Variable yet vague: Questioning the utility of PHYB for barcoding in Potamogeton

Abstract

Abstract Potamogeton is a cosmopolitan genus of aquatic plants comprising ca. 72 species and 99 hybrids. Hybridization and polyploidization events are characteristic of its evolutionary history, thus molecular approach is desirable for confirmation of species and hybrids determinations. In this study, we tested the suitability of low-copy nuclear gene PHYB as a barcoding marker, as this gene was shown to have sufficient level of variability in Potamogeton in preceding studies. We cloned and sequenced part of gene PHYB exon 1 for 19 samples of 8 Potamogeton species. Our sampling took place in East Europe, Siberia, Russian Far East and NE North America. The obtained sequences were used to construct a genetic network. We report some features of PHYB which hamper its application as a barcode in Potamogeton. Most of the tetraploid species provided two sets of dissimilar PHYB sequences, which probably stand for two paralogs. PCR-derived errors, such as recombination and random substitutions, shifted the position of some sequences in the network. In addition, one haplotype was shared between two closely related species, breaking the species-specificity of PHYB barcode. Even though it may provide higher resolution for hybrid identification than ITS or 5S-NTS, using it as a marker for standard barcoding in this genus is not the best option.