Metabarcoding Reflection
This week we discussed the paper by Collins et al 2019 that compared several universal primer sets for fish biodiversity. I have never had much of an interest in fish so I learned a lot about what primer sets are out there for detecting fish and how effective they are. One thing I got out of the paper is the need for a fine balance of degenerate bases in the primer sets that allows for the right amount of specificity. In this case the COI primers had a lot of degenerate bases compared to the 12S primers, and they were also a lot less specific. This makes me wonder what a good threshold number of degenerate bases is when designing primers.
In my group we were also discussing the different markers that will be used on the index sites and how we think that it is going to be difficult for everyone to agree on which primer sets to actually use. We also discussed that if people are using other genetic markers on their own that are separate from the three chosen for the sites, data and sequences should be put into an open database to be made available to others in the eDNA group. Those three universal markers won’t cover what is necessary for everyone’s projects so it might be helpful to share data to cover more ground. This ties back to one of our first discussions we had as a class about the advantages of open access data.
My own work is primarily focused on species specific primers but in the future I am hoping to do metabarcoding work on blue mussel guts to understand the composition of their diet and how much sugar kelp detritus contributes to that diet. This paper made me wonder what universal marker I should use for this type of work, and based off of the lecture ITS, rbcL and tmL might be good options. I also wonder if the sugar kelp signal will be overpowered by mussel DNA signal. If this happens, perhaps a partial blocker will help with the problem of sample swamping and allow for weaker signals to be read.