Rapid Evolution by Positive Selection and Gene Gain and Loss: PLA2 Venom Genes in Closely Related Sistrurus Rattlesnakes with Divergent Diets

Abstract

Rapid evolution of snake venom genes by positive selection has been reported previously but key features of this process such as the targets of selection, rates of gene turnover, and functional diversity of toxins generated remain unclear. This is especially true for closely related species with divergent diets. We describe the evolution of PLA(2) gene sequences isolated from genomic DNA from four taxa of Sistrurus rattlesnakes which feed on different prey. We identified four to seven distinct PLA(2 )sequences in each taxon and phylogenetic analyses suggest that these sequences represent a rapidly evolving gene family consisting of both paralogous and homologous loci with high rates of gene gain and loss. Strong positive selection was implicated as a driving force in the evolution of these protein coding sequences. Exons coding for amino acids that make up mature proteins have levels of variation two to three times greater than those of the surrounding noncoding intronic sequences. Maximum likelihood models of coding sequence evolution reveal that a high proportion (approximately 30%) of all codons in the mature protein fall into a class of codons with an estimated d(N)/d(S) (omega) ratio of at least 2.8. An analysis of selection on individual codons identified nine residues as being under strong (p < 0.01) positive selection, with a disproportionately high proportion of these residues found in two functional regions of the PLA(2) protein (surface residues and putative anticoagulant region). This is direct evidence that diversifying selection has led to high levels of functional diversity due to structural differences in proteins among these snakes. Overall, our results demonstrate that both gene gain and loss and protein sequence evolution via positive selection are important evolutionary forces driving adaptive divergence in venom proteins in closely related species of venomous snakes.

Cloning of a novel acidic phospholipase A2 from the venom gland of Crotalus durissus cascavella (Brazilian northeastern rattlesnake)

“…Acidic IIA phospholipases A 2 present multiple isoforms, generally associated with intra-specific geographic variation, as well as adaptation to prey diversity (43,44,54,55). On the other hand, some PLA 2 clones apparently not translated into venom proteins has been reported, since not-expressing toxin mRNA may be a repository for snake survival under an ever-changing environment (54,55).…”

“…On the other hand, some PLA 2 clones apparently not translated into venom proteins has been reported, since not-expressing toxin mRNA may be a repository for snake survival under an ever-changing environment (54,55).…”

Venoms, venomics, antivenomics

“…Gene duplication followed by functional divergence is the main source of molecular novelty. Gene duplication creates redundancy and allows a gene copy to be selectively expressed in the venom gland, escaping the pressure of negative selection and evolving a new function through positive selection and adaptative molecular evolution [31][32][33]. The occurrence of multiple isoforms within each major toxin family evidences the emergence of paralogous groups of multigene families across taxonomic lineages where gene duplication events occurred prior to their divergence, and suggests an important role for balancing selection in maintaining high levels of functional variation in venom proteins within populations.…”

Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution

“…Venoms are composed of mixtures of toxic proteins and peptides that are usually encoded directly by a handful of known gene families (Kordis and Gubensek 2000;Fry et al 2009;Casewell et al 2013). Exceptionally high estimated rates of gene duplication and diversifying selection across these venom genes families are thought to contribute to the evolution of novel proteins and thus changes in venom composition (Duda and Palumbi 1999;Gibbs and Rossiter 2008;Chang and Duda 2012), allowing venomous taxa to specialize and adapt onto different prey species (Kohn 1959a;Daltry et al 1996;Li et al 2005;Barlow et al 2009;Chang and Duda 2016;Phuong et al 2016). Therefore, the study of venomous taxa can facilitate understanding of the genetic contributions to ecologically relevant traits and subsequent diversification.…”