PJB-2012-195
EVALUATION OF THE CHLOROPLAST BARCODING MARKERS BY MEAN AND SMALLEST INTERSPECIFIC DISTANCES
DA-CHENG HAO1*, PEI-GEN XIAO2*, YONG PENG2, JINGQUN DONG1 AND WENXIA LIU1
Abstract
It is more difficult in plants than in animals to distinguish between species using barcoding loci, thus it is vital to investigate the barcoding potential of various chloroplast (cp) regions besides the well-known plastid markers. It is also crucial to investigate whether the analytical metrics and depths of taxon sampling affect assessments of the barcoding utility. Here, we collected more than 9100 plant sequences, representing ten cp non-coding regions, by experiments and GenBank search. The inter- and intra-specific variations of the individual genus were calculated. The correlation between the number of sampled congeneric species and mean/smallest interspecific distance was quantitated. In addition, a selection of published barcoding data sets was reviewed to compare species discrimination of trnH-psbA in various plants. By comparing the barcoding gaps, we found that species pairs for different cp markers have variable size gaps between intra and interspecific genetic distances and the approach based on mean interspecific distances results in overblown estimates and may lead to misidentification of closely related species, which is problematic for all cp markers examined. It is also found that the smallest interspecific distances decrease with the number of species sampled in 6 out of 10 cp markers examined. The differences in the size of barcode gaps based on mean versus smallest interspecific distances may have major implications for the plant DNA barcoding. This study presents the first empirical evidence to advocate the simultaneous use of mean and smallest interspecific distances in assessing plant barcoding markers.
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