The sequencing of the 16S rRNA gene is a routine method for the taxonomic classification and identification of Cyanobacteria. Using the sequence identity between an unknown strain and strains with known taxonomic identification, conclusions about their relatedness can be drawn. For species identification, we use a 99% identity cutoff and include literature research if available.
We propose the sequencing of a partial 16S rRNA sequence using 359F/781R primers, which usually allows identification up to genus level, or of a complete 16S rRNA sequence with the 27F/23S30R primers, which usually allows identification up to species level. For the identification via the 16S rRNA gene sequences, we use the BLAST tool of NCBI to obtain closely related species based on their identity. Additionally, an in-depth phylogenetic study is added to complement the BLAST analysis. The phylogenetic analysis is performed with the software program MEGA7 (Kumar et al., 2016). Closely related 16S rRNA sequences are collected from Genbank (NCBI) and aligned and a phylogenetic tree will be inferred using the Neighbor-joining method.
The report will comprise the obtained sequence(s) and a list of the most related species based on the sequence identity with a scientific conclusion on the family, genus and potentially also up to species level. The report also includes a similarity matrix and a phylogenetic tree. If present, we also provide a small literature study on the identified species.
For this analysis, a unicyanobacterial culture is required.
- Kumar, S., Stecher, G., and Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870-1874. doi: 10.1093/molbev/msw054.