1
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Ruschig M, Nerlich J, Becker M, Meier D, Polten S, Cervantes-Luevano K, Kuhn P, Licea-Navarro AF, Hallermann S, Dübel S, Schubert M, Brown J, Hust M. Human antibodies neutralizing the alpha-latrotoxin of the European black widow. Front Immunol 2024; 15:1407398. [PMID: 38933276 PMCID: PMC11199383 DOI: 10.3389/fimmu.2024.1407398] [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: 03/26/2024] [Accepted: 04/29/2024] [Indexed: 06/28/2024] Open
Abstract
Poisoning by widow-spider (genus Latrodectus) bites occurs worldwide. The illness, termed latrodectism, can cause severe and persistent pain and can lead to muscle rigidity, respiratory complications, and cardiac problems. It is a global health challenge especially in developing countries. Equine serum-derived polyclonal anti-sera are commercially available as a medication for patients with latrodectism, but the use of sera imposes potential inherent risks related to its animal origin. The treatment may cause allergic reactions in humans (serum sickness), including anaphylactic shock. Furthermore, equine-derived antivenom is observed to have batch-to-batch variability and poor specificity, as it is always an undefined mix of antibodies. Because latrodectism can be extremely painful but is rarely fatal, the use of antivenom is controversial and only a small fraction of patients is treated. In this work, recombinant human antibodies were selected against alpha-latrotoxin of the European black widow (Latrodectus tredecimguttatus) by phage display from a naïve antibody gene library. Alpha-Latrotoxin (α-LTX) binding scFv were recloned and produced as fully human IgG. A novel alamarBlue assay for venom neutralization was developed and used to select neutralizing IgGs. The human antibodies showed in vitro neutralization efficacy both as single antibodies and antibody combinations. This was also confirmed by electrophysiological measurements of neuronal activity in cell culture. The best neutralizing antibodies showed nanomolar affinities. Antibody MRU44-4-A1 showed outstanding neutralization efficacy and affinity to L. tredecimguttatus α-LTX. Interestingly, only two of the neutralizing antibodies showed cross-neutralization of the venom of the Southern black widow (Latrodectus mactans). This was unexpected, because in the current literature the alpha-latrotoxins are described as highly conserved. The here-engineered antibodies are candidates for future development as potential therapeutics and diagnostic tools, as they for the first time would provide unlimited supply of a chemically completely defined drug of constant quality and efficacy, which is also made without the use of animals.
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Affiliation(s)
- Maximilian Ruschig
- Departments of Biotechnology and Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jana Nerlich
- Faculty of Medicine, Carl-Ludwig-Institute of Physiology, Leipzig University, Leipzig, Germany
| | - Marlies Becker
- Departments of Biotechnology and Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Doris Meier
- Departments of Biotechnology and Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Saskia Polten
- Departments of Biotechnology and Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Karla Cervantes-Luevano
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | | | - Alexei Fedorovish Licea-Navarro
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Stefan Hallermann
- Faculty of Medicine, Carl-Ludwig-Institute of Physiology, Leipzig University, Leipzig, Germany
| | - Stefan Dübel
- Departments of Biotechnology and Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maren Schubert
- Departments of Biotechnology and Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jeffrey Brown
- PETA Science Consortium International e.V., Stuttgart, Germany
| | - Michael Hust
- Departments of Biotechnology and Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
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2
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Jiang H, Wang Y, Zhang G, Jia A, Wei Z, Wang Y. Identification and Evolutionary Analysis of the Widely Distributed CAP Superfamily in Spider Venom. Toxins (Basel) 2024; 16:240. [PMID: 38922134 PMCID: PMC11209345 DOI: 10.3390/toxins16060240] [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: 04/05/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
Venom plays a crucial role in the defense and predation of venomous animals. Spiders (Araneae) are among the most successful predators and have a fascinating venom composition. Their venom mainly contains disulfide-rich peptides and large proteins. Here, we analyzed spider venom protein families, utilizing transcriptomic and genomic data, and highlighted their similarities and differences. We show that spiders have specific combinations of toxins for better predation and defense, typically comprising a core toxin expressed alongside several auxiliary toxins. Among them, the CAP superfamily is widely distributed and highly expressed in web-building Araneoidea spiders. Our analysis of evolutionary relationships revealed four subfamilies (subA-subD) of the CAP superfamily that differ in structure and potential functions. CAP proteins are composed of a conserved CAP domain and diverse C-terminal domains. CAP subC shares similar domains with the snake ion channel regulator svCRISP proteins, while CAP subD possesses a sequence similar to that of insect venom allergen 5 (Ag5). Furthermore, we show that gene duplication and selective expression lead to increased expression of CAP subD, making it a core member of the CAP superfamily. This study sheds light on the functional diversity of CAP subfamilies and their evolutionary history, which has important implications for fully understanding the composition of spider venom proteins and the core toxin components of web-building spiders.
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Affiliation(s)
- Hongcen Jiang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Yiru Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Guoqing Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Anqiang Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Zhaoyuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Yi Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
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3
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Miles LS, Waterman H, Ayoub NA, Garb JE, Haney RA, Rosenberg MS, Krabbenhoft TJ, Verrelli BC. Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider. J Hered 2024; 115:241-252. [PMID: 38567866 DOI: 10.1093/jhered/esae018] [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: 12/01/2023] [Accepted: 03/19/2024] [Indexed: 05/12/2024] Open
Abstract
Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.
