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. 2020 Jan 28;18:11. doi: 10.1186/s12915-019-0731-8

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© The Author(s). 2020

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 10. — Phylogenetic tree of the NACHT domain and Leucine-rich Repeat containing receptor (NLR) nucleotide-binding domain sequences in round goby, blue-spotted mudskipper (Boleophthalmus pectinirostris), zebrafish (Danio rerio), (Ictalurus punctatus), miiuy croaker (Miichthys miiuy), and human (Homo sapiens). Maximum Likelihood phylogenetic tree with 500 bootstraps rooted at the split between NB-ARC (found in APAF) and NACHT domains (present in all the other NLRs). NB-ARC domains from APAF1 orthologs were used as an outgroup. Bootstrap values are shown for nodes that determine an entire cluster. The tree resolves all three major classes of vertebrate NLRs (NLR-A, NLR-B, NLR-C). NLR-A genes were conserved in all analyzed species; no NLR-B genes were found in the gobies. Six groups of NLR-C genes were identified, four of which are exclusive to zebrafish (Danio rerio) (groups 1–4) and two contain only sequences from gobies (groups 5 and 6, gray boxes and bold print). Lineage-specific expansions are displayed with colored endpoints. Within the goby-specific groups, lineage-specific expansions can be seen for both round goby (orange) and blue-spotted mudskipper (Boleophthalmus pectinirostris) (brown). The placement of sparse miiuy croaker genes in group 3 and round goby genes in NLR-A clusters is not well supported and presumably an artifact. The characteristic Walker A motifs are shown next to each subgroup, with group 5 featuring 2 different motifs