Jack Clarke, Vicki Thomson & Richard Edwards
Abstract
Snakes are one of the most venomous animals on the planet, using their venom for defence and the capturing of prey. Snake venoms have evolved independently of other venoms in other vertebrates, and there is considerable variation between species in their proteomic composition. One of the primary mechanisms through which snake venoms are thought to evolve is the duplication, recruitment and specialisation of proteins from other tissues. In some cases, this evolution is known to involve the tandem duplication of genes resulting in chromosomal clusters of venom genes in some gene families. We have recently sequenced and assembled the genomes of two highly venomous Australian snakes: Notechis scutatus (mainland tiger snake) and Pseudonaja textilis (eastern brown snake). In conjunction with publicly available proteomes from 10 other venomous snakes and 2 non-venomous snakes, these genomes provide an excellent opportunity to examine the role that duplication and neofunctionalisation has played in snake venom evolution.
We have analysed 43 protein families known to play a role in snake venom and examined their pattern of duplication in snakes, compared to high quality reference genomes of other reptiles and non-venomous vertebrates. We find evidence for extensive duplications across some of these families, but no clear enrichment for duplication in the evolution of venom specifically. Instead, we identify a trend where numerous duplications specific to venomous snakes occur in proteins that seem predisposed to evolve by duplication and specialisation, even in non-venomous vertebrates. A subset of high-quality snake genomes was then used to further explore the nature of duplications. While tandem gene duplication is evident in some larger families, it remains absent in many.
The snake venom metalloproteinase (SVMP) family provides an excellent case study, with multiple duplication events throughout its evolutionary history in vertebrates. Part of the broader ADAM (“a disintegrin and metalloproteinase”) family of single-pass transmembrane and secreted zinc proteases, SVMP appears to have expanded by independent tandem duplications in different snake lineages. We also identify a second ADAM subfamily, ADAM20, with an abundance of venomous snake-specific duplications. Ongoing work in exploring the possible role of ADAM20 proteins in snake venoms and the role that genome assembly quality has played in our ability to robustly detect the presence or absence of gene duplication events.
