ITS1: a DNA barcode better than ITS2 in eukaryotes?

A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants, and has been widely used in DNA barcoding analyses for other biological groups, e.g. algae, protists, and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85,345 sequence pairs in ten major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects, and fishes, covering 611 families, 3,694 genera, and 19,060 species, were analyzed. Using similarity-based me...