Identification of Daboia siamensis venome using integrated multi-omics data

Abstract

Snakebite, classified by World Health Organization as a neglected tropical disease, causes more than 100,000 deaths and 2 million injuries per year. Currently, available antivenoms do not bind with strong specificity to target toxins, which means that severe complications can still occur despite treatment. Moreover, the cost of antivenom is expensive. Knowledge of venom compositions is fundamental for producing a specific antivenom that has high effectiveness, low side effects, and ease of manufacture. With advances in mass spectrometry techniques, venom proteomes can now be analyzed in great depth at high efficiency. However, these techniques require genomic and transcriptomic data for interpreting mass spectrometry data. This study aims to establish and incorporate genomics, transcriptomics, and proteomics data to study venomics of a venomous snake, Daboia siamensis. Multiple proteins that have not been reported as venom components of this snake such as hyaluronidase-1, phospholipase B, and waprin were discovered. Thus, multi-omics data are advantageous for venomics studies. These findings will be valuable not only for antivenom production but also for the development of novel therapeutics.

Figure 1

Workflow of our integrated multi-omics approach. The full-size figure of venom SDS-PAGE gel is shown in supplement Fig. S1.

Figure 2

Comparisons of snake genome assemblies. The overall assembly sizes (A) and contig and scaffold statistics (B) of Daboia siamensis (this study), Crotalus horridus, Crotalus pyrrhus, Protobothrops flavoviridis, Protobothrops mucrosquamatus, Vipera berus (GenBank assembly accession: GCA_000800605.1), Thamnophis sirtalis, Ophiophagus Hannah, and Python bivittatus.

Figure 3

Percentages of CDSs (A) and proteins (B) categorized in enzymatic and non-enzymatic groups.

Figure 4

Multiple alignment of waprin protein from various venomous snakes. The NCBI reference sequence/GenBank accession numbers for Daboia russelii, Protobothrops mucrosquamatus, Pseudonaja textilis, Crotalus tigris, Notechis scutatus, Thamnophis elegans, and Thamnophis sirtalis waprins are ASU45069, XP_029139923, XP_026557480, XP_039199862, XP_026523009, XP_032094882, and XP_013912228, respectively. The single peptide of Daboia siamensis waprin identified in this study is highlighted in the yellow box.

Figure 5

Percentages of functional group-based GO terms calculated from Daboia siamensis venom proteome according to cellular component terms (A), biological process terms (B), and molecular function terms (C).

Figure 6

Pairwise sequence alignment of Thai (TH) and Myanmar (MM) DSAIP proteins. The grey, green, orange, and purple boxes denote regions of propeptide, peptidase, disintegrin, and ADAM cys-rich, respectively. Alphabets in red indicate differences between Thai and Myanmar DSAIP proteins. Blue-highlighted alphabets are regions covered by SMSNet search results. Red diamonds denote conserved cysteine residues.