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Affiliation(s)
- Lindsay S Miles
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Hannah Waterman
- Department of Biological Sciences and Research and Education in Energy, Environment, and Water Institute, University at Buffalo, Buffalo, NY, United States
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Robert A Haney
- Department of Biology, Ball State University, Muncie, IN, United States
| | - Michael S Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Trevor J Krabbenhoft
- Department of Biological Sciences and Research and Education in Energy, Environment, and Water Institute, University at Buffalo, Buffalo, NY, United States
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
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4
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Touchard A, Barassé V, Malgouyre JM, Treilhou M, Klopp C, Bonnafé E. The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles. BMC Genomics 2024; 25:84. [PMID: 38245722 PMCID: PMC10800049 DOI: 10.1186/s12864-024-10012-y] [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: 08/28/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Venoms have evolved independently over a hundred times in the animal kingdom to deter predators and/or subdue prey. Venoms are cocktails of various secreted toxins, whose origin and diversification provide an appealing system for evolutionary researchers. Previous studies of the ant venom of Tetramorium bicarinatum revealed several Myrmicitoxin (MYRTX) peptides that gathered into seven precursor families suggesting different evolutionary origins. Analysis of the T. bicarinatum genome enabling further genomic approaches was necessary to understand the processes underlying the evolution of these myrmicitoxins. RESULTS Here, we sequenced the genome of Tetramorium bicarinatum and reported the organisation of 44 venom peptide genes (vpg). Of the eleven chromosomes that make up the genome of T. bicarinatum, four carry the vpg which are organized in tandem repeats. This organisation together with the ML evolutionary analysis of vpg sequences, is consistent with evolution by local duplication of ancestral genes for each precursor family. The structure of the vpg into two or three exons is conserved after duplication events while the promoter regions are the least conserved parts of the vpg even for genes with highly identical sequences. This suggests that enhancer sequences were not involved in duplication events, but were recruited from surrounding regions. Expression level analysis revealed that most vpg are highly expressed in venom glands, although one gene or group of genes is much more highly expressed in each family. Finally, the examination of the genomic data revealed that several genes encoding transcription factors (TFs) are highly expressed in the venom glands. The search for binding sites (BS) of these TFs in the vpg promoters revealed hot spots of GATA sites in several vpg families. CONCLUSION In this pioneering investigation on ant venom genes, we provide a high-quality assembly genome and the annotation of venom peptide genes that we think can fosters further genomic research to understand the evolutionary history of ant venom biochemistry.
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Affiliation(s)
- Axel Touchard
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Valentine Barassé
- BTSB-UR 7417, Université Fédérale de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000, Albi, France
| | - Jean-Michel Malgouyre
- BTSB-UR 7417, Université Fédérale de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000, Albi, France
| | - Michel Treilhou
- BTSB-UR 7417, Université Fédérale de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000, Albi, France
| | - Christophe Klopp
- INRAE, BioinfOmics, Université Fédérale de Toulouse, GenoToul Bioinformatics Facility, Sigenae, 31326, Castanet-Tolosan, France
| | - Elsa Bonnafé
- BTSB-UR 7417, Université Fédérale de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000, Albi, France.
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5
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Fan Z, Wang LY, Xiao L, Tan B, Luo B, Ren TY, Liu N, Zhang ZS, Bai M. Lampshade web spider Ectatosticta davidi chromosome-level genome assembly provides evidence for its phylogenetic position. Commun Biol 2023; 6:748. [PMID: 37463957 PMCID: PMC10354039 DOI: 10.1038/s42003-023-05129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
The spider of Ectatosticta davidi, belonging to the lamp-shade web spider family, Hypochilidae, which is closely related to Hypochilidae and Filistatidae and recovered as sister of the rest Araneomorphs spiders. Here we show the final assembled genome of E. davidi with 2.16 Gb in 15 chromosomes. Then we confirm the evolutionary position of Hypochilidae. Moreover, we find that the GMC gene family exhibit high conservation throughout the evolution of true spiders. We also find that the MaSp genes of E. davidi may represent an early stage of MaSp and MiSp genes in other true spiders, while CrSp shares a common origin with AgSp and PySp but differ from MaSp. Altogether, this study contributes to addressing the limited availability of genomic sequences from Hypochilidae spiders, and provides a valuable resource for investigating the genomic evolution of spiders.
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Affiliation(s)
- Zheng Fan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lu-Yu Wang
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lin Xiao
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bing Tan
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bin Luo
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Tian-Yu Ren
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Ning Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Zhi-Sheng Zhang
- School of Life Sciences, Southwest University, 400700, Chongqing, China.
