Development of species-specific environmental DNA (eDNA) markers for invasive aquatic plants

• Environmental DNA (eDNA) has been used for surveillance of invasive animals.
• We tested 3 chloroplast regions as possible eDNA markers for invasive aquatic plants.
• We found that matK was a more useful eDNA marker than either rbcL or trnL–psbA.
• We were able to identify diagnostic invasive aquatic plant DNA from water eDNA.
• This is the first study to test eDNA as potential tool for monitoring aquatic plants.

Environmental DNA (eDNA) has recently been employed as a surveillance tool for invasive species, although its use has so far been limited to animals. We investigated the possibility of using eDNA to monitor aquatic invasive plants by assessing the potential utility of three regions of the chloroplast genome- matK, rbcL, and trnH–psbA- in ten aquatic invasive plant species. Of the three regions, matK was most likely to harbor putatively species-specific nucleotides in candidate primer-binding sites, and the potentially diagnostic primers that we designed for this region were least likely to amplify DNA from non-target species. A lack of species-specific nucleotides precluded the design of appropriate rbcL primers in most of our species, and amplification of non-target DNA often precluded the use of trnH–psbA markers. We, therefore, suggest that of the three regions, matK is the most useful starting point for designing eDNA markers for aquatic plants. We also demonstrated that these markers can identify species from eDNA that has been extracted from water samples. Our results should be useful to the ongoing development of eDNA as a tool for the early detection and ongoing surveillance of aquatic invasive plants.