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Avella I, Schulte L, Hurka S, Damm M, Eichberg J, Schiffmann S, Henke M, Timm T, Lochnit G, Hardes K, Vilcinskas A, Lüddecke T. Proteogenomics-guided functional venomics resolves the toxin arsenal and activity of Deinagkistrodon acutus venom. Int J Biol Macromol 2024; 278:135041. [PMID: 39182889 DOI: 10.1016/j.ijbiomac.2024.135041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Snakebite primarily impacts rural communities of Africa, Asia, and Latin America. The sharp-nosed viper (Deinagkistrodon acutus) is among the snakes of highest medical importance in Asia. Despite various studies on its venom using modern venomics techniques, a comprehensive understanding of composition and function of this species' venom remains lacking. We combined proteogenomics with extensive bioactivity profiling to present the first genome-level catalogue of D. acutus venom proteins and their exochemistry. Our analysis identified an unusually simple venom containing 45 components from 20 distinct protein families. Relative toxin abundances indicate that C-type lectin and C-type lectin-related protein (CTL), snake venom metalloproteinase (svMP), snake venom serine protease (svSP), and phospholipase A2 (PLA2) constitute 90 % of the venom. Bioassays targeting key aspects of viperid envenomation showed considerable concentration-dependent cytotoxicity, particularly in kidney and lung cells, and potent protease and PLA2 activity. Factor Xa and thrombin activities were minor, and no plasmin activity was observed. Effects on haemolysis, intracellular calcium (Ca2+) release, and nitric oxide (NO) synthesis were negligible. Our analysis provides the first holistic genome-based overview of the toxin arsenal of D. acutus, predicting the molecular and functional basis of its life-threatening effects, and opens novel avenues for treating envenomation by this highly dangerous snake.
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Affiliation(s)
- Ignazio Avella
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
| | - Lennart Schulte
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany
| | - Sabine Hurka
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Bioeconomy (BioKreativ) "SymBioÖkonomie", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Maik Damm
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Johanna Eichberg
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Susanne Schiffmann
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 60596 Frankfurt am Main, Germany
| | - Marina Henke
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 60596 Frankfurt am Main, Germany
| | - Thomas Timm
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Günther Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Kornelia Hardes
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany
| | - Tim Lüddecke
- Animal Venomics Lab, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Natural Product Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany.
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Dresler J, Herzig V, Vilcinskas A, Lüddecke T. Enlightening the toxinological dark matter of spider venom enzymes. NPJ BIODIVERSITY 2024; 3:25. [PMID: 39271930 PMCID: PMC11399385 DOI: 10.1038/s44185-024-00058-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/15/2024] [Indexed: 09/15/2024]
Abstract
Spiders produce highly adapted venoms featuring a complex mixture of biomolecules used mainly for hunting and defense. The most prominent components are peptidic neurotoxins, a major focus of research and drug development, whereas venom enzymes have been largely neglected. Nevertheless, investigation of venom enzymes not only reveals insights into their biological functions, but also provides templates for future industrial applications. Here we compared spider venom enzymes validated at protein level contained in the VenomZone database and from all publicly available proteo-transcriptomic spider venom datasets. We assigned reported enzymes to cellular processes and known venom functions, including toxicity, prey pre-digestion, venom preservation, venom component activation, and spreading factors. Our study unveiled extensive discrepancy between public databases and publications with regard to enzyme coverage, which impedes the development of novel spider venom enzyme-based applications. Uncovering the previously unrecognized abundance and diversity of venom enzymes will open new avenues for spider venom biodiscovery.
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Affiliation(s)
- Josephine Dresler
- Animal Venomics Lab, Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Gießen, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt a. M., Germany.
| | - Volker Herzig
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Andreas Vilcinskas
- Animal Venomics Lab, Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Gießen, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt a. M., Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Gießen, Germany
| | - Tim Lüddecke
- Animal Venomics Lab, Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Gießen, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt a. M., Germany.
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Krämer J, Hölker P, Predel R. How to Overcome a Snail? Identification of Putative Neurotoxins of Snail-Feeding Firefly Larvae (Coleoptera: Lampyridae, Lampyris noctiluca). Toxins (Basel) 2024; 16:272. [PMID: 38922166 PMCID: PMC11209139 DOI: 10.3390/toxins16060272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
The larvae of some lampyrid beetles are highly specialized predators of snails. They have been observed to climb on the shells of their prey and use this exposed position to bite and inject secretions potentially originating from the midgut. Besides serving the purpose of extra-oral digestion (EOD), injected compounds also seem to have a paralyzing effect. Up to now, the toxins causing this paralyzing activity have not been identified. In the current study, we provide a first compositional analysis of the midgut secretion from lampyrid larvae, with a focus on identifying putative neurotoxins causing the observed paralyzing effect. For this purpose, we utilized a combined proteo-transcriptomic approach to characterize the compounds present in the midgut secretion of larval stages of Lampyris noctiluca. In terms of the absolute numbers of identified compounds, the midgut secretion is dominated by hydrolyzing enzymes comprising peptidases, carboxylesterases, and glycosidases. However, when considering expression levels, a few rather short cysteine-rich peptides exceed all other compounds. Some of these compounds show moderate similarity to putative neurotoxins identified in the venom of other arthropods and could be responsible for paralyzing effects. In addition to these potential toxins, we provide a list of peptides typical of the midgut secretion of L. noctiluca, supplemented by the corresponding precursor sequences.
