The golden lancehead genome reveals distinct selective processes acting on venom genes of an island endemic snake

Pedro G Nachtigall , Andrew J Mason , Darin R Rokyta , H Lisle Gibbs , Felipe G Grazziotin , Inácio L M Junqueira-de-Azevedo. Genome Biology and Evolution, evaf243, DOI: 10.1093/gbe/evaf243

Abstract

High-quality genomic resources are important for accurate assessments of adaptive evolution in rapidly evolving island endemic species. The golden lancehead (Bothrops insularis) is a critically endangered venomous species endemic to the Queimada Grande island located on the southeast coast of Brazil, with no reference genome available. Here, we present a high-quality near chromosome-level and well-annotated genome for the golden lancehead. A macrosyntenic analysis using genomes from other viper species revealed that microchromosomes present higher rearrangements consisting of fission and fusion events. Using our genome and genomic data from eight individuals, we conducted a survey of the genetic variation of toxin genes, which included the nucleotide diversity and copy-number variation (CNV). We also inferred a demographic history for the species in the last 100,000 years. The genetic variation analysis revealed that major components of B. insularis venom appear to be evolving largely under natural selection processes rather than genetic drift as expected for an insular species. PLA2s and CTLs are under balancing selection, whereas SVMPs and SVSPs are under positive selection. The CNV suggests recent duplication events in SVMPs and CTLs and deletion events in SVSPs and PLA2s. The demographic history indicates a stable population size over the last 10,000 years, suggesting that B. insularis is both genetically and demographically healthy. Altogether, we provide a genomic resource to better understand the differentiation of an iconic snake and evidence that selection has driven the evolution of diverse venom genes over short evolutionary timescales in an insular species.