Testing eight barcoding markers for Potamogeton species at intraspecific levels

•Potamogetonaceae is one of the most difficult groups to clarify in aquatic plants.•Promising markers are poor to discriminate intraspecific genetic variety in Potamogeton.•Seven cpDNA and two nuclear markers were tested for intraspecific divergence in Potamogeton.•PHYB is the most efficient candidate for intraspecific divergence in Potamogeton.

Potamogetonaceae is one of the most difficult groups to clarify in aquatic plants. The current studies are mostly concentrated on interspecific identification in Potamogeton. Promising barcoding markers are poor to discriminate intraspecific genetic variety in Potamogeton. In this present study, we tested eight barcoding markers for intraspecific divergence in Potamogeton, including seven cpDNA barcodes (trnL-trnL-trnF, rpl20-rps12, trnG intron, trnH-psbA, matK and rbcL) and two nuclear markers (ITS and PHYB). The results demonstrated that PHYB showed a significantly higher degree of intraspecific divergence in Potamogeton than the others. Five barcodes including trnL-trnL-trnF, trnG intron, matK，rbcL and ITS exhibited a low level of intraspecific variability in Potamogeton. In addition, rpl20-rps12 and trnH-psbA did not show an intraspecific variability in this genus. Thus, PHYB is the most efficient candidate for intraspecific divergence in Potamogeton. This study provides a solid foundation for Potamogeton to explore evolutionary process, and contributes to investigating the relationships between species distribution and geographic arrangement in Potamogeton.