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Affiliation(s)
- Jonas Krämer
- Institute of Zoology, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Patrick Hölker
- Institute of Zoology, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany
| | - Reinhard Predel
- Institute of Zoology, University of Cologne, Zuelpicher Strasse 47b, 50674 Cologne, Germany
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Guo R, Guo G, Wang A, Xu G, Lai R, Jin H. Spider-Venom Peptides: Structure, Bioactivity, Strategy, and Research Applications. Molecules 2023; 29:35. [PMID: 38202621 PMCID: PMC10779620 DOI: 10.3390/molecules29010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
Spiders (Araneae), having thrived for over 300 million years, exhibit remarkable diversity, with 47,000 described species and an estimated 150,000 species in existence. Evolving with intricate venom, spiders are nature's skilled predators. While only a small fraction of spiders pose a threat to humans, their venoms contain complex compounds, holding promise as drug leads. Spider venoms primarily serve to immobilize prey, achieved through neurotoxins targeting ion channels. Peptides constitute a major part of these venoms, displaying diverse pharmacological activities, and making them appealing for drug development. Moreover, spider-venom peptides have emerged as valuable tools for exploring human disease mechanisms. This review focuses on the roles of spider-venom peptides in spider survival strategies and their dual significance as pharmaceutical research tools. By integrating recent discoveries, it provides a comprehensive overview of these peptides, their targets, bioactivities, and their relevance in spider survival and medical research.
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Affiliation(s)
- Ruiyin Guo
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
| | - Gang Guo
- The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming 650118, China;
| | - Aili Wang
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
| | - Gaochi Xu
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
| | - Ren Lai
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
- Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, Kunming-Primate Research Center, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Sino-African Joint Research Center and Engineering Laboratory of Peptides, Kunming Institute of Zoology, Kunming 650107, China
| | - Hui Jin
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (R.G.)
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Digestive enzymes and sphingomyelinase D in spiders without venom (Uloboridae). Sci Rep 2023; 13:2661. [PMID: 36792649 PMCID: PMC9932164 DOI: 10.1038/s41598-023-29828-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Spiders have distinct predatory behaviours selected along Araneae's evolutionary history but are mainly based on the use of venom for prey paralysis. Uloboridae spiders have lost their venom glands secondarily during evolution. Because of this, they immobilise their prey by extensively wrapping, and digestion starts with the addition of digestive fluid. During the extra-oral digestion, the digestive fluid liquefies both the prey and the AcSp2 spidroins from the web fibres. Despite the efficiency of this process, the cocktail of enzymes involved in digestion in Uloboridae spiders remains unknown. In this study, the protein content in the midgut of Uloborus sp. was evaluated through enzymatic, proteomic, and phylogenetic analysis. Hydrolases such as peptidases (endo and exopeptidases: cysteine, serine, and metallopeptidases), carbohydrases (alpha-amylase, chitinase, and alpha-mannosidase), and lipases were biochemically assayed, and 50 proteins (annotated as enzymes, structural proteins, and toxins) were identified, evidencing the identity between the digestive enzymes present in venomous and non-venomous spiders. Even enzymes thought to be unique to venom, including enzymes such as sphingomyelinase D, were found in the digestive system of non-venomous spiders, suggesting a common origin between digestive enzymes and enzymes present in venoms. This is the first characterization of the molecules involved in the digestive process and the midgut protein content of a non-venomous spider.
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Neto OBS, Valladão R, Coelho GR, Dias R, Pimenta DC, Lopes AR. Spiders' digestive system as a source of trypsin inhibitors: functional activity of a member of atracotoxin structural family. Sci Rep 2023; 13:2389. [PMID: 36765114 PMCID: PMC9918498 DOI: 10.1038/s41598-023-29576-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Spiders are important predators of insects and their venoms play an essential role in prey capture. Spider venoms have several potential applications as pharmaceutical compounds and insecticides. However, transcriptomic and proteomic analyses of the digestive system (DS) of spiders show that DS is also a rich source of new peptidase inhibitor molecules. Biochemical, transcriptomic and proteomic data of crude DS extracts show the presence of molecules with peptidase inhibitor potential in the spider Nephilingis cruentata. Therefore, the aims of this work were to isolate and characterize molecules with trypsin inhibitory activity. The DS of fasting adult females was homogenized under acidic conditions and subjected to heat treatment. After that, samples were submitted to ion exchange batch and high-performance reverse-phase chromatography. The fractions with trypsin inhibitory activity were confirmed by mass spectrometry, identifying six molecules with inhibitory potential. The inhibitor NcTI (Nephilingis cruentata trypsin inhibitor) was kinetically characterized, showing a KD value of 30.25 nM ± 8.13. Analysis of the tertiary structure by molecular modeling using Alpha-Fold2 indicates that the inhibitor NcTI structurally belongs to the MIT1-like atracotoxin family. This is the first time that a serine peptidase inhibitory function is attributed to this structural family and the inhibitor reactive site residue is identified. Sequence analysis indicates that these molecules may be present in the DS of other spiders and could be associated to the inactivation of prey trypsin (serine peptidase) ingested by the spiders.
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Affiliation(s)
- Oscar Bento Silva Neto
- Laboratory of Biochemistry, Instituto Butantan, São Paulo, 05503900, Brazil.,Programa Interunidades (USP, Instituto Butantan, IPT) de pós-graduação em Biotecnologia, Universidade de São Paulo, São Paulo, 05508000, Brazil
| | - Rodrigo Valladão
- Laboratory of Biochemistry, Instituto Butantan, São Paulo, 05503900, Brazil.,Programa Interunidades (USP, Instituto Butantan, IPT) de pós-graduação em Biotecnologia, Universidade de São Paulo, São Paulo, 05508000, Brazil
| | | | - Renata Dias
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiás, Brazil
| | | | - Adriana Rios Lopes
- Laboratory of Biochemistry, Instituto Butantan, São Paulo, 05503900, Brazil. .,Programa Interunidades (USP, Instituto Butantan, IPT) de pós-graduação em Biotecnologia, Universidade de São Paulo, São Paulo, 05508000, Brazil.
