Abstract
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, ycf1a and ycf1b, 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 ycf1b, which was slightly better than the combination of matK and rbcL. For the well-sampled representative plant groups, ycf1b generally performed better than any of the matK, rbcL and trnH-psbA. We concluded that ycf1a or ycf1b is the most variable plastid genome region and can serve as a core barcode of land plants.
Highlights
A DNA barcode is a DNA fragment used to identify species
The candidate barcodes are selected from markers used in molecular systematics due to the limited knowledge of genome variations; we know little about mitochondrial genomes, much less nuclear genomes
Several plastid genome regions such as atpF-H, matK, psbK-I, rbcL, ropC1, rpoB, trnH-psbA, and trnL-F that are frequently used in plant molecular systematics have been extensively evaluated[2,3,4], and the rbcL and matK genes were selected as core plant barcodes by the CBOL Plant Working Group[5]
Summary
A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. The section of ycf[1] in the SSC region has high sequence variability in seed plants This region of the ycf[1] gene is more variable than matK in most taxa investigated far[11,12] and has been used in molecular systematics at low taxonomic levels[13,14,15,16,17]. Because ycf[1] is too long (5709 bp in Nicotiana tabacum) and too variable to permit the design of universal primers[9], it has received little attention for DNA barcoding or molecular systematic purposes at low taxonomic www.nature.com/scientificreports levels; the high variability of ycf[1] indicates its potential value in DNA barcoding of land plants. We (1) generated primers for PCR amplification of ycf1a and ycf1b, and (2) tested the performance of ycf1a or ycf1b in discriminating between species compared with the plastid genes rbcL, matK and trnH-psbA
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