Environmental DNA (eDNA) metabarcoding targets sequences with interspecific
variation that can be amplified using universal primers allowing simultaneous detection
of multiple species from environmental samples. I developed novel primers for three
barcodes commonly used to identify plant species, and compared amplification success
for aquatic plant DNA against pre-existing primers. Control eDNA samples of 45 plant
species showed that species-level identification was highest for novel matK and preexisting
ITS2 primers (42% each); remaining primers each identified between 24% and
33% of species. Novel matK, rbcL, and pre-existing ITS2 primers combined identified
88% of aquatic species. The novel matK primers identified the largest number of species
from eDNA collected from the Black River, Ontario; 21 aquatic plant species were
identified using all primers. This study showed that eDNA metabarcoding allows for
simultaneous detection of aquatic plants including invasive species and species-at-risk,
thereby providing a biodiversity assessment tool with a variety of applications.
Author Keywords: aquatic plants, biodiversity, bioinformatics, environmental DNA (eDNA), high-throughput sequencing, metabarcoding