Integrative Multi-omics Analysis Reveals the Contribution of NeoVTX Genes to Venom Diversity of Synanceia Verrucosa

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2024 Dec 19

PMID 39695923

Authors

Zhiwei Zhang

Qian Li

Hao Li

Shichao Wei

Wen Yu

Zhaojie Peng

Fuwen Wei

Wenliang Zhou

Affiliations

Soon will be listed here.

Abstract

Background: Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish are the most venomous and dangerous fish because of severe human envenomation and occasionally fatalities, whereas the genomic background of their venom has not been fully explored compared with that in 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 was annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, the transcriptome of the venom gland, and the proteome of crude venom revealed mechanisms underlying the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were identified as the major source for the neoVTX protein production. Further isoform sequencing revealed massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, which further contributed to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of which were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant. 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 function in housekeeping or hemostasis maintaining roles in the venom gland. Notably, gastrotropin like non-toxin proteins were the second highest abundant proteins in the venom, which have not been reported in other venomous animals and contribute to the unique venom properties of S. verrucosa.

Conclusions: The results identified the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to the diversity of venom composition through tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are important for understanding the adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit the venom components of S. verrucosa for pharmaceutical innovation.

References

Fritzinger D, Bredehorst R, Vogel C . Molecular cloning and derived primary structure of cobra venom factor. Proc Natl Acad Sci U S A. 1994; 91(26):12775-9. PMC: 45522. DOI: 10.1073/pnas.91.26.12775. View

Pertea M, Pertea G, Antonescu C, Chang T, Mendell J, Salzberg S . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-5. PMC: 4643835. DOI: 10.1038/nbt.3122. View

Martinson E, Mrinalini , Kelkar Y, Chang C, Werren J . The Evolution of Venom by Co-option of Single-Copy Genes. Curr Biol. 2017; 27(13):2007-2013.e8. PMC: 5719492. DOI: 10.1016/j.cub.2017.05.032. View

Silva de Franca F, Tambourgi D . Hyaluronan breakdown by snake venom hyaluronidases: From toxins delivery to immunopathology. Front Immunol. 2023; 14:1125899. PMC: 10064005. DOI: 10.3389/fimmu.2023.1125899. View

Margres M, Rautsaw R, Strickland J, Mason A, Schramer T, Hofmann E . The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proc Natl Acad Sci U S A. 2021; 118(4). PMC: 7848695. DOI: 10.1073/pnas.2014634118. View

Zhang Z, Lv Y, Wu W, Yan C, Tang C, Peng C . The structural and functional divergence of a neglected three-finger toxin subfamily in lethal elapids. Cell Rep. 2022; 40(2):111079. DOI: 10.1016/j.celrep.2022.111079. View

Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer C . Fast alignment and preprocessing of chromatin profiles with Chromap. Nat Commun. 2021; 12(1):6566. PMC: 8589834. DOI: 10.1038/s41467-021-26865-w. View

Haas B, Salzberg S, Zhu W, Pertea M, Allen J, Orvis J . Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008; 9(1):R7. PMC: 2395244. DOI: 10.1186/gb-2008-9-1-r7. View

Calvete J, Fasoli E, Sanz L, Boschetti E, Righetti P . Exploring the venom proteome of the western diamondback rattlesnake, Crotalus atrox, via snake venomics and combinatorial peptide ligand library approaches. J Proteome Res. 2009; 8(6):3055-67. DOI: 10.1021/pr900249q. View

10.

McKillop I, Girardi C, Thompson K . Role of fatty acid binding proteins (FABPs) in cancer development and progression. Cell Signal. 2019; 62:109336. DOI: 10.1016/j.cellsig.2019.06.001. View

11.

Bao W, Kojima K, Kohany O . Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015; 6:11. PMC: 4455052. DOI: 10.1186/s13100-015-0041-9. View

12.

MORRISSETTE J, Kratzschmar J, Haendler B, Martin B, Patel J, Moss R . Primary structure and properties of helothermine, a peptide toxin that blocks ryanodine receptors. Biophys J. 1995; 68(6):2280-8. PMC: 1282138. DOI: 10.1016/S0006-3495(95)80410-8. View

13.

Ma H, Xiao-Peng T, Yang S, Lu Q, Lai R . Protease inhibitor in scorpion (Mesobuthus eupeus) venom prolongs the biological activities of the crude venom. Chin J Nat Med. 2016; 14(8):607-14. DOI: 10.1016/S1875-5364(16)30071-1. View

14.

Herraez-Perez A, Pardos-Blas J, Afonso C, Tenorio M, Zardoya R . Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics. Gigascience. 2023; 12. PMC: 10541794. DOI: 10.1093/gigascience/giad075. View

15.

Cai L, Yang F, Wang Y, Yang J, Zhu Y, Ma X . A combined protein toxin screening based on the transcriptome and proteome of Solenopsis invicta. Proteome Sci. 2022; 20(1):15. PMC: 9494847. DOI: 10.1186/s12953-022-00197-z. View

16.

Rokyta D, Lemmon A, Margres M, Aronow K . The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus). BMC Genomics. 2012; 13:312. PMC: 3472243. DOI: 10.1186/1471-2164-13-312. View

17.

Ellisdon A, Reboul C, Panjikar S, Huynh K, Oellig C, Winter K . Stonefish toxin defines an ancient branch of the perforin-like superfamily. Proc Natl Acad Sci U S A. 2015; 112(50):15360-5. PMC: 4687532. DOI: 10.1073/pnas.1507622112. View

18.

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

19.

Saggiomo S, Firth C, Wilson D, Seymour J, Miles J, Wong Y . The Geographic Distribution, Venom Components, Pathology and Treatments of Stonefish ( spp.) Venom. Mar Drugs. 2021; 19(6). PMC: 8225006. DOI: 10.3390/md19060302. View

20.

Almeida D, Scortecci K, Kobashi L, Agnez-Lima L, Medeiros S, Silva-Junior A . Profiling the resting venom gland of the scorpion Tityus stigmurus through a transcriptomic survey. BMC Genomics. 2012; 13:362. PMC: 3444934. DOI: 10.1186/1471-2164-13-362. View