Verbenaceae family).