Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa

Abstract Background Animal venom systems have been considered as valuable model for investigating molecular mechanisms underlying phenotypic evolution. The stonefish were reported as the most venomous and dangerous fish due to sever human envenomation and occasionally fatality, whereas the genomic background of their venom remained under investigated and poorly explored compared with other venomous animals. Results In this study, we followed modern venomic pipelines to decode the Synanceia verrucosa venom components. A catalog of 478 toxin genes were annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, transcriptome of venom gland and proteome of crude venom revealed a mechanism underlined the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were evidenced as the major source for the neoVTX protein production. Further isoform sequencing enabled us to uncover massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, further contributing to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of them were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant for granted. Other major venom proteins included a presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, and hyaluronidase. Besides, a few of highly abundant non-toxin proteins were also characterized and they were hypothesized to imply housekeeping or hemostasis maintaining roles in the venom gland. Notably, a gastrotropin like non-toxin proteins ranked as the second highest abundant proteins in the venom, which had never been reported in other venomous animals, contributing to the unique venom property of S. verrucosa. Conclusions The results decoded the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to venom composition diversity by demonstrating tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are hypothesized to be pivotal to understand adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit venom components of S. verrucosa for pharmaceutical innovation.