*3.2. Super- and Ultrabarcoding*

Much of the expanding role of barcodes in the past decade has been driven by the rapid growth of high-throughput sequencing technology. As opposed to traditional DNA barcodes, which target individual loci or a set of short loci with universal primers, "superbarcodes" and "ultra-barcodes" have been proposed as alternatives that compare information from entire organellar genomes and/or other long regions [12,13]. For plants, whole chloroplast sequencing has been common for over a decade [196]. Super- and ultrabarcoding provide some unique advantages over traditional barcoding. For example, in some large clades (e.g., the green plant tree of life), traditional DNA barcode loci are not present in all taxa [197] and universal PCR primers often don't exist for some taxa in a given clade (see [8]). In these cases, ultra-barcoding provides a simple solution to chal-

lenges with traditional DNA barcodes, in which the entire chloroplast genome can serve as one single, long barcode locus or in combination with other loci (e.g., nuclear ribosomal DNA, [14]). Moreover, some traditional DNA barcode loci (e.g., *matK*, ca. 1000 bp) are simply too long for amplicon-based approaches using short-read sequencing platforms. Lastly, chloroplast genomes are abundant and typically easy to sequence even from recalcitrant (i.e., old and/or preserved) tissues and it's increasingly common to assemble whole organellar genomes from off-target reads even in targeted/capture-based sequencing applications [198].

As sequence databases grow, the concept of super- or ultra-barcodes is certain to follow. Rather than viewing alternative barcoding strategies as either/or choices, novel DNA barcoding strategies are complementary to locus-based markers, and each contributes to a growing, cumulative database of well-curated data for molecular species identification.
