Design and use of a new primer pair for the characterization of the cyanobacteria and communities targeting petB gene through metabarcoding approaches.

During the last years, the application of next-generation sequencing (NGS) technologies to search for specific genetic markers has become a crucial method for the characterization of microbial communities. Illumina MiSeq, likely the most widespread NGS platform for metabarcoding experiments and taxonomic classification, allows processing shorter reads than the classical SANGER sequencing method and therefore requires specific primer pairs that produce shorter amplicons. Specifically, for the analysis of the commonly studied and communities, the marker gene has recently stood out as able to provide deep coverage to determine the microdiversity of the community. However, current primer set produce a 597 bp amplicon that is not suitable for MiSeq chemistry. Here, we designed and tested a primer pair that targets both and communities producing an appropriate amplicon to be used with state-of-the-art Illumina MiSeq. This new primer set allows the classification of both groups to a low taxonomic level and is therefore suitable for high throughput experiments using MiSeq technologies, therefore constituting a useful, novel tool to facilitate further studies on and communities. •This work describes the design of a and -specific primer pair, allowing the characterization of both populations to a low taxonomic level.•This primer pair is suitable for widespread Illumina MiSeq sequencing technologies.• was confirmed as an adequate target for the characterization of both picocyanobacteria.