True Lies: Using Proteomics to Assess the Accuracy of Transcriptome-Based Venomics in Centipedes Uncovers False Positives and Reveals Startling Intraspecific Variation in Scolopendra Subspinipes.

Jennifer Smith,Eivind Undheim

doi:10.3390/toxins10030096

Abstract

Centipede venoms have emerged as a rich source of novel bioactive compounds. However, most centipede species are commonly considered too small for venom extraction and transcriptomics is likely to be an attractive way of probing the molecular diversity of these venoms. Examining the venom composition of Scolopendra subspinipes, we test the accuracy of this approach. We compared the proteomically determined venom profile with four common toxin transcriptomic toxin annotation approaches: BLAST search against toxins in UniProt, lineage-specific toxins, or species-specific toxins and comparative expression analyses of venom and non-venom producing tissues. This demonstrated that even toxin annotation based on lineage-specific homology searches is prone to substantial errors compared to a proteomic approach. However, combined comparative transcriptomics and phylogenetic analysis of putative toxin families substantially improves annotation accuracy. Furthermore, comparison of the venom composition of S. subspinipes with the closely related S. subspinipes mutilans revealed a surprising lack of overlap. This first insight into the intraspecific venom variability of centipedes contrasts the sequence conservation expected from previous findings that centipede toxins evolve under strong negative selection. Our results highlight the importance of proteomic data in studies of even comparably well-characterized venoms and warrants caution when sourcing venom from centipedes of unknown origin.

Highlights

Animal venoms contain a plethora of bioactive peptides and proteins, many of which have the potential for application as pharmacological tools [1] and in some cases lead molecules for the development of novel therapeutics [2] or agrochemical products [3]
S. subspinipes as our model species we show that the most accurate annotation of toxins in venom transcriptomic datasets results from combining comparative expression and phylogenetic analyses, as compared to BLAST-only methods that lead to high rates of false positives
We found a surprisingly low overlap between venom from different members of the S. subspinipes species complex, contrasting previous findings suggesting that high conservation exists between subspecies in centipedes

Summary

Introduction

Animal venoms contain a plethora of bioactive peptides and proteins, many of which have the potential for application as pharmacological tools [1] and in some cases lead molecules for the development of novel therapeutics [2] or agrochemical products [3]. Toxins 2018, 10, 96 interest in the field of venom research to investigate the diversity of putative toxins in venomous organisms. One method of probing this molecular diversity is through transcriptomic analysis of venom glands [4]. Over the past ten years, DNA sequencing costs have dramatically decreased and the technologies required to generate transcriptomes are widely accessible. Venom gland transcriptomes have been acquired for over 100 species worldwide, including snakes, scorpions, sea anemones and spiders. A group of venomous animals that are attracting increasing research interest are the centipedes

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