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, 150040, Harbin, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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6
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Krugner R, Espindola C, Justus N, Hatton RL. Web Vibrations in Intraspecific Contests of Female Black Widow Spiders, Latrodectus hesperus. ENVIRONMENTAL ENTOMOLOGY 2023; 52:169-174. [PMID: 36727725 DOI: 10.1093/ee/nvad003] [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: 08/12/2022] [Indexed: 06/18/2023]
Abstract
Female black widow spiders, Latrodectus hesperus Chamberlin and Ivie (Araneae: Theridiidae), are solitary predators of arthropods with no tolerance for intruders on the webs. In California, L. hesperus are found in urban and agricultural settings and can be a phytosanitary pest in fresh produce. Spatial separation of L. hesperus webs could be determined by seasonal population densities, with territorial competition expected under high densities in the environment. However, little is known about female-female communication behaviors in this species. In 1-hr laboratory observations, displays of female-female rivalry included production of vibrational signals in a majority (20 of 30) of trials. The number of signals produced by both females was highest during the initial 10 min of trials, with signaling rate (time interval between signals) peaking during the 40-50 min observation period. The overall ratio of signals produced by the resident female and the introduced female was about 5:1, with the number of signals produced by the resident female higher than the number of signals produced by the introduced female. Analysis of rivalry signals showed a peak in magnitude (about 0.4 m/s) ranging from 6 to 23 Hz and smaller peaks at about 29, 38, and 47 Hz. Collectively, these results demonstrate that female L. hesperus exhibit territorial rivalry and that female-female rivalry is mediated by emission of vibrational signals through the web. Understanding the mechanisms of intraspecific competition in L. hesperus is required for elucidating interspecific interactions in the environment and may lead to development of novel methods to prevent spiders from colonizing crops.
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Affiliation(s)
- Rodrigo Krugner
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648, USA
| | - Crystal Espindola
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648, USA
| | - Nathan Justus
- School of Mechanical, Industrial, and Manufacturing Engineering, Collaborative Robotics and Intelligent Systems Institute, College of Engineering, Oregon State University, 101 Covell Hall, Corvallis, OR 97331, USA
| | - Ross L Hatton
- School of Mechanical, Industrial, and Manufacturing Engineering, Collaborative Robotics and Intelligent Systems Institute, College of Engineering, Oregon State University, 101 Covell Hall, Corvallis, OR 97331, USA
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7
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Dugon MM, Lawton C, Sturgess D, Dunbar JP. Predation on a pygmy shrew,
Sorex minutus
, by the noble false widow spider,
Steatoda nobilis. Ecosphere 2023. [DOI: 10.1002/ecs2.4422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Michel M. Dugon
- Venom Systems & Proteomics Lab School of Natural Sciences, Ryan Institute, University of Galway Galway Ireland
| | - Colin Lawton
- Animal Ecology and Conservation Group School of Natural Sciences, Ryan Institute, University of Galway Galway Ireland
| | - Dawn Sturgess
- Venom Systems & Proteomics Lab School of Natural Sciences, Ryan Institute, University of Galway Galway Ireland
| | - John P. Dunbar
- Venom Systems & Proteomics Lab School of Natural Sciences, Ryan Institute, University of Galway Galway Ireland
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8
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Thill VL, Moniz HA, Teglas MB, Wasley MJ, Feldman CR. Preying dangerously: black widow spider venom resistance in sympatric lizards. ROYAL SOCIETY OPEN SCIENCE 2022; 9:221012. [PMID: 36277837 PMCID: PMC9579766 DOI: 10.1098/rsos.221012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Lizards and spiders are natural adversaries, yet little is known of adaptations that lizards might possess for dealing with the venomous defences of spider prey. In the Western USA, two lizard species (Elgaria multicarinata and Sceloporus occidentalis) are sympatric with and predate western black widow spiders (Latrodectus hesperus). The consequences of black widow spider venom (BWSV) can be severe, and are well understood for mammals but unknown for reptiles. We evaluated potential resistance to BWSV in the lizards that consume black widows, and a potentially susceptible species (Uta stansburiana) known as prey of widows. We investigated BWSV effects on whole-animal performance (sprint) and muscle tissue at two venom doses compared with control injections. Sprint speed was not significantly decreased in E. multicarinata or S. occidentalis in any treatment, while U. stansburiana suffered significant performance reductions in response to BWSV. Furthermore, E. multicarinata showed minimal tissue damage and immune response, while S. occidentalis and U. stansburiana exhibited increased muscle damage and immune system infiltration in response to BWSV. Our data suggest predator-prey relationships between lizards and spiders are complex, possibly leading to physiological and molecular adaptations that allow some lizards to tolerate or overcome the dangerous defences of their arachnid prey.
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Affiliation(s)
- Vicki L. Thill
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV 89557, USA
| | - Haley A. Moniz
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV 89557, USA
| | - Mike B. Teglas
- Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV 89557, USA
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA
| | - McKenzie J. Wasley
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- United States Fish and Wildlife Service, Klamath Falls Fish and Wildlife Office, Klamath Falls, OR 97602, USA
| | - Chris R. Feldman
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV 89557, USA
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9
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Wang Z, Zhu K, Li H, Gao L, Huang H, Ren Y, Xiang H. Chromosome-level genome assembly of the black widow spider Latrodectus elegans illuminates composition and evolution of venom and silk proteins. Gigascience 2022; 11:6593146. [PMID: 35639632 PMCID: PMC9154082 DOI: 10.1093/gigascience/giac049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The black widow spider has both extraordinarily neurotoxic venom and three-dimensional cobwebs composed of diverse types of silk. However, a high-quality reference genome for the black widow spider was still unavailable, which hindered deep understanding and application of the valuable biomass. FINDINGS We assembled the Latrodectus elegans genome, including a genome size of 1.57 Gb with contig N50 of 4.34 Mb and scaffold N50 of 114.31 Mb. Hi-C scaffolding assigned 98.08% of the genome to 14 pseudo-chromosomes, and with BUSCO, completeness analysis revealed that 98.4% of the core eukaryotic genes were completely present in this genome. Annotation of this genome identified that repetitive sequences account for 506.09 Mb (32.30%) and 20,167 protein-coding genes, and specifically, we identified 55 toxin genes and 26 spidroins and provide preliminary analysis of their composition and evolution. CONCLUSIONS We present the first chromosome-level genome assembly of a black widow spider and provide substantial toxin and spidroin gene resources. These high-qualified genomic data add valuable resources from a representative spider group and contribute to deep exploration of spider genome evolution, especially in terms of the important issues on the diversification of venom and web-weaving pattern. The sequence data are also firsthand templates for further application of the spider biomass.
