Extended Data Fig. 6: Phylogenetic reconstruction of rDsrA peptides from marine bacteria. | Nature Microbiology

Extended Data Fig. 6: Phylogenetic reconstruction of rDsrA peptides from marine bacteria.

From: A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

Extended Data Fig. 6

The maximum-likelihood tree was built with IQ-TREE. Sequences represent the reverse dissimilatory sulfite reductase subunits A (rDsrA), for sulfite oxidation. A total of 458 Arenicellales genomes were predicted to have the rdsrA gene, while 528 Arenicellales were predicted to contain recA. The gene was found in the families UBA868 (433 genomes), UBA5680 (present in all but one of the 23 genomes), BMS3Bbin11 (represented by one genome) and LS-SOB (present in two of the four genomes). UBA5680 peptides are within the Gammaproteobacteria 2 and LS-SOB in the Gammaproteobacteria 3 subclusters in the tree. This reference tree was used to predict the function and taxonomy of metatranscriptome reads by placing the corresponding peptides on the tree. The metatranscriptome peptides were taxonomically classified after placement in one of the subclusters as shown in the smaller phylogenetic tree to the left that represents part of the UBA868 subcluster and some of the Ocean Microbial Reference Gene Catalog (OM-RGC) rDsrA peptides. The names in bigger fonts belong to the subclusters in Figs. 1 and 6, which include the taxa with smaller fonts. Circles at nodes are proportional to the bootstrap values ≥70% based on 100 replicates. Scale bar indicates number of substitutions per site.

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