Figure 1.

Scheme of the method of oligonucleotide indexing. PUP: Partial Universal Primer; RS: Read Start sequence; CP: Cocktail Portion; UP: Universal Primer. Sequence polymorphisms are represented by vertical bars; the ones localized in the cocktail portion are used to design the primer cocktail composition and the sequencing primers (Table 2). The PCR generates an amplicon population; each individual amplicon harbours species-specific polymorphisms in the target region (shadowed). Individual amplicons are sequenced using the sequencing primers. Sequences are aligned using the read start reference and analyzed to determine the species content.