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Affiliation(s)
- Zhongkai Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.,School of Ecology and Environment, Northwestern Polytechnical University, Xian, 710072, PR China
| | - Kesen Zhu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xian, 710072, PR China
| | - Lei Gao
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Huanying Huang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xian, 710072, PR China
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
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10
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von Reumont BM, Anderluh G, Antunes A, Ayvazyan N, Beis D, Caliskan F, Crnković A, Damm M, Dutertre S, Ellgaard L, Gajski G, German H, Halassy B, Hempel BF, Hucho T, Igci N, Ikonomopoulou MP, Karbat I, Klapa MI, Koludarov I, Kool J, Lüddecke T, Ben Mansour R, Vittoria Modica M, Moran Y, Nalbantsoy A, Ibáñez MEP, Panagiotopoulos A, Reuveny E, Céspedes JS, Sombke A, Surm JM, Undheim EAB, Verdes A, Zancolli G. Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research. Gigascience 2022; 11:giac048. [PMID: 35640874 PMCID: PMC9155608 DOI: 10.1093/gigascience/giac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.
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Affiliation(s)
- Bjoern M von Reumont
- Goethe University Frankfurt, Institute for Cell Biology and Neuroscience, Department for Applied Bioinformatics, 60438 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Naira Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbeli ave. 22, 0028 Yerevan, Armenia
| | - Dimitris Beis
- Developmental Biology, Centre for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 11527, Greece
| | - Figen Caliskan
- Department of Biology, Faculty of Science and Letters, Eskisehir Osmangazi University, TR-26040 Eskisehir, Turkey
| | - Ana Crnković
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Maik Damm
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Hannah German
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Trg Republike Hrvatske 14, 10000 Zagreb, Croatia
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nasit Igci
- Nevsehir Haci Bektas Veli University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 50300 Nevsehir, Turkey
| | - Maria P Ikonomopoulou
- Madrid Institute for Advanced Studies in Food, Madrid,E28049, Spain
- The University of Queensland, St Lucia, QLD 4072, Australia
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
| | - Ivan Koludarov
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Tim Lüddecke
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35392 Gießen, Germany
| | - Riadh Ben Mansour
- Department of Life Sciences, Faculty of Sciences, Gafsa University, Campus Universitaire Siidi Ahmed Zarrouk, 2112 Gafsa, Tunisia
| | - Maria Vittoria Modica
- Dept. of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Via Po 25c, I-00198 Roma, Italy
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - María Eugenia Pachón Ibáñez
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexios Panagiotopoulos
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
- Animal Biology Division, Department of Biology, University of Patras, Patras, GR-26500, Greece
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Javier Sánchez Céspedes
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Andy Sombke
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eivind A B Undheim
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Postboks 1066 Blindern 0316 Oslo, Norway
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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11
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Mason AJ, Holding ML, Rautsaw RM, Rokyta DR, Parkinson CL, Gibbs HL. Venom gene sequence diversity and expression jointly shape diet adaptation in pitvipers. Mol Biol Evol 2022; 39:6567549. [PMID: 35413123 PMCID: PMC9040050 DOI: 10.1093/molbev/msac082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the joint roles of protein sequence variation and differential expression during adaptive evolution is a fundamental, yet largely unrealized goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom-gland transcriptome dataset spanning three genera of pitvipers to identify the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey.
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Affiliation(s)
- Andrew J Mason
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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12
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Cerca J, Armstrong EE, Vizueta J, Fernández R, Dimitrov D, Petersen B, Prost S, Rozas J, Petrov D, Gillespie RG. The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders. Genome Biol Evol 2021; 13:evab262. [PMID: 34849853 PMCID: PMC8693713 DOI: 10.1093/gbe/evab262] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 01/07/2023] Open
Abstract
Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find expansions associated with the sensory perception of taste, immunity, and metabolism. In addition, we report strikingly different histories of chemosensory, venom, and silk gene families, with the first two evolving much earlier, affected by the ancestral whole genome duplication in Arachnopulmonata (∼450 Ma) and exhibiting higher numbers. Together, our findings reveal that spider genomes are highly variable and that genomic novelty may have been driven by the burst of an ancient whole genome duplication, followed by gene family and transposable element expansion.
