Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of
the most commonly used DNA markers in plant phylogenetic and DNA barcoding
analyses, and it has been recommended as a core plant DNA barcode. Despite
this popularity, the universality and specificity of PCR primers for the
ITS region are not satisfactory, resulting in amplification and sequencing
difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S
sequences of Plantae and Fungi from GenBank, we designed new universal and
plant-specific PCR primers for amplifying the whole ITS region and a part
of it (ITS1 or ITS2) of plants. In silico analyses of the new and the
existing ITS primers based on these highly representative data sets
indicated that (i) the newly designed universal primers are suitable for
over 95% of plants in most groups; and (ii) the plant-specific primers are
suitable for over 85% of plants in most groups without amplification of
fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm
families, 24 fern and lycophyte families, 16 moss families and 17 fungus
families were used to test the performances of these primers. In vitro PCR
produced similar results to those from the in silico analyses. Our new
primer pairs gave PCR improvements up to 30% compared with common-used
ones. The new universal ITS primers will find wide application in both
plant and fungal biology, and the new plant-specific ITS primers will, by
eliminating PCR amplification of nonplant templates, significantly improve
the quality of ITS sequence information collections in plant molecular
systematics and DNA barcoding.