Taxon-specific COI primer design and visualization

Advisor:
Mehrdad Hajibabaei (IB)

COI metabarcoding is a popular method for surveying biological diversity from environmental samples such as soil, water, and trap samples. In biomonitoring studies in particular, DNA-based survey methods are used as a scalable technique to rapidly assess samples repeatedly over time and space.  Of key interest, are taxa known to play crucial roles in ecosystems such as mites (Orabatida) and springtails (Collembola) (sensitive to disturbance and can be used as indicators of soil biodiversity), as well as the Ephemeroptera-Plectopera-Trichoptera (EPT) group (sensitive to pollution and used as water quality indicators). There is a need for improved primer specificity to facilitate the detection of these target taxa from environmental DNA in the midst of competing DNA from non-target arthropods.

The objective of this project would be three-fold: 1) Design new COI primers to target taxa crucial for biomonitoring and assessing soil/water quality, ex. Orabatida, Collembola, EPT, 2) Verify the performance of these primers using in silico PCR, 3) Design an online tool to visualize primer binding sites on the COI barcoding region, ex. R Shiny.