Molecular Evolution and Diversity of Conus Peptide Toxins, as Revealed by Gene Structure and Intron Sequence Analyses

Abstract

Cone snails, which are predatory marine gastropods, produce a cocktail of venoms used for predation, defense and competition. The major venom component, conotoxin, has received significant attention because it is useful in neuroscience research, drug development and molecular diversity studies. In this study, we report the genomic characterization of nine conotoxin gene superfamilies from 18 Conus species and investigate the relationships among conotoxin gene structure, molecular evolution and diversity. The I1, I2, M, O2, O3, P, S, and T superfamily precursors all contain three exons and two introns, while A superfamily members contain two exons and one intron. The introns are conserved within a certain gene superfamily, and also conserved across different Conus species, but divergent among different superfamilies. The intronic sequences contain many simple repeat sequences and regulatory elements that may influence conotoxin gene expression. Furthermore, due to the unique gene structure of conotoxins, the base substitution rates and the number of positively selected sites vary greatly among exons. Many more point mutations and trinucleotide indels were observed in the mature peptide exon than in the other exons. In addition, the first example of alternative splicing in conotoxin genes was found. These results suggest that the diversity of conotoxin genes has been shaped by point mutations and indels, as well as rare gene recombination or alternative splicing events, and that the unique gene structures could have made a contribution to the evolution of conotoxin genes.

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

“…A previous analysis of patterns of conotoxin divergence suggested that introns within contoxoin gene superfamilies were similar across species within a gene superfamily (Wu et al 2013). Our results partially corroborate this suggestion, as the ratio of exon to noncoding divergence depended on what conotoxin region was encoded by the exon.…”

“…In addition, the number of exons per gene within a gene superfamily align with results previous studies based on a relatively smaller number of sequences (Wu et al 2013;Barghi et al 2015a). For example, Barghi et al (2015a) found that the J superfamily consisted of a single exon and (Wu et al 2013) found several gene superfamilies (i.e., I1, I2, and M) consisting of three exons, which are identical to the results presented here.…”

“…However, we found that the prepro region was distributed across multiple exons, conflicting with earlier hypotheses. Although not explicitly quantified, these results are also seen in earlier work examining the genomic architecture from conotoxin genes (Wu et al 2013;Barghi et al 2015a). …”

“…We note that our final conotoxin data set consists of exon fragments (conotoxin exons with any assembled adjacent noncoding regions), rather than full conotoxin genes. As described in (Wu et al 2013), conotoxin introns can often be several kilobases in length, which is much longer than the average insert size of our sequencing experiment ($350 bp).…”

“…1). However, past studies have shown that noncoding regions (i.e., introns, untranslated regions [UTRs]) adjacent to hypervariable mature toxin exons are conserved between species (Nakashima et al 1993(Nakashima et al , 1995Gibbs and Rossiter 2008;Wu et al 2013), suggesting that these conserved regions can be used for probe design to potentially recover all venom genes across clades of venomous taxa.…”