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7
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Avella I, Wüster W, Luiselli L, Martínez-Freiría F. Toxic Habits: An Analysis of General Trends and Biases in Snake Venom Research. Toxins (Basel) 2022; 14:toxins14120884. [PMID: 36548781 PMCID: PMC9783912 DOI: 10.3390/toxins14120884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Biases in snake venom research have been partially identified but seldomly quantified. Using the Google Scholar web search engine, we collected a total of 267 articles published between 1964 and 2021, and reviewed them to assess the main trends in this field of study. We developed a 4-category classification of the harmful potential of each of the 298 snake species retrieved from the analysed publications, and tested whether taxonomy, realm of origin, and/or assigned hazard category could affect how often each of them appeared in the articles considered. Overall, viperids were significantly more represented than any other snake taxon retrieved. The Neotropics were the most represented biogeographic realm for number of studied species, whereas information about the country of origin of the analysed specimens was often incomplete. The vast majority of the publications focused on snake venom characterisation, whereas more ecology-related topics were rarely considered. Hazard category and biogeographic realm of origin of each species had a significant effect on the number of articles dedicated to it, suggesting that a snake's harmful potential and place of origin influence its popularity in venom studies. Our analysis showed an overall positive trend in the number of snake venom studies published yearly, but also underlined severe neglect of snake families of supposedly minor medical relevance (e.g., Atractaspididae), underrepresentation of some of the areas most impacted by snakebite (i.e., Indomalayan and Afrotropic realms), and limited interest in the ecological and functional context of snake venom.
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Affiliation(s)
- Ignazio Avella
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Correspondence:
| | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Luca Luiselli
- Institute for Development, Ecology, Conservation & Cooperation, Via G. Tomasi di Lampedusa 33, I-00144 Rome, Italy
- Department of Zoology, University of Lomé, Lomé 01BP1515, Togo
- Department of Environmental and Applied Biology, Rivers State University of Science and Technology, Port Harcourt P.M.B. 5080, Nigeria
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
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8
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Perrotta BG, Kidd KA, Walters DM. PCB exposure is associated with reduction of endosymbionts in riparian spider microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156726. [PMID: 35716742 DOI: 10.1016/j.scitotenv.2022.156726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities, including endosymbionts, play diverse and critical roles in host biology and reproduction, but contaminant exposure may cause an imbalance in the microbiome composition with subsequent impacts on host health. Here, we examined whether there was a significant alteration of the microbiome community within two taxa of riparian spiders (Tetragnathidae and Araneidae) from a site with historical polychlorinated biphenyl (PCB) contamination in southern Ontario, Canada. Riparian spiders specialize in the predation of adult aquatic insects and, as such, their contaminant levels closely track those of nearby aquatic ecosystems. DNA from whole spiders from sites with either low or high PCB contamination was extracted, and spider microbiota profiled by partial 16S rRNA gene amplicon sequencing. The most prevalent shift in microbial communities we observed was a large reduction in endosymbionts in spiders at the high PCB site. The abundance of endosymbionts at the high PCB site was 63 % and 98 % lower for tetragnathids and araneids, respectively, than at the low PCB site. Overall, this has potential implications for spider reproductive success and food webs, as riparian spiders are critical gatekeepers of energy and material fluxes at the land-water interface.
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Affiliation(s)
- Brittany G Perrotta
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; Contractor, U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Karen A Kidd
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; School of Earth, Environment and Society, McMaster University, Hamilton, Ontario, Canada.
| | - David M Walters
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
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Trabuco Amaral D, Mitani Y, Aparecida Silva Bonatelli I, Cerri R, Ohmiya Y, Viviani V. Genome analysis of Phrixothrix hirtus (Phengodidae) railroad worm shows the expansion of odorant-binding gene families and positive selection on morphogenesis and sex determination genes. Gene X 2022; 850:146917. [PMID: 36174905 DOI: 10.1016/j.gene.2022.146917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022] Open
Abstract
Among bioluminescent beetles of the Elateroidea superfamily, Phengodidae is the third largest family, with 244 bioluminescent species distributed only in the Americas, but is still the least studied from the phylogenetic and evolutionary points of view. The railroad worm Phrixothrix hirtus is an essential biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing the first source of genomic information and a framework for comparative analyses of the bioluminescent system in Elateroidea. This is the largest genome described in the Elateroidea superfamily, with an estimated size of ∼3.4 Gb, displaying 32 % GC content, and 67 % transposable elements. Comparative genomic analyses showed a positive selection of genes and gene family expansion events of growths and morphogenesis gene products, which could be associated with the atypical anatomical development and morphogenesis found in paedomorphic females and underdeveloped males. We also observed gene family expansion among distinct odorant-binding receptors, which could be associated with the pheromone communication system typical of these beetles, and retrotransposable elements. Common genes putatively regulating bioluminescence production and control, including two luciferase genes corresponding to lateral lanterns green-emitting and head lanterns red-emitting luciferases with 7 exons and 6 introns, and genes potentially involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea.
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Affiliation(s)
- Danilo Trabuco Amaral
- Programa de Pós-Graduação em Biotecnociência, Centro de Ciências Naturais e Humanas. Universidade Federal do ABC (UFABC), Santo André, Brazil
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | | | - Ricardo Cerri
- Department of Computational Science, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Ikeda-Osaka, Japan; Osaka Institute of Technology, OIT, Osaka, Japan
| | - Vadim Viviani
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil; Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil.