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Affiliation(s)
- José Cerca
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ellie E Armstrong
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
- Department of Biology, Stanford University, California, USA
| | - Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
| | - Rosa Fernández
- Institute of Evolutionary Biology (CSIC—Universitat Pompeu Fabra), Barcelona, Spain
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Norway
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Stefan Prost
- Central Research Laboratories, Natural History Museum Vienna, Vienna, Austria
- University of Veterinary Medicine, Konrad Lorenz Institute of Ethology, Vienna, Austria
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Dmitri Petrov
- Department of Biology, Stanford University, California, USA
| | - Rosemary G Gillespie
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, California, USA
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13
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Lüddecke T, Herzig V, von Reumont BM, Vilcinskas A. The biology and evolution of spider venoms. Biol Rev Camb Philos Soc 2021; 97:163-178. [PMID: 34453398 DOI: 10.1111/brv.12793] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022]
Abstract
Spiders are diverse, predatory arthropods that have inhabited Earth for around 400 million years. They are well known for their complex venom systems that are used to overpower their prey. Spider venoms contain many proteins and peptides with highly specific and potent activities suitable for biomedical or agrochemical applications, but the key role of venoms as an evolutionary innovation is often overlooked, even though this has enabled spiders to emerge as one of the most successful animal lineages. In this review, we discuss these neglected biological aspects of spider venoms. We focus on the morphology of spider venom systems, their major components, biochemical and chemical plasticity, as well as ecological and evolutionary trends. We argue that the effectiveness of spider venoms is due to their unprecedented complexity, with diverse components working synergistically to increase the overall potency. The analysis of spider venoms is difficult to standardize because they are dynamic systems, fine-tuned and modified by factors such as sex, life-history stage and biological role. Finally, we summarize the mechanisms that drive spider venom evolution and highlight the need for genome-based studies to reconstruct the evolutionary history and physiological networks of spider venom compounds with more certainty.
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Affiliation(s)
- Tim Lüddecke
- Department for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Gießen, 35392, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Volker Herzig
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Björn M von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, Frankfurt am Main, 60325, Germany.,Institute for Insect Biotechnology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26-32, Gießen, 35392, Germany
| | - Andreas Vilcinskas
- Department for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Gießen, 35392, Germany.,LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, Frankfurt am Main, 60325, Germany.,Institute for Insect Biotechnology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26-32, Gießen, 35392, Germany
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14
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de Tranaltes C, Dunn J, Martin JM, Johnson JC. Siblicide in the city: the urban heat island accelerates sibling cannibalism in the black widow spider (Latrodectus hesperus). Urban Ecosyst 2021. [DOI: 10.1007/s11252-021-01148-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Fan Z, Yuan T, Liu P, Wang LY, Jin JF, Zhang F, Zhang ZS. A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. Gigascience 2021; 10:6178709. [PMID: 33739402 PMCID: PMC7976613 DOI: 10.1093/gigascience/giab016] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/25/2021] [Accepted: 02/18/2021] [Indexed: 12/11/2022] Open
Abstract
Background The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event. Results We present a chromosome‐level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi‐C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes. Conclusions The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.
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Affiliation(s)
- Zheng Fan
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing 400715, China
| | - Tao Yuan
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing 400715, China
| | - Piao Liu
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing 400715, China
| | - Lu-Yu Wang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing 400715, China
| | - Jian-Feng Jin
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Zhi-Sheng Zhang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing 400715, China
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16
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Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer. Nat Commun 2021; 12:818. [PMID: 33547293 PMCID: PMC7864903 DOI: 10.1038/s41467-021-21093-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
Venoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show that centipede venoms have recruited at least five gene families from bacterial and fungal donors, involving at least eight horizontal gene transfer events. These results establish centipedes as currently the only known animals with venoms used in predation and defence that contain multiple gene families derived from horizontal gene transfer. The results also provide the first evidence for the implication of horizontal gene transfer in the evolutionary origin of venom in an animal lineage. Three of the bacterial gene families encode virulence factors, suggesting that horizontal gene transfer can provide a fast track channel for the evolution of novelty by the exaptation of bacterial weapons into animal venoms.
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17
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Yang ZM, Yu N, Wang SJ, Korai SK, Liu ZW. Characterization of ecdysteroid biosynthesis in the pond wolf spider, Pardosa pseudoannulata. INSECT MOLECULAR BIOLOGY 2021; 30:71-80. [PMID: 33131130 DOI: 10.1111/imb.12678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/02/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
Ecdysteroids, as the key growth hormones, regulate moulting, metamorphosis and reproduction in arthropods. Ecdysteroid biosynthesis is catalysed by a series of cytochrome P450 monooxygenases (CYP450s) encoded by Halloween genes, including spook (spo), phantom (phm), disembodied (dib), shadow (sad) and shade (shd). The ecdysteroid biosynthesis in insects is clear with 20-hydroxyecdysone (20E) as the main ecdysteroid. However, the information on the major ecdysteroids in arachnids is limited. In this study, Halloween genes spo, dib, sad and shd, but not phm, were identified in the pond wolf spider, Pardosa pseudoannulata. Phylogenetic analysis grouped arachnid and insect Halloween gene products into two CYP450 clades, the CYP2 clan (spo and phm) and the mitochondrial clan (dib, sad, and shd). In P. pseudoannulata, the temporal expression profile of the four Halloween genes in concurrence with spiderling moulting with steady increase in the course of the 2nd instar followed by a rapid dropdown once moulting was completed. Spatially, the four Halloween genes were highly expressed in spiderling abdomen and in the ovaries of female adults. In parallel, ponasterone A (PA), but not 20E, was detected by LC-MS/MS analysis in P. pseudoannulata, and it was demonstrated as a functional ecdysteroid in the spider by accelerating of moulting with PA addition. The present study revealed the different ecdysteroid biosynthesis pathways in spiders and insects.
