Computational protocol: Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean

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Protocol publication

[…] All our new sequences were blasted and the closest relative(s) for each sequence were included in the phylogenetic trees. For the phylogenetic analyses, we selected sequences (>900 bp) belonging to non-heterocytous taxa to examine phylogenetic position of our strains. Multiple sequence alignments were conducted using the CLUSTAL W program []. Phylogenetic trees were constructed in Mega 6.06 [] using (1) the Neighbour-Joining (NJ) method on a Jukes and Cantor distance matrix model, (2) the Maximum-Likelihood (ML) applying a GTR + G + I model of nucleotide substitution. The robustness of the inferred phylogenies was determined by bootstrap analysis based on 1000 resamplings of data.Phylogenetic relationships among coccoid and filamentous cyanobacteria strains were examined separately. For coccoid cyanobacteria we included free-living Synechococcus strains and the closely related Prochlorococcus, clones of the specific sponge symbiont “Candidatus Synechococcus spongiarum” and representatives of all the genera of Pleurocapsales order. For filamentous cyanobacteria we included marine filamentous cyanobacteria strains of Synechococcales order and almost all available sequences of the genera Symploca and Schizothrix. To ascertain the precise phylogenetic position of our filamentous strains, we conducted a detailed phylogenetic analysis employing a comprehensive selection of 16S rRNA gene sequences from all genera of Leptolyngbyaceae family, the closely affiliated Heteroleibleiniaceae (the only available sequence belongs to Tapinothrix) and sequences from Pseudanabaenaceae. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics