Screening potential DNA barcode regions for Urticaceae plants

【Objective】Identification ability of DNA barcode sequences for Urticaceae plants was evaluated to provide references for Urticaceae plants identification. 【Method】DNA fragments of 4 hot regions(ITS,matK,rbcL and psbA-trnH) were amplified by PCR and sequenced using universal primers from Urticaceae family to compare PCR amplification efficiency and sequencing success rate. The nucleotide constitution and mutation of sequences were analyzed to compare inter-and intraspecific divergences and estimate barcoding gap. 【Result】psbA-trnH region had the highest amplification efficiency(100.0%) in 30 plant samples belonging to 13 Urticaceae species. The sequencing efficiency rate was the highest for psbA-trnH region, which was 95.4%. It was 92.3%, 90.1%, and 0 for ITS, rbcL and matK, respectively. The genetic distance of ITS sequences was from 0 to 0.508. The genetic distance of psbA-trnH sequence was from 0 to 0.522. The genetic distance of rbcL sequence was from 0 to 0.532. ITS region had better inter-and intraspecific divergences and DNA barcoding gap than other tested regions(rbcL and psbA-trnH). The phylogenetic tree based on ITS sequence had the highest percentage on a monophyletic clade for different species, and followed by psbA-trnH and rbcL sequences. The clustering results showed that the best method was MP, followed by UPGMA, ML and NJ. NJ method was the most unsatisfactory. 【Conclusion】The interspecific divergences were significantly bigger than the intraspecific divergences in Urticaceae plants. DNA barcode was suitable for identifying Urticaceae plants. Among all sequences in this study, no any single sequence could completely identify different types of Urticaceae species. ITS,rbcL and psbA-trnH can be used as a combination of DNA barcode sequence to identify the species in Urticaceae.