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Affiliation(s)
- Z-M Yang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - N Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - S-J Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - S K Korai
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Z-W Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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18
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Sheffer MM, Hoppe A, Krehenwinkel H, Uhl G, Kuss AW, Jensen L, Jensen C, Gillespie RG, Hoff KJ, Prost S. Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation. Gigascience 2021; 10:giaa148. [PMID: 33410470 PMCID: PMC7788392 DOI: 10.1093/gigascience/giaa148] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/17/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Argiope bruennichi, the European wasp spider, has been investigated intensively as a focal species for studies on sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies. FINDINGS We generated, de novo, a 1.67 Gb genome assembly of A. bruennichi using 21.8× Pacific Biosciences sequencing, polished with 19.8× Illumina paired-end sequencing data, and proximity ligation (Hi-C)-based scaffolding. This resulted in an N50 scaffold size of 124 Mb and an N50 contig size of 288 kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high-quality assembly. CONCLUSIONS We present the first chromosome-level genome assembly in the order Araneae. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation not only in A. bruennichi but also in arachnids overall, shedding light on questions such as the genomic architecture of traits, whole-genome duplication, and the genomic mechanisms behind silk and venom evolution.
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Affiliation(s)
- Monica M Sheffer
- Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, 17489 Greifswald, Germany
| | - Anica Hoppe
- Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489 Greifswald, Germany
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Henrik Krehenwinkel
- Department of Biogeography, University of Trier, Universitätsring 15, 54296 Trier, Germany
| | - Gabriele Uhl
- Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, 17489 Greifswald, Germany
| | - Andreas W Kuss
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Lars Jensen
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Corinna Jensen
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Rosemary G Gillespie
- Department of Environmental Science Policy and Management, University of California Berkeley, 130 Mulford Hall #3114, Berkeley, CA, 94720, USA
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17489 Greifswald, Germany
- Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorf-Str. 8, 17489 Greifswald, Germany
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Gardens of South Africa, 232 Boom St., Pretoria 0001, South Africa
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19
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Dunbar JP, Khan NA, Abberton CL, Brosnan P, Murphy J, Afoullouss S, O'Flaherty V, Dugon MM, Boyd A. Synanthropic spiders, including the global invasive noble false widow Steatoda nobilis, are reservoirs for medically important and antibiotic resistant bacteria. Sci Rep 2020; 10:20916. [PMID: 33262382 PMCID: PMC7708416 DOI: 10.1038/s41598-020-77839-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
The false widow spider Steatoda nobilis is associated with bites which develop bacterial infections that are sometimes unresponsive to antibiotics. These could be secondary infections derived from opportunistic bacteria on the skin or infections directly vectored by the spider. In this study, we investigated whether it is plausible for S. nobilis and other synanthropic European spiders to vector bacteria during a bite, by seeking to identify bacteria with pathogenic potential on the spiders. 11 genera of bacteria were identified through 16S rRNA sequencing from the body surfaces and chelicerae of S. nobilis, and two native spiders: Amaurobius similis and Eratigena atrica. Out of 22 bacterial species isolated from S. nobilis, 12 were related to human pathogenicity among which Staphylococcus epidermidis, Kluyvera intermedia, Rothia mucilaginosa and Pseudomonas putida are recognized as class 2 pathogens. The isolates varied in their antibiotic susceptibility: Pseudomonas putida, Staphylococcus capitis and Staphylococcus edaphicus showed the highest extent of resistance, to three antibiotics in total. On the other hand, all bacteria recovered from S. nobilis were susceptible to ciprofloxacin. Our study demonstrates that S. nobilis does carry opportunistic pathogenic bacteria on its body surfaces and chelicerae. Therefore, some post-bite infections could be the result of vector-borne bacterial zoonoses that may be antibiotic resistant.
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Affiliation(s)
- John P Dunbar
- Venom Systems & Proteomics Lab, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.
