Journal Article

ycf1, the most promising plastid DNA barcode of land plants

Dong, Wenpan, Li, Changhao, Zhou, Shiliang, Guo, Junjie, Xu, Chao, Cheng, Tao, Zuo, Yunjuan, Sun, Jiahui, Shi, Shuo

2015

Overview

A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid candidate barcodes lack species-level resolution. The identification of DNA barcodes of high resolution at species level is critical to the success of DNA barcoding in plants. We searched the available plastid genomes for the most variable regions and tested the best candidates using both a large number of tree species and seven well-sampled plant groups. Two regions of the plastid gene ycf1 , ycf1 a and ycf1 b, were the most variable loci that were better than existing plastid candidate barcodes and can serve as a barcode of land plants. Primers were designed for the amplification of these regions and the PCR success of these primers ranged from 82.80% to 98.17%. Of 420 tree species, 357 species could be distinguished using ycf1 b, which was slightly better than the combination of matK and rbcL . For the well-sampled representative plant groups, ycf1 b generally performed better than any of the matK , rbcL and trnH-psbA . We concluded that ycf1 a or ycf1 b is the most variable plastid genome region and can serve as a core barcode of land plants.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/181/2480 / 631/449/2669 / Chlorophyll / Deoxyribonucleic acid / DNA / DNA Barcoding, Taxonomic / Embryophyta - classification / Embryophyta - genetics / Genes, Plant / Genome, Plant / Genomes / Humanities and Social Sciences / multidisciplinary / Plant species / Plastids - genetics / Polymerase chain reaction / Primers / Reproducibility of Results / Science / Species / Trees - classification / Trees - genetics