The Deep Origin and Recent Loss of Venom Toxin Genes in Rattlesnakes Noah L. Dowell, Matt W. Giorgianni, Victoria A. Kassner, Jane E. Selegue, Elda E. Sanchez, Sean B. Carroll  Current Biology  Volume 26, Issue 18, Pages 2434-2445 (September 2016) DOI: 10.1016/j.cub.2016.07.038 Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 The Different Structures and Expression of the PLA2 Gene Complexes of C. scutulatus, C. atrox, and C. adamanteus (A–C) The relative positions and orientations (denoted with arrowheads) of the C. scutulatus (A), C. atrox (B), and C. adamanteus (C) full-length PLA2 genes between the conserved Otud3 and Mul1 genes are indicated. The identities of each major expressed venom gland PLA2 gene are indicated above the schematic. Below each schematic are the strand-specific coverage plots for aligned venom gland RNA-seq reads that overlap exons. Exons for each gene (color matched) are shown between the coverage plots. The predicted translation products of the expressed gene models (mapped reads) are identical (100% amino acid identity) to proteins previously detected in venom. Pla2-gB2 encodes Mojave toxin subunit B (Mtx B); Pla2-gA2 encodes Mojave toxin subunit A (Mtx A); for other gene nomenclature, see text. Note that the complement of genes differs between species and that each species expresses different major transcripts in the venom gland. See also Figures S1 and S4 and Table S1. Current Biology 2016 26, 2434-2445DOI: (10.1016/j.cub.2016.07.038) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 The Most Recent Common Ancestor of Rattlesnakes Was Neurotoxic Trimmed species phylogeny with venom type represented as black (neurotoxic) or white (non-neurotoxic) boxes. Within this clade, the most parsimonious interpretation of the neurotoxic venom distribution is that the most recent common ancestor (MRCA) possessed neurotoxic venom and three lineages (x) have independently lost neurotoxicity. See also Figures S2–S4 and Tables S1 and S2. Current Biology 2016 26, 2434-2445DOI: (10.1016/j.cub.2016.07.038) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 Venom Pla2 Genes Arose via Sequential Duplications (A–C) Blocks of high sequence identity that overlap the venom genes in C. scutulatus (A), C. adamanteus (B), and C. atrox (C) are shown as gray boxes linked by arcs above the PLA2 group 2 complex (drawn to scale). The duplication identifiers are to the left of each sequence pair (SD14, etc.). The duplications are ordered from top to bottom by the level of sequence divergence. Dashed arcs link duplicated regions on opposite strands. Solid arcs link duplicated regions on the same strand. (D) Model of the expansion of the PLA2 group 2 complex that gave rise to the inferred, ancestral rattlesnake complex with at least seven Pla2-g genes, based on the sequence divergence of specific duplicated regions and protein phylogeny. Genes are colored according to the naming convention of modern genes. Boxes on left are color matched to the duplicated genes. (i) The ancestral chromosome is inferred to have four distinct Pla2 group 2 family members, including a single Pla2-g gene, which is most similar to the gC gene in modern rattlesnakes. (ii) The earliest duplication gave rise to gC and the basic Pla2s (SD9, SD11, SD13). (iii) Tandem duplication of basic-Pla2s (SD7). (iv) Inversion of a basic Pla2 yields the head-to-head basic:acidic (gC::gA) Pla2 unit (SD10, 27, 40, 42). (v) A large duplication of the gC::gA unit expanded the Pla2 complex to seven genes (SD14). See Figure S5 for evolutionary distances between duplicated sequences. Current Biology 2016 26, 2434-2445DOI: (10.1016/j.cub.2016.07.038) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 4 Conserved, Dispersed Repetitive Sequence Blocks May Facilitate Gene Duplication and Deletion (A) All three rattlesnake species PLA2 complexes have conserved sequence blocks (boxes) that can include conserved clusters of transposable element (TE) sequences (white boxes, expanded below locus) and that share individual TE components, orientation and location. Gray boxes share high identity with gray regions of large conserved sequence blocks outside of the TE clusters. These elements may serve as permissive substrates for NAHR-mediated gene duplications and deletions. Pla2-g genes are depicted by arrows with color scheme, and abbreviations are the same as in Figure 1; the position of lineage-specific deletions is denoted by parentheses. TE abbreviations are as follows: ERV, endogenous retrovirus 1-10 Ami; hAT, DNA transposon; CR1, LINE CR1-1 element. (B) A rearranged C. atrox PLA2 complex with a duplicated gC1::gA1 gene pair was discovered in one of four specimens analyzed. Orange bar indicates the novel sequence relative to the standard C.atrox chromosome. Four exons (white arrow) of an Otud3 pseudogene (ψ Otud3) are between gA1′ and gB1, while an intact Otud3 gene is still present downstream of Pla2-e. Current Biology 2016 26, 2434-2445DOI: (10.1016/j.cub.2016.07.038) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 5 The Deep Origin and Recent Independent Losses of Rattlesnake Venom Toxin Genes Model depicting the evolution of the PLA2 group 2G gene complex. Significant evolutionary events are mapped onto a simplified cladogram of venomous snakes, and the PLA2 complexes of various species are shown. The complex is inferred to have expanded from a single Pla2-g gene as is present today in the elapid O. hannah (top). The number of Pla2-g genes expanded in viperids, and some gained expression in venom. Further duplication and the differentiation of distinct Pla2-g types, including the components of the neurotoxic heterodimer (gA2 and gB2) and the Lys49 myotoxin (gK), occurred in the pit viper (Crotalinae) lineage (middle). The MRCA of rattlesnakes possessed at least seven Pla2-g genes, which has been reduced by unique lineage-specific losses (gray circles) in extant rattlesnakes (bottom, deleted genes denoted by faded colors in brackets). See also Figure S3 and Table S1. Current Biology 2016 26, 2434-2445DOI: (10.1016/j.cub.2016.07.038) Copyright © 2016 Elsevier Ltd Terms and Conditions