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10
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Marchi FC, Mendes-Silva E, Rodrigues-Ribeiro L, Bolais-Ramos LG, Verano-Braga T. Toxinology in the proteomics era: a review on arachnid venom proteomics. J Venom Anim Toxins Incl Trop Dis 2022; 28:20210034. [PMID: 35291269 PMCID: PMC8893269 DOI: 10.1590/1678-9199-jvatitd-2021-0034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/01/2021] [Indexed: 11/22/2022] Open
Abstract
The word venomics was coined to acknowledge the studies that use omics to investigate venom proteins and peptides. Venomics has evolved considerably over the last 20 years. The first works on scorpion or spider venomics were published in the early 2000's. Such studies relied on peptide mass fingerprinting (PMF) to characterize venom complexity. After the introduction of new mass spectrometers with higher resolution, sensitivity and mass accuracy, and the next-generation nucleotide sequencing, the complexity of data reported in research on scorpion and spider venomics increased exponentially, which allowed more comprehensive studies. In the present review article, we covered key publications on scorpion venomics and spider venomics, presenting historical grounds and implemented technologies over the last years. The literature presented in this review was selected after searching the PubMed database using the terms "(scorpion venom) AND (proteome)" for scorpion venomics, and "(spider venom) AND (proteome)" for publications on spider venomics. We presented the key aspects related to proteomics in the covered papers including, but not restricted to, the employed proteomic strategy (i.e., PMF, two-dimensional gel electrophoresis, shotgun/bottom-up and/or top-down/peptidome), and the type of mass spectrometer used. Some conclusions can be drawn from the present study. For example, the scorpion genus Tityus is the most studied concerning venomics, followed by Centruroides; whereas for spiders the studied genera were found more equally distributed. Another interesting conclusion is the lack of high throughput studies on post-translational modifications (PTMs) of scorpion and spider proteins. In our opinion, PTMs should be more studied as they can modulate the activity of scorpion and spider toxins.
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Affiliation(s)
- Filipi Calbaizer Marchi
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Edneia Mendes-Silva
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Lucas Rodrigues-Ribeiro
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Lucas Gabriel Bolais-Ramos
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Thiago Verano-Braga
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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11
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Arroyave-Muñoz A, Meijden AVD, Estrada-Gómez S, García LF. Linking toxicity and predation in a venomous arthropod: the case of Tityus fuhrmanni (Scorpiones: Buthidae), a generalist predator scorpion. J Venom Anim Toxins Incl Trop Dis 2022; 28:e20210036. [PMID: 35082841 PMCID: PMC8747031 DOI: 10.1590/1678-9199-jvatitd-2021-0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
Background: Scorpions are arachnids that have a generalist diet, which use venom to
subdue their prey. The study of their trophic ecology and capture behavior
is still limited compared to other organisms, and aspects such as trophic
specialization in this group have been little explored. Methods: In order to determine the relationship between feeding behavior and venom
toxicity in the scorpion species Tityus fuhrmanni, 33
specimens were offered prey with different morphologies and defense
mechanisms: spiders, cockroaches and crickets. In each of the experiments we
recorded the following aspects: acceptance rate, immobilization time and the
number of capture attempts. The median lethal dose of T.
fuhrmanni venom against the three different types of prey was
also evaluated. Results: We found that this species does not have a marked difference in acceptance
for any of the evaluated prey, but the number of capture attempts of spiders
is higher when compared to the other types of prey. The immobilization time
is shorter in spiders compared to other prey and the LD50 was
higher for cockroaches. Conclusions: These results indicate that T. fuhrmanni is a scorpion with
a generalist diet, has a venom with a different potency among prey and is
capable of discriminating between prey types and employing distinct
strategies to subdue them.
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12
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Fuzita FJ, Palmisano G, Pimenta DC, Terra WR, Ferreira C. A proteomic approach to identify digestive enzymes, their exocytic and microapocrine secretory routes and their compartmentalization in the midgut of Spodoptera frugiperda. Comp Biochem Physiol B Biochem Mol Biol 2021; 257:110670. [PMID: 34438074 DOI: 10.1016/j.cbpb.2021.110670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022]
Abstract
A proteomic approach was used to identify the digestive enzymes secreted by exocytosis and by microapocrine vesicles and enzyme midgut compartmentalization in Spodoptera frugiperda larvae. For this, proteomic analyses were performed in isolated midgut enterocyte microvillar membrane, in a fraction enriched in microapocrine vesicles (separated in soluble and membrane fractions), in the washings of the peritrophic membrane to isolate its loosely- and tightly-bound proteins, and in the peritrophic membrane contents. PM washings correspond to proteins extracted from the mucus layer surrounding PM. Serine endopeptidases (trypsins, chymotrypsins and serine endopeptidase homologs that have substitutions in the catalytic residues) and lipases are mainly secreted by exocytosis. Aminopeptidases are mainly microvillar enzymes and some are secreted membrane-bound to microapocrine vesicles, whereas carboxypeptidase isoforms follow different secretory routes. The results also showed that most polymer hydrolases (such as amylase and endopeptidases) are not retained in the ectoperitrophic fluid (found in PM washings but absent from PM contents). On the contrary, most enzymes involved in intermediate digestion (exemplified by carboxypeptidase and aminopeptidase) do not pass through the peritrophic membrane. Finally, the data revealed that the protein composition of PM includes peritrophins classified as peritrophic membrane proteins, PMP, and chitin deacetylase.
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Affiliation(s)
- Felipe J Fuzita
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil
| | - Giuseppe Palmisano
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000 São Paulo, Brazil
| | - Daniel C Pimenta
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo 05503-900, Brazil
| | - Walter R Terra
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil
| | - Clélia Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil.
