Phylogenetic Tree of PR Proteins from the Mediterranean and Red Seas along with PR Homologs in GenBank

<p>The tree was divided into what we propose are distinct subfamilies of sequences, based on bootstrap values significance. The tree was constructed as follows: (i) All homologs of PR proteins were identified in GenBank including predicted proteins from the Sargasso Sea assemblies using BLASTp [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030273#pbio-0030273-b36" target="_blank">36</a>] searches with representatives of previously identified PR-like protein families as query sequences. (ii) All sequences greater than 300 nucleotides in length were aligned to each other using CLUSTALx [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030273#pbio-0030273-b37" target="_blank">37</a>], and a neighbor-joining phylogenetic tree was inferred using the neighbor programs of PAUP* [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030273#pbio-0030273-b38" target="_blank">38</a>]. Bootstrap resampling (1,000 pseudoreplications) of neighbor-joining and maximum parsimony trees were performed in all analyses to provide confidence estimation for the inferred topologies. Bootstraps values greater than 50% are indicated above the branches (neighbor-joining/maximum parsimony). The scale bar represents the number of substitutions per site. The sequences are colored according to the type of sample in which they were found: blue, cultured species; orange, sequences from uncultured organisms obtained using PCR-based methods; and red, BAC-derived sequences from uncultured species in the Mediterranean Sea and Red Sea (this study) or from previously reported Pacific, Antarctic, and Red Sea [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030273#pbio-0030273-b01" target="_blank">1</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030273#pbio-0030273-b07" target="_blank">7</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030273#pbio-0030273-b08" target="_blank">8</a>] BAC/fosmids. Black squares mark sequenced BACs in this study; red squares label BACs sequenced in previous reports. α, <i>Alphaproteobacteria</i>; γ, <i>Gammaproteobacteria</i>. Red circles mark the two abundant PR groups discussed in the manuscript.