| | - Neyaz A Khan
- Discipline of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Cathy L Abberton
- Westway Health Ltd., Unit 120, Business Innovation Centre, National University of Ireland Galway, Galway, Ireland
| | - Pearce Brosnan
- Westway Health Ltd., Unit 120, Business Innovation Centre, National University of Ireland Galway, Galway, Ireland
| | - Jennifer Murphy
- Westway Health Ltd., Unit 120, Business Innovation Centre, National University of Ireland Galway, Galway, Ireland
| | - Sam Afoullouss
- Marine Biodiscovery, School of Chemistry, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Vincent O'Flaherty
- Discipline of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland.,Westway Health Ltd., Unit 120, Business Innovation Centre, National University of Ireland Galway, Galway, Ireland
| | - Michel M Dugon
- Venom Systems & Proteomics Lab, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Aoife Boyd
- Discipline of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
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Dunaj SJ, Bettencourt BR, Garb JE, Brucker RM. Spider phylosymbiosis: divergence of widow spider species and their tissues' microbiomes. BMC Evol Biol 2020; 20:104. [PMID: 32811423 PMCID: PMC7433143 DOI: 10.1186/s12862-020-01664-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Microbiomes can have profound impacts on host biology and evolution, but to date, remain vastly understudied in spiders despite their unique and diverse predatory adaptations. This study evaluates closely related species of spiders and their host-microbe relationships in the context of phylosymbiosis, an eco-evolutionary pattern where the microbial community profile parallels the phylogeny of closely related host species. Using 16S rRNA gene amplicon sequencing, we characterized the microbiomes of five species with known phylogenetic relationships from the family Theridiidae, including multiple closely related widow spiders (L. hesperus, L. mactans, L. geometricus, S. grossa, and P. tepidariorum). RESULTS We compared whole animal and tissue-specific microbiomes (cephalothorax, fat bodies, venom glands, silk glands, and ovary) in the five species to better understand the relationship between spiders and their microbial symbionts. This showed a strong congruence of the microbiome beta-diversity of the whole spiders, cephalothorax, venom glands, and silk glands when compared to their host phylogeny. Our results support phylosymbiosis in these species and across their specialized tissues. The ovary tissue microbial dendrograms also parallel the widow phylogeny, suggesting vertical transfer of species-specific bacterial symbionts. By cross-validating with RNA sequencing data obtained from the venom glands, silk glands and ovaries of L. hesperus, L. geometricus, S. grossa, and P. tepidariorum we confirmed that several microbial symbionts of interest are viably active in the host. CONCLUSION Together these results provide evidence that supports the importance of host-microbe interactions and the significant role microbial communities may play in the evolution and adaptation of their hosts.
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Affiliation(s)
- Sara J Dunaj
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | | | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Robert M Brucker
- The Rowland Institute of Harvard University, Cambridge, MA, USA.
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21
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Dunbar JP, Fort A, Redureau D, Sulpice R, Dugon MM, Quinton L. Venomics Approach Reveals a High Proportion of Lactrodectus-Like Toxins in the Venom of the Noble False Widow Spider Steatoda nobilis. Toxins (Basel) 2020; 12:E402. [PMID: 32570718 PMCID: PMC7354476 DOI: 10.3390/toxins12060402] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 01/26/2023] Open
Abstract
The noble false widow spider Steatoda nobilis originates from the Macaronesian archipelago and has expanded its range globally. Outside of its natural range, it may have a negative impact on native wildlife, and in temperate regions it lives in synanthropic environments where it frequently encounters humans, subsequently leading to envenomations. S. nobilis is the only medically significant spider in Ireland and the UK, and envenomations have resulted in local and systemic neurotoxic symptoms similar to true black widows (genus Latrodectus). S. nobilis is a sister group to Latrodectus which possesses the highly potent neurotoxins called α-latrotoxins that can induce neuromuscular paralysis and is responsible for human fatalities. However, and despite this close relationship, the venom composition of S. nobilis has never been investigated. In this context, a combination of transcriptomic and proteomic cutting-edge approaches has been used to deeply characterise S. nobilis venom. Mining of transcriptome data for the peptides identified by proteomics revealed 240 annotated sequences, of which 118 are related to toxins, 37 as enzymes, 43 as proteins involved in various biological functions, and 42 proteins without any identified function to date. Among the toxins, the most represented in numbers are α-latrotoxins (61), δ-latroinsectotoxins (44) and latrodectins (6), all of which were first characterised from black widow venoms. Transcriptomics alone provided a similar representation to proteomics, thus demonstrating that our approach is highly sensitive and accurate. More precisely, a relative quantification approach revealed that latrodectins are the most concentrated toxin (28%), followed by α-latrotoxins (11%), δ-latroinsectotoxins (11%) and α-latrocrustotoxins (11%). Approximately two-thirds of the venom is composed of Latrodectus-like toxins. Such toxins are highly potent towards the nervous system of vertebrates and likely responsible for the array of symptoms occurring after envenomation by black widows and false widows. Thus, caution should be taken in dismissing S. nobilis as harmless. This work paves the way towards a better understanding of the competitiveness of S. nobilis and its potential medical importance.
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Affiliation(s)
- John P. Dunbar
- Venom Systems & Proteomics Lab, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland; (J.P.D.); (M.M.D.)
| | - Antoine Fort
- Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.F.); (R.S.)
| | - Damien Redureau
- Mass Spectrometry Laboratory, MolSys RU, University of Liège, 4000 Liège, Belgium;
| | - Ronan Sulpice
- Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.F.); (R.S.)
| | - Michel M. Dugon
- Venom Systems & Proteomics Lab, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland; (J.P.D.); (M.M.D.)
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys RU, University of Liège, 4000 Liège, Belgium;
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22
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Paiva ALB, Matavel A, Silva BCS, Guerra-Duarte C, Diniz MRV. Gene sequence analysis of toxins from the spider Phoneutria nigriventer revealed an intronless feature. J Venom Anim Toxins Incl Trop Dis 2020; 26:e20190075. [PMID: 32395122 PMCID: PMC7199488 DOI: 10.1590/1678-9199-jvatitd-2019-0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/18/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Phoneutria nigriventer spider venom contains several cysteine-rich peptide toxins that act on different ion channels. Despite extensive studies on its venom and description of cDNA sequences of several of its toxin precursors, the gene structure of these toxins remains unknown. METHODS Genomic regions encoding the precursors of three previously characterized P. nigriventer toxins - PnTx1, PnTx2-5 and PnTx4(5-5) - were amplified by PCR using specific primers. PCR fragments were cloned and sequenced. Obtained sequences were compared with their corresponding cDNA sequences. RESULTS The size of PCR fragments obtained and sequences corresponding to genomic regions encoding for the toxin precursors matched their cDNA sequences. CONCLUSIONS Despite a few nucleotide substitutions in the genomic regions encoding for the toxin precursors when compared with cDNA sequences, the results of the present work indicate that P. nigriventer toxins do not contain introns in their genes sequences.