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13
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Nakamura S, Miyazaki T, Park EY. α-L-Fucosidase from Bombyx mori has broad substrate specificity and hydrolyzes core fucosylated N-glycans. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 124:103427. [PMID: 32561391 DOI: 10.1016/j.ibmb.2020.103427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/25/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
N-glycans play a role in physiological functions, including glycoprotein conformation, signal transduction, and antigenicity. Insects display both α-1,6- and α-1,3-linked fucose residues bound to the innermost N-acetylglucosamine of N-glycans whereas core α-1,3-fucosylated N-glycans are not found in mammals. Functions of insect core-fucosylated glycans are not clear, and no α-L-fucosidase related to the N-glycan degradation has been identified. In the genome of the domestic silkworm, Bombyx mori, a gene for a protein, BmFucA, belonging to the glycoside hydrolase family 29 is a candidate for an α-L-fucosidase gene. In this study, BmFucA was cloned and recombinantly expressed as a glutathione-S-transferase tagged protein (GST-BmFucA). Recombinant GST-BmFucA exhibited broad substrate specificity and hydrolyzed p-nitrophenyl α-L-fucopyranoside, 2'-fucosyllactose, 3-fucosyllactose, 3-fucosyl-N,N'-diacetylchitobiose, and 6-fucosyl-N,N'-diacetylchitobiose. Further, GST-BmFucA released fucose from both pyridylaminated complex-type and paucimannose-type glycans that were core-α-1,6-fucosylated. GST-BmFucA also shows hydrolysis activity for core-fucosylated glycans attached to phospholipase A2 from bee venom. BmFucA may be involved in the catabolism of core-fucosylated N-glycans in B. mori.
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Affiliation(s)
- Shuntaro Nakamura
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takatsugu Miyazaki
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Enoch Y Park
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
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14
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Becchimanzi A, Avolio M, Bostan H, Colantuono C, Cozzolino F, Mancini D, Chiusano ML, Pucci P, Caccia S, Pennacchio F. Venomics of the ectoparasitoid wasp Bracon nigricans. BMC Genomics 2020; 21:34. [PMID: 31924169 PMCID: PMC6954513 DOI: 10.1186/s12864-019-6396-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Venom is one of the most important sources of regulation factors used by parasitic Hymenoptera to redirect host physiology in favour of the developing offspring. This has stimulated a number of studies, both at functional and "omics" level, which, however, are still quite limited for ectophagous parasitoids that permanently paralyze and suppress their victims (i.e., idiobiont parasitoids). RESULTS Here we present a combined transcriptomic and proteomic study of the venom of the generalist idiobiont wasp Bracon nigricans, an ectophagous larval parasitoid of different lepidopteran species, for which we recently described the host regulation strategy and the functional role of the venom in the induction of physiological changes in parasitized hosts. The experimental approach used led to the identification of the main components of B. nigricans venom involved in host regulation. Enzymes degrading lipids, proteins and carbohydrates are likely involved in the mobilization of storage nutrients from the fat body and may concurrently be responsible for the release of neurotoxic fatty acids inducing paralysis, and for the modulation of host immune responses. CONCLUSION The present work contributes to fill the gap of knowledge on venom composition in ectoparasitoid wasps, and, along with our previous physiological study on this species, provides the foundation on which to develop a functional model of host regulation, based both on physiological and molecular data. This paves the way towards a better understanding of parasitism evolution in the basal lineages of Hymenoptera and to the possible exploitation of venom as source of bioinsecticidal molecules.
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Affiliation(s)
- Andrea Becchimanzi
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Maddalena Avolio
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
- Present address: Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
- Present address: Infrastrutture di Ricerca per le Risorse Biologiche Marine, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences and CEINGE Biotecnologie Avanzate, University of Napoli Federico II, Napoli, Italy
| | - Donato Mancini
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Pietro Pucci
- Department of Chemical Sciences and CEINGE Biotecnologie Avanzate, University of Napoli Federico II, Napoli, Italy
| | - Silvia Caccia
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
| | - Francesco Pennacchio
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, NA Italy
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15
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Medina-Santos R, Guerra-Duarte C, de Almeida Lima S, Costal-Oliveira F, Alves de Aquino P, Oliveira do Carmo A, Ferreyra CB, Gonzalez-Kozlova EE, Kalapothakis E, Chávez-Olórtegui C. Diversity of astacin-like metalloproteases identified by transcriptomic analysis in Peruvian Loxosceles laeta spider venom and in vitro activity characterization. Biochimie 2019; 167:81-92. [PMID: 31476328 DOI: 10.1016/j.biochi.2019.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/28/2019] [Indexed: 11/25/2022]
Abstract
Loxosceles spiders are found in almost all countries of South America. In Peru, Loxosceles laeta species is the main responsible for the accidents caused by poisonous animals, being known as "killer spiders", due to the large number of fatal accidents observed. Astacin-like metalloproteases, named LALPs (Loxosceles astacin-like metalloproteases) are highly expressed in Loxosceles spiders venom gland. These proteases may be involved in hemorrhage and venom spreading, being relevant to the envenoming proccess. Thus, the aim of this work was to analyze Peruvian L. laeta venom gland transcripts using bioinformatics tools, focusing on LALPs. A cDNA library from Peruvian L. laeta venom glands was constructed and sequenced by MiSeq (Illumina) sequencer. After assembly, the resulting sequences were annotated, seeking out for similarity with previously described LALPs. Nine possible LALPs isoforms from Peruvian L. laeta venom were identified and the results were validated by in silico and in vitro experiments. This study contributes to a better understanding of the molecular diversity of Loxosceles venom and provide insights about the action of LALPs.
