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. 2021 Aug 19;10:e65394. doi: 10.7554/eLife.65394

Figure 2. The pathogen recognition receptor (PRR) repertoire of whale shark.

Nodes supported ≥95% UFBOOT indicated with a dot. For NOD-like receptors, NLRs in whale shark with a NACHT domain are indicated by a dot at the tip. See also Figure 2—figure supplements 1–2. For RIG-like receptors (RLRs), branches are colored by gene, except for RLRs in whale shark which are colored distinctly and labeled by a dot at each tip. See also Figure 2—figure supplement 3. For toll-like receptors (TLRs), each clade represents a separate TLR except families found within TLR13 are also labeled a (TLR13a), b (TLR32), and c (TLR33). TLR families are also labeled by stars indicating whether they were present in the whale shark genome, present in jawed vertebrate ancestor, present in the vertebrate ancestor, and novel to this study. See also Figure 2—figure supplement 4.

Figure 2.

Figure 2—figure supplement 1. Phylogenetic analysis of NOD-like receptors (NLRs) from whale shark, zebrafish, and human.

Figure 2—figure supplement 1.

Branches leading to human sequences are shown in black, to zebrafish in blue-green, and whale shark in red. Whale shark sequences with a detectable NACHT have ‘_NACHT’ at the end of the sequence identifier (except for transcriptome sequence which all contain NACHT domains; all NACHT domain containing sequences are also noted with ‘*’ in Supplementary file 12).
Figure 2—figure supplement 2. Detailed analysis of NOD1 evolution.

Figure 2—figure supplement 2.

(A) Phylogenetic analysis of NOD1 focused NOD-like receptor (NLR) dataset. (B) Domain structure of NOD1 duplicates in whale shark. (C) Synteny analysis of jawed vertebrate NOD1s.
Figure 2—figure supplement 3. Phylogenetic analyses of whale shark and jawed vertebrate RIG-like receptors (RLRs), DICER, and mitochondrial antiviral signaling (MAVS).

Figure 2—figure supplement 3.

(A) Tree of the RLR and DICER DEAD-Helicase domains. (B) Tree of the RLR and MAVS CARD domains. Whale shark sequences are highlighted in blue.
Figure 2—figure supplement 4. Phylogenetic tree of vertebrate toll-like receptors (TLRs), including new whale shark sequences.

Figure 2—figure supplement 4.

The tree is rooted according to the minimal ancestor deviation method (Tria et al., 2017).