Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment

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Subsection “Symbiont-specific DNA found in environmental samples”: Please add whether the 198 bp locus in cheA that was used to detect the symbionts in seawater was well-conserved or highly variable (or something else).

This is an important point and we took several measures to ensure that, as much as possible, we were amplifying a symbiont specific marker while not excluding symbionts that might vary in sequence. We targeted the cheA region because it is very conserved within each symbiont species, with greater than >99% nucleotide identity among the 10 E. escacola sequences available and the 6 E. luxaltus sequences available. However, this region is only 78% similar when sequences from the two symbiont species are compared to each other. This pattern was confirmed with the addition of 8 unique sequences from the water samples, which show >99% similarity to the sequences extracted from genomes. We conclude that the cheA locus is highly conserved in each symbiont species and therefore that sequences amplified from the water are unlikely to come from other organisms (see phylogenetic tree in Figure 1). This information was more explicitly stated in the revised manuscript in the Discussion.

To confirm that our primers would not amplify non-target organisms from the environmental samples, we BLASTed this locus against the GenBank nr, reference genomes, and wgs databases. Either no significantly similar sequences were found (in the case of E. escacola) or the top hits had <81% sequence identity (E. luxaltus). We cannot rule out the possibility that sequences from other microbes in the environment could be amplified with our methods, but we think that non-target species are unlikely to contribute to the pattern we show. We have clarified this in the Discussion.