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Affiliation(s)
- Raíssa Medina-Santos
- Biochemistry and Immunology Department, Federal University of Minas Gerais, Brazil; Genetic, Ecology and Evolution Department, Federal University of Minas Gerais, Brazil
| | | | | | | | | | | | - César Bonilla Ferreyra
- Univesidad Nacional Mayor de San Marcos, Facultad de Odontología, Lima, Peru; Instituto Nacional de Salud, Lima, Peru
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16
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Zobel-Thropp PA, Mullins J, Kristensen C, Kronmiller BA, David CL, Breci LA, Binford GJ. Not so Dangerous After All? Venom Composition and Potency of the Pholcid (Daddy Long-Leg) Spider Physocyclus mexicanus. Front Ecol Evol 2019; 7:256. [PMID: 33235882 PMCID: PMC7682650 DOI: 10.3389/fevo.2019.00256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pholcid spiders (Araneae: Pholcidae), officially "cellar spiders" but popularly known as "daddy long-legs," are renown for the potential of deadly toxic venom, even though venom composition and potency has never formally been studied. Here we detail the venom composition of male Physocyclus mexicanus using proteomic analyses and venom-gland transcriptomes ("venomics"). We also analyze the venom's potency on insects, and assemble available evidence regarding mammalian toxicity. The majority of the venom (51% of tryptic polypeptides and 62% of unique tryptic peptides) consists of proteins homologous to known venom toxins including enzymes (astacin metalloproteases, serine proteases and metalloendopeptidases, particularly neprilysins) and venom peptide neurotoxins. We identify 17 new groups of peptides (U1-17-PHTX) most of which are homologs of known venom peptides and are predicted to have an inhibitor cysteine knot fold; of these, 13 are confirmed in the proteome. Neprilysins (M13 peptidases), and astacins (M12 peptidases) are the most abundant venom proteins, respectively representing 15 and 11% of the individual proteins and 32 and 20% of the tryptic peptides detected in crude venom. Comparative evidence suggests that the neprilysin gene family is expressed in venoms across a range of spider taxa, but has undergone an expansion in the venoms of pholcids and may play a central functional role in these spiders. Bioassays of crude venoms on crickets resulted in an effective paralytic dose of 3.9 µg/g, which is comparable to that of crude venoms of Plectreurys tristis and other Synspermiata taxa. However, crickets exhibit flaccid paralysis and regions of darkening that are not observed after P. tristis envenomation. Documented bites on humans make clear that while these spiders can bite, the typical result is a mild sting with no long-lasting effects. Together, the evidence we present indicates pholcid venoms are a source of interesting new peptides and proteins, and effects of bites on humans and other mammals are inconsequential.
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Affiliation(s)
| | - Jennifer Mullins
- Department of Biology, Lewis & Clark College, Portland, OR, United States
| | | | - Brent A. Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Cynthia L. David
- Arizona Proteomics Consortium, University of Arizona, Tucson, AZ, United States
| | - Linda A. Breci
- Arizona Proteomics Consortium, University of Arizona, Tucson, AZ, United States
| | - Greta J. Binford
- Department of Biology, Lewis & Clark College, Portland, OR, United States
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17
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The Dual Prey-Inactivation Strategy of Spiders-In-Depth Venomic Analysis of Cupiennius salei. Toxins (Basel) 2019; 11:toxins11030167. [PMID: 30893800 PMCID: PMC6468893 DOI: 10.3390/toxins11030167] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 02/08/2023] Open
Abstract
Most knowledge of spider venom concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The here presented comprehensive analysis of the venom gland transcriptome and proteome of Cupiennius salei focusses on proteins and cysteine-containing peptides and offers new insight into the structure and function of spider venom, here described as the dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to a major disturbance of the cellular homeostasis. Hyaluronidase and cytolytic peptides destroy tissue and membranes, thus supporting the spread of other venom compounds. We detected 81 transcripts of neurotoxins from 13 peptide families, whereof two families comprise 93.7% of all cysteine-containing peptides. This raises the question of the importance of the other low-expressed peptide families. The identification of a venom gland-specific defensin-like peptide and an aga-toxin-like peptide in the hemocytes offers an important clue on the recruitment and neofunctionalization of body proteins and peptides as the origin of toxins.
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18
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Bowman CE. The gut epithelium from feeding to fasting in the predatory soil mite Pergamasus longicornis (Mesostigmata: Parasitidae): one tissue, two roles. EXPERIMENTAL & APPLIED ACAROLOGY 2019; 77:253-357. [PMID: 30895556 DOI: 10.1007/s10493-019-00356-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
A review of acarine gut physiology based on published narratives dispersed over the historical international literature is given. Then, in an experimental study of the free-living predatory soil mite Pergamasus longicornis (Berlese), quantitative micro-anatomical changes in the gut epithelium are critically assessed from a temporal series of histological sections during and after feeding on larval dipteran prey. An argued functional synthesis based upon comparative kinetics is offered for verification in other mesostigmatids. Mid- and hind-gut epithelia cell types interconvert in a rational way dependent upon the physical consequences of ingestion, absorption and egestion. The fasted transitional pseudo-stratified epithelium rapidly becomes first squamous on prey ingestion (by stretching), then columnar during digestion before confirmed partial disintegration (gut 'lumenation') during egestion back to a pseudo-stratified state. Exponential processes within the mid- and endodermic hind-gut exhibit 'stiff' dynamics. Cells expand rapidly ([Formula: see text] 22.9-49.5 min) and vacuolate quickly ([Formula: see text] 1.1 h). Cells shrink very slowly ([Formula: see text] 4.9 days) and devacuolate gently ([Formula: see text] 1.0-1.7 days). Egestive cellular degeneration has an initial [Formula: see text] 7.7 h. Digestion appears to be triggered by maximum gut expansion-estimated at 10 min post start of feeding. Synchrony with changes in gut lumen contents suggests common changes in physiological function over time for the cells as a whole tightly-coupled epithelium. Distinct in architecture as a tissue over time the various constituent cell types appear functionally the same. Functional phases are: early fluid transportation (0-1 h) and extracellular activity (10-90 min); through rising food absorption (10 min to [Formula: see text] day); to slow intracellular meal processing and degenerative egestive waste material production (1 to [Formula: see text] days) much as in ticks. The same epithelium is both absorptive and degenerative in role. The switch in predominant physiology begins 4 h after the start of feeding. Two separate pulses of clavate cells appear to be a mechanism to facilitate transport by increasing epithelial surface area in contact with the lumen. Free-floating cells may augment early extracellular lumenal digestion. Possible evidence for salivary enzyme alkaline-related extra-corporeal digestion was found. Giant mycetome-like cells were found embedded in the mid-gut wall. Anteriorly, the mid-gut behaves like a temporally expendable food processing tissue and minor long-term resistive store. Posteriorly the mid-gut behaves like a major assimilative/catabolic tissue and 'last-out' food depot (i.e., a 'hepatopancreas' function) allowing the mite to resist starvation for up to 3.5 weeks after a single meal. A 'conveyor-belt' wave of physiology (i.e., feeding and digestion, then egestion and excretion) sweeps posteriorly but not necessarily pygidially over time. Assimilation efficiency is estimated at 82%. The total feeding cycle time histologically from a single meal allowing for the bulk of intracellular digestion and egestive release is not 52.5 h but of the order of 6 days ([Formula: see text] total gut emptyings per day), plus typically a further 3 days for subsequent excretion to occur. Final complete gut system clearance in this cryptozooid may take much longer ([Formula: see text] days). A common physiology across the anactinotrichid acarines is proposed. A look to the future of this field is included.
