Abstract
Venoms have traditionally been studied from a proteomic and/or transcriptomic perspective, often overlooking the true genetic complexity underlying venom production. The recent surge in genome-based venom research (sometimes called "venomics") has proven to be instrumental in deepening our understanding of venom evolution at the molecular level, particularly through the identification and mapping of toxin-coding loci across the broader chromosomal architecture. Although venomous snakes are a model system in venom research, the number of high-quality reference genomes in the group remains limited. In this study, we present a chromosome-resolution reference genome for the Arabian horned viper Cerastes gasperettii (NCBI: txid110202), a venomous snake native to the Arabian Peninsula. Our highly contiguous genome (genome size: 1.63 Gbp; contig N50: 45.6 Mbp; BUSCO: 92.8%) allowed us to explore macrochromosomal rearrangements within the Viperidae family, as well as across squamates. We identified the main highly expressed toxin genes within the venom glands comprising the venom's core, in line with our proteomic results. We also compared microsyntenic changes in the main toxin gene clusters with those of other venomous snake species, highlighting the pivotal role of gene duplication and loss in the emergence and diversification of snake venom metalloproteinases and snake venom serine proteases for C. gasperettii. Using Illumina short-read sequencing data, we reconstructed the demographic history and genome-wide heterozigosity of the species, revealing how historical aridity likely drove population expansions. Finally, this study highlights the importance of using long-read sequencing as well as chromosome-level reference genomes to disentangle the origin and diversification of toxin gene families in venomous snake species.