Transcriptome annotation and characterization of novel toxins in six scorpion species

D.G.B. Grashof; H.M.I. Kerkkamp; S. Afonso; J. Archer; D.J. Harris; M.K. Richardson; F.J. Vonk; A. Van Der Meijden

doi:10.1186/s12864-019-6013-6

Transcriptome annotation and characterization of novel toxins in six scorpion species

D.G.B. Grashof, H.M.I. Kerkkamp, S. Afonso, J. Archer, D.J. Harris, M.K. Richardson, F.J. Vonk, A. Van Der Meijden

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

© 2019 The Author(s).Background: Venom has evolved in parallel in multiple animals for the purpose of self-defense, prey capture or both. These venoms typically consist of highly complex mixtures of toxins: diverse bioactive peptides and/or proteins each with a specific pharmacological activity. Because of their specificity, they can be used as experimental tools to study cell mechanisms and develop novel medicines and drugs. It is therefore potentially valuable to explore the venoms of various animals to characterize their toxins and identify novel toxin-families. This study focuses on the annotation and exploration of the transcriptomes of six scorpion species from three different families. The transcriptomes were annotated with a custom-built automated pipeline, primarily consisting of Basic Local Alignment Search Tool searches against UniProt databases and filter steps based on transcript coverage. Results: We annotated the transcriptomes of four scorpions from the family Buthidae, one from Iuridae and one from Diplocentridae using our annotation pipeline. We found that the four buthid scorpions primarily produce disulfide-bridged ion-channel targeting toxins, while the non-buthid scorpions have a higher abundance of non-disulfide-bridged toxins. Furthermore, analysis of the "unidentified" transcripts resulted in the discovery of six novel putative toxin families containing a total of 37 novel putative toxins. Additionally, 33 novel toxins in existing toxin-families were found. Lastly, 19 novel putative secreted proteins without toxin-like disulfide bonds were found. Conclusions: We were able to assign most transcripts to a toxin family and classify the venom composition for all six scorpions. In addition to advancing our fundamental knowledge of scorpion venomics, this study may serve as a starting point for future research by facilitating the identification of the venom composition of scorpions and identifying novel putative toxin families.

Original language	English
Article number	645
Journal	BMC Genomics
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s12864-019-6013-6
Publication status	Published - 13 Aug 2019
Externally published	Yes

Funding

AvdM was supported through FCT – Fundação para a Ciência e a Tecnologia, I.P. under contract number DL57/2016/CP1440/CT0009. This work is funded by FEDER funds through the Operational Program for Competitiveness Factors - COMPETE and by National Funds through FCT - Foundation for Science and Technology under the project FCT-PTDC/BIA-EVF/ 2687/2012 and FCOMP-01-0124-FEDER-028340. HMIK was supported by the Top Sector Syngenopep grant (nr. 731.014.206) from the Netherlands Organization for Scientific Research (NWO) and by Naturalis Biodiversity Center. The funding bodies were not involved in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Funders	Funder number
Netherlands Organization for Scientific Research
Top Sector Syngenopep	731.014.206
Fundação para a Ciência e a Tecnologia	FCOMP-01-0124-FEDER-028340, FCT-PTDC/BIA-EVF/ 2687/2012
Nederlandse Organisatie voor Wetenschappelijk Onderzoek
Instituto Nacional de Ciência e Tecnologia para Excitotoxicidade e Neuroproteção	DL57/2016/CP1440/CT0009
Naturalis Biodiversity Center

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title = "Transcriptome annotation and characterization of novel toxins in six scorpion species",

abstract = "{\textcopyright} 2019 The Author(s).Background: Venom has evolved in parallel in multiple animals for the purpose of self-defense, prey capture or both. These venoms typically consist of highly complex mixtures of toxins: diverse bioactive peptides and/or proteins each with a specific pharmacological activity. Because of their specificity, they can be used as experimental tools to study cell mechanisms and develop novel medicines and drugs. It is therefore potentially valuable to explore the venoms of various animals to characterize their toxins and identify novel toxin-families. This study focuses on the annotation and exploration of the transcriptomes of six scorpion species from three different families. The transcriptomes were annotated with a custom-built automated pipeline, primarily consisting of Basic Local Alignment Search Tool searches against UniProt databases and filter steps based on transcript coverage. Results: We annotated the transcriptomes of four scorpions from the family Buthidae, one from Iuridae and one from Diplocentridae using our annotation pipeline. We found that the four buthid scorpions primarily produce disulfide-bridged ion-channel targeting toxins, while the non-buthid scorpions have a higher abundance of non-disulfide-bridged toxins. Furthermore, analysis of the {"}unidentified{"} transcripts resulted in the discovery of six novel putative toxin families containing a total of 37 novel putative toxins. Additionally, 33 novel toxins in existing toxin-families were found. Lastly, 19 novel putative secreted proteins without toxin-like disulfide bonds were found. Conclusions: We were able to assign most transcripts to a toxin family and classify the venom composition for all six scorpions. In addition to advancing our fundamental knowledge of scorpion venomics, this study may serve as a starting point for future research by facilitating the identification of the venom composition of scorpions and identifying novel putative toxin families.",

author = "D.G.B. Grashof and H.M.I. Kerkkamp and S. Afonso and J. Archer and D.J. Harris and M.K. Richardson and F.J. Vonk and {Van Der Meijden}, A.",

year = "2019",

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doi = "10.1186/s12864-019-6013-6",

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AU - Grashof, D.G.B.

AU - Kerkkamp, H.M.I.

AU - Afonso, S.

AU - Archer, J.

AU - Harris, D.J.

AU - Richardson, M.K.

AU - Vonk, F.J.

AU - Van Der Meijden, A.

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AB - © 2019 The Author(s).Background: Venom has evolved in parallel in multiple animals for the purpose of self-defense, prey capture or both. These venoms typically consist of highly complex mixtures of toxins: diverse bioactive peptides and/or proteins each with a specific pharmacological activity. Because of their specificity, they can be used as experimental tools to study cell mechanisms and develop novel medicines and drugs. It is therefore potentially valuable to explore the venoms of various animals to characterize their toxins and identify novel toxin-families. This study focuses on the annotation and exploration of the transcriptomes of six scorpion species from three different families. The transcriptomes were annotated with a custom-built automated pipeline, primarily consisting of Basic Local Alignment Search Tool searches against UniProt databases and filter steps based on transcript coverage. Results: We annotated the transcriptomes of four scorpions from the family Buthidae, one from Iuridae and one from Diplocentridae using our annotation pipeline. We found that the four buthid scorpions primarily produce disulfide-bridged ion-channel targeting toxins, while the non-buthid scorpions have a higher abundance of non-disulfide-bridged toxins. Furthermore, analysis of the "unidentified" transcripts resulted in the discovery of six novel putative toxin families containing a total of 37 novel putative toxins. Additionally, 33 novel toxins in existing toxin-families were found. Lastly, 19 novel putative secreted proteins without toxin-like disulfide bonds were found. Conclusions: We were able to assign most transcripts to a toxin family and classify the venom composition for all six scorpions. In addition to advancing our fundamental knowledge of scorpion venomics, this study may serve as a starting point for future research by facilitating the identification of the venom composition of scorpions and identifying novel putative toxin families.

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DO - 10.1186/s12864-019-6013-6

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VL - 20

JO - BMC Genomics

JF - BMC Genomics

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M1 - 645

ER -

Transcriptome annotation and characterization of novel toxins in six scorpion species

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