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Affiliation(s)
- Clive E Bowman
- Mathematical Institute, University of Oxford, Oxford, OX2 6GG, United Kingdom.
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19
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Perrella NN, Withers SG, Lopes AR. Identity and role of the non-conserved acid/base catalytic residue in the GH29 fucosidase from the spider Nephilingis cruentata. Glycobiology 2019; 28:925-932. [PMID: 30204861 DOI: 10.1093/glycob/cwy083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
α-l-Fucosidases are widely occurring enzymes that remove fucose residues from N- and O-fucosylated glycoproteins. Comparison of amino acid sequences of fucosidases reveals that although the nucleophile is conserved among all α-l-fucosidases, the position of the acid/base residue is quite variable. Although several site-directed mutation studies have previously been performed on bacterial fucosidases, the only eukaryotic fucosidase so studied was the human fucosidase. Recent alignments indicate that human and Arthropoda α-l-fucosidases share at least 50% identity and the acid/base residue seems to be conserved among them suggesting a common acid/base residue in Metazoa. Here we describe the cloning and expression in Pichia pastoris of a very active α-l-fucosidase from the spider Nephilingis cruentata (NcFuc) with a Km value for pNPFuc of 0.4 mM. NcFuc hydrolyzed fucoidan, 2´fucosyllactose and also lacto-N-difucohexaose II. Mutants modified at the conserved residues D214N, E209A, E59A were expressed and characterized. The 500-fold lower kcat of D214N than the wild type was consistent with a role in catalysis, as was the 8000-fold lower kcat value of E59A. This was supported by the 57-fold increase in the kcat of E59A upon addition of azide. A complex pH/rate profile was seen for the wild-type and mutant forms of NcFuc, similar to those measured previously for the Sulfolobus fucosidase. The non-conservative catalytic structure and distinct active site organization reinforce the necessity of structural studies of new fucosidases.
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Affiliation(s)
- Natalia N Perrella
- Laboratory of Biochemistry, Instituto Butantan, Sao Paulo, Brazil.,Biotechnology Graduate Program, University of Sao Paulo, Sao Paulo, Brazil
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Adriana R Lopes
- Laboratory of Biochemistry, Instituto Butantan, Sao Paulo, Brazil
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20
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Wilson D, Daly NL. Venomics: A Mini-Review. High Throughput 2018; 7:E19. [PMID: 30041430 PMCID: PMC6164461 DOI: 10.3390/ht7030019] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/23/2018] [Accepted: 07/18/2018] [Indexed: 02/06/2023] Open
Abstract
Venomics is the integration of proteomic, genomic and transcriptomic approaches to study venoms. Advances in these approaches have enabled increasingly more comprehensive analyses of venoms to be carried out, overcoming to some extent the limitations imposed by the complexity of the venoms and the small quantities that are often available. Advances in bioinformatics and high-throughput functional assay screening approaches have also had a significant impact on venomics. A combination of all these techniques is critical for enhancing our knowledge on the complexity of venoms and their potential therapeutic and agricultural applications. Here we highlight recent advances in these fields and their impact on venom analyses.
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Affiliation(s)
- David Wilson
- Centre for Biodiscovery and Molecular, Development of Therapeutics, AITHM, James Cook University, Cairns, QLD 4878, Australia.
| | - Norelle L Daly
- Centre for Biodiscovery and Molecular, Development of Therapeutics, AITHM, James Cook University, Cairns, QLD 4878, Australia.
