Species discrimination in Pedicularis (Orobanchaceae) based on the
chloroplast genome
Abstract
Complete plastid genomes have recently been proposed as ”super-barcodes”
for genetic identification and delineation in plants, for which standard
DNA barcodes may fail. However, relatively few studies have fully
considered the genetic mechanisms inherent to the taxonomic complexity
of specious genera and how this may affect species resolution via
complete plastome barcodes. Pedicularis is a highly diversified group of
plants whose floral traits have undergone rapid radiation in the
Himalaya-Hengduan Mountains, which can complicate identification and
classification within the group based on morphological traits alone. In
this study, we analyzed 292 plastomes representing 96 species of
Pedicularis to compare species discrimination rates with those based on
standard DNA barcodes. The results show that the traditional standard
barcode (nrITS+matK+rbcL+trnH-psbA) and the large single copy (LSC)
region of the plastid genome share the highest discrimination rates
(80.21%), followed by the plastid genome, the supermatrixes of
protein-coding genes and high variable regions (79.17%), and the matK
gene and ycf1 gene alone could discriminate 78.13% of species. Further,
we found that the sequence length and percentage of
parsimony-informative sites significantly influence species
discrimination rates, and genes with higher species discrimination rates
are more likely to be conservative in selection. Given the extra costs
and time required for generating such “super-barcodes” to try to
discern species in taxonomically complex genera, this study questions
their use and calls for more efforts to explore nuclear markers that may
improve discrimination rates in future studies with relatively low-cost
and effort.