[Review] Refinements for the amplification and sequencing of red algal DNA barcode and RedToL phylogenetic markers: a summary of current primers, profiles and strategies

doi:2013.28.1.31

Algae > Volume 28(1); 2013 > Article

Algae 2013;28(1): 31-43. doi: https://doi.org/10.4490/algae.2013.28.1.031

Gary W. Saunders¹^,* and Tanya E. Moore¹

¹Centre for Environmental and Molecular Algal Research, Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada

*Corresponding Author

Email: gws@unb.ca

ABSTRACT

This review provides a comprehensive summary of the PCR primers and profiles currently in use in our laboratory for red algal DNA barcoding and phylogenetic research. While work focuses on florideophyte taxa, many of the markers have been applied successfully to the Bangiales, as well as other lineages previously assigned to the Bangiophyceae sensu lato. All of the primers currently in use with their respective amplification profiles and strategies are provided, which can include full fragment, overlapping fragments and what might best be called “informed overlapping fragments”, i.e., a fragment for a marker is amplified and sequenced for a taxon and those sequence data are then used to identify the best primers to amplify the remaining fragment(s) for that marker. We extend this strategy for the more variable markers with sequence from the external PCR primers used to “inform” the selection of internal sequencing primers. This summary will hopefully serve as a useful resource to systematists in the red algal community.

Key words: DNA barcode; Florideophyceae; molecular markers; phylogeny; polymerase chain reaction; primers; RedToL