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21
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Perrella NN, Fuzita FJ, Moreti R, Verhaert PDEM, Lopes AR. First characterization of fucosidases in spiders. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2018; 98:e21462. [PMID: 29600526 DOI: 10.1002/arch.21462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
l-fucose is a constituent of glycoconjugates in different organisms. Fucosidases catalyze the removal of fucose residues, and have been correlated to different physiological and pathological processes, such as fertilization, cancer, fucosidosis, and digestion in molluscs and ticks. An α-l-fucosidase sequence was identified from the transcriptome and proteome from the midgut diverticula of the synanthropic spider Nephilingis cruentata. In this article, we describe the isolation of this α-l-fucosidase and the characterization of its activity using substrates and inhibitors demonstrating different specificities among fucosidases. The enzyme had a Km of 32 and 400 μM for 4-methylumbelliferyl α-l-fucopyranoside and 4-nitrophenyl α-l-fucopyranoside, respectively; and was unable to hydrolyze fucoidan. Nephilingis cruentata α-l-fucosidase was inhibited competitively by fucose and fuconojyrimycin. The fucosidase had two distinct pH optima even in the isolated form, due to oligomerization dependent on pH, as previously described to other fucosidases. Alignment and molecular homology modeling of the protein sequence with other fucosidases indicated that the active sites and catalytic residues were different, including residues involved in acid/base catalysis. Phylogenetic analysis showed, for the first time, gene-duplication events for fucosidases in Arachnida species. All these data reveal that studies on fucosidases in organisms distinct from bacteria, fungi, and humans are important.
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Affiliation(s)
- Natalia N Perrella
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, Brazil
- Biotechnology Program, University of São Paulo, São Paulo, Brazil
| | - Felipe J Fuzita
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Rodrigo Moreti
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, Brazil
- Biotechnology Program, University of São Paulo, São Paulo, Brazil
| | - Peter D E M Verhaert
- Laboratory of Analytical Biotechnology & Innovative Peptide Biology, Delft University of Technology, Delft, The Netherlands
| | - Adriana R Lopes
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, Brazil
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Zhang Y, DeLaney K, Hui L, Wang J, Sturm RM, Li L. A Multifaceted Mass Spectrometric Method to Probe Feeding Related Neuropeptide Changes in Callinectes sapidus and Carcinus maenas. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:948-960. [PMID: 29435768 PMCID: PMC5959843 DOI: 10.1007/s13361-017-1888-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 05/07/2023]
Abstract
Food intake is regulated by various neuromodulators, including numerous neuropeptides. However, it remains elusive at the molecular and cellular level as to how these important chemicals regulate internal processes and which regions of the neuronal organs are responsible for regulating the behavior. Here we report a comparative neuropeptidomic analysis of the brain and pericardial organ (PO) in response to feeding in two well-studied crustacean physiology model organisms, Callinectes sapidus and Carcinus maenas, using mass spectrometry (MS) techniques. A multifaceted MS-based approach has been developed to obtain complementary information on the expression changes of a large array of neuropeptides in the brain and PO. The method employs stable isotope labeling of brain and PO extracts for relative MS quantitation, capillary electrophoresis (CE)-MS for fractionation and high-specificity analysis, and mass spectrometric imaging (MSI) for in-situ molecular mapping of peptides. A number of neuropeptides, including RFamides, B-type allatostatins (AST-B), RYamides, and orcokinins exhibit significant changes in abundance after feeding in this investigation. Peptides from the AST-B family found in PO tissue were shown to have both altered expression and localization changes after feeding, indicating that they may be a class of vital neuropeptide regulators involved in feeding behavior. Graphical Abstract ᅟ.
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Affiliation(s)
- Yuzhuo Zhang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI, 53706-1322, USA
| | - Limei Hui
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Junhua Wang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI, 53706-1322, USA
| | - Robert M Sturm
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705-2222, USA.
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI, 53706-1322, USA.
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23
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New findings from the first transcriptome of the Bothrops moojeni snake venom gland. Toxicon 2017; 140:105-117. [DOI: 10.1016/j.toxicon.2017.10.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 11/18/2022]
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24
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Walter A, Bechsgaard J, Scavenius C, Dyrlund TS, Sanggaard KW, Enghild JJ, Bilde T. Characterisation of protein families in spider digestive fluids and their role in extra-oral digestion. BMC Genomics 2017; 18:600. [PMID: 28797246 PMCID: PMC5553785 DOI: 10.1186/s12864-017-3987-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/01/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Spiders are predaceous arthropods that are capable of subduing and consuming relatively large prey items compared to their own body size. For this purpose, spiders have evolved potent venoms to immobilise prey and digestive fluids that break down nutrients inside the prey's body by means of extra-oral digestion (EOD). Both secretions contain an array of active proteins, and an overlap of some components has been anecdotally reported, but not quantified. We systematically investigated the extent of such protein overlap. As venom injection and EOD succeed each other, we further infer functional explanations, and, by comparing two spider species belonging to different clades, assess its adaptive significance for spider EOD in general. RESULTS We describe the protein composition of the digestive fluids of the mygalomorph Acanthoscurria geniculata and the araneomorph Stegodyphus mimosarum, in comparison with previously published data on a third spider species. We found a number of similar hydrolases being highly abundant in all three species. Among them, members of the family of astacin-like metalloproteases were particularly abundant. While the importance of these proteases in spider venom and digestive fluid was previously noted, we now highlight their widespread use across different spider taxa. Finally, we found species specific differences in the protein overlap between venom and digestive fluid, with the difference being significantly greater in S. mimosarum compared to A. geniculata. CONCLUSIONS The injection of venom precedes the injection with digestive fluid, and the overlap of proteins between venom and digestive fluid suggests an early involvement in EOD. Species specific differences in the overlap may reflect differences in ecology between our two study species. The protein composition of the digestive fluid of all the three species we compared is highly similar, suggesting that the cocktail of enzymes is highly conserved and adapted to spider EOD.
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Affiliation(s)
- André Walter
- Department of Bioscience, Aarhus University, Aarhus, Denmark.
| | | | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Thomas S Dyrlund
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kristian W Sanggaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Aarhus, Denmark
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25
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017. [PMID: 28756775 DOI: 10.1186/s12915-017-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. RESULTS We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. CONCLUSIONS Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
- Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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26
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017; 15:62. [PMID: 28756775 PMCID: PMC5535294 DOI: 10.1186/s12915-017-0399-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.,Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark.,Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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