Hi Jonathan M Adams There is a commonly used barcoding primer for eukaryotes called the COI (Cytochrome c oxidase subunit I) gene. This gene is a part of the mitochondrial genome and is considered a "standard" barcoding marker for eukaryotes due to its high level of diversity and conservation across a wide range of taxa.

There are several commonly used COI primers, including the following:

-Folmer: 5'-GCATTTAGTTTGGTGGTGC-3' (forward) and 5'-TAAAGAAACTTCAGGGTGACC-3' (reverse)

-LCO1490: 5'-GGTCAACAAATCATAAAGATATTGG-3' (forward) and 5'-TAAACTTCAGGGTGACCAAAAAATCA-3' (reverse)

-HCO2198: 5'-GTTTAAACTYGGTCCRAARAAYCA-3' (forward) and 5'-TAAACTTCAGGGTGACCAAAAAATCA-3' (reverse)

It is recommended to select the most appropriate primer based on the taxonomic group and target organism you are studying, as some primers may work better for certain groups than others. Additionally, it is always a good idea to check the local and global COI sequence databases to ensure the primers you choose are suitable for your specific study system.

Hope this helps.

A commonly used eukaryotic primer for the amplification of 18S ribosomal RNA is the universal eukaryotic primer pair, "Eukaryotic 18S" (EukA) 5'-CGCCTGTTTATCAAAAACAT-3' and "Eukaryotic 18S" (EukB) 5'-GCTGCGTTCTTCATCGATGC-3'.

This primer pair has been shown to have broad specificity, and has been used to amplify 18S ribosomal RNA from a wide range of eukaryotic microorganisms, including many protists and single-celled algae. However, as with any primer pair, the specificity can vary depending on the sample, so it is always a good idea to check the specificity of the primers for your specific sample using techniques such as agarose gel electrophoresis or by sequencing the amplicon.

It's important to note that the use of a single primer pair may not result in the amplification of all eukaryotic species in a sample. In such cases, using a combination of primers or using multiplex PCR may be necessary. Additionally, it is always recommended to validate the specificity of the primers in your sample before beginning any downstream analysis.

Hi Jonathan,

See https://app.pr2-primers.org/pr2-primers/ for all the options.

For algae/protists barcoding primers 18S EukA/ EuKB as recommended above.

For metabarcoding I have previously used, 18S V4 region:

(Stoeck et al., 2010) TAReuk454FWD1 (5´-CAGCASCYGCGGTAATTCC-3´) and TAReukREV3 (5´-ACTTTCGTTCTTGATYRA-3´) - these are the most widely used. Length 417bp

or

E572F (5′-CYGCGGTAATTCCAGCTC-3′) and reverse primer E1009R (5′-AYGGTATCTRATCRTCTTYG-3′) (Comeau et al. 2011)- this set sends to be easier to amplify. Length 438bp

18S V9 a shorter option ~159bp

1391F (5´-GTACACACCGCCCGTC-3´) and Euk B (5´-TGATCCTTCTGCAGGTTCACCTAC-3´) Amarel-zettler et al. 2009 used by the Earth microbiome project.

COI is a poor marker for most algae and some protists and the reference databases are very sparse.

Drop me a message if you need any further info.

Hi Jonathan

On a similar vein to Joe's response, look at

Vaulot, D., Geisen, S., Mahé, F., & Bass, D. (2022). pr2-primers: An 18S rRNA primer database for protists. Molecular Ecology Resources, 22, 168– 179. https://doi.org/10.1111/1755-0998.13465

Hola Jonathan

I recommend the universal primers Eu565F (5'-CCA GCA SCY GCG GTA ATT CC-3') and Eu981R (5'-ACT TTC GTT CTT GAT YRA TGA-3') for the amplification of eukaryotic 18S rRNA gene (Stoeck et al., 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology. 19, 21–31).