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Affiliation(s)
| | - Alessandra Matavel
- Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias
(FUNED), Belo Horizonte, MG, Brazil
| | - Bruno César Souza Silva
- Universidade Federal de Minas Gerais (UFMG), Programa Interunidades
de Pós-graduação em Bioinformática (ICB), Belo Horizonte, MG, Brazil
| | - Clara Guerra-Duarte
- Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias
(FUNED), Belo Horizonte, MG, Brazil
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23
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Cordellier M, Schneider JM, Uhl G, Posnien N. Sex differences in spiders: from phenotype to genomics. Dev Genes Evol 2020; 230:155-172. [PMID: 32052129 PMCID: PMC7127994 DOI: 10.1007/s00427-020-00657-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/31/2020] [Indexed: 01/26/2023]
Abstract
Sexual reproduction is pervasive in animals and has led to the evolution of sexual dimorphism. In most animals, males and females show marked differences in primary and secondary sexual traits. The formation of sex-specific organs and eventually sex-specific behaviors is defined during the development of an organism. Sex determination processes have been extensively studied in a few well-established model organisms. While some key molecular regulators are conserved across animals, the initiation of sex determination is highly diverse. To reveal the mechanisms underlying the development of sexual dimorphism and to identify the evolutionary forces driving the evolution of different sexes, sex determination mechanisms must thus be studied in detail in many different animal species beyond the typical model systems. In this perspective article, we argue that spiders represent an excellent group of animals in which to study sex determination mechanisms. We show that spiders are sexually dimorphic in various morphological, behavioral, and life history traits. The availability of an increasing number of genomic and transcriptomic resources and functional tools provides a great starting point to scrutinize the extensive sexual dimorphism present in spiders on a mechanistic level. We provide an overview of the current knowledge of sex determination in spiders and propose approaches to reveal the molecular and genetic underpinnings of sexual dimorphism in these exciting animals.
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Affiliation(s)
- Mathilde Cordellier
- Department of Biology, Institute of Zoology, Universität Hamburg, Martin-Luther-King Platz 3, 20146, Hamburg, Germany.
| | - Jutta M Schneider
- Department of Biology, Institute of Zoology, Universität Hamburg, Martin-Luther-King Platz 3, 20146, Hamburg, Germany.
| | - Gabriele Uhl
- Zoological Institute and Museum, Research Group General and Systematic Zoology, Universität Greifswald, Loitzer Straße 26, 17489, Greifswald, Germany.
| | - Nico Posnien
- Department of Developmental Biology, Göttingen Center for Molecular Biosciences (GZMB), University Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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24
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Ovarian Transcriptomic Analyses in the Urban Human Health Pest, the Western Black Widow Spider. Genes (Basel) 2020; 11:genes11010087. [PMID: 31940922 PMCID: PMC7017306 DOI: 10.3390/genes11010087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/06/2019] [Accepted: 01/07/2020] [Indexed: 11/23/2022] Open
Abstract
Due to their abundance and ability to invade diverse environments, many arthropods have become pests of economic and health concern, especially in urban areas. Transcriptomic analyses of arthropod ovaries have provided insight into life history variation and fecundity, yet there are few studies in spiders despite their diversity within arthropods. Here, we generated a de novo ovarian transcriptome from 10 individuals of the western black widow spider (Latrodectus hesperus), a human health pest of high abundance in urban areas, to conduct comparative ovarian transcriptomic analyses. Biological processes enriched for metabolism—specifically purine, and thiamine metabolic pathways linked to oocyte development—were significantly abundant in L. hesperus. Functional and pathway annotations revealed overlap among diverse arachnid ovarian transcriptomes for highly-conserved genes and those linked to fecundity, such as oocyte maturation in vitellogenin and vitelline membrane outer layer proteins, hormones, and hormone receptors required for ovary development, and regulation of fertility-related genes. Comparative studies across arachnids are greatly needed to understand the evolutionary similarities of the spider ovary, and here, the identification of ovarian proteins in L. hesperus provides potential for understanding how increased fecundity is linked to the success of this urban pest.
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25
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Yu N, Han C, Liu Z. In silico identification of the neuropeptidome of the pond wolf spider Pardosa pseudoannulata. Gen Comp Endocrinol 2020; 285:113271. [PMID: 31525378 DOI: 10.1016/j.ygcen.2019.113271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/27/2019] [Accepted: 09/12/2019] [Indexed: 01/09/2023]
Abstract
Neuropeptides have been successfully documented in numerous arthropod species via in silico prediction from transcriptomic and genomic data. We recently sequenced the genome and nine transcriptomes of a chelicerate species, the pond wolf spider, Pardosa pseudoannulata. Here 43 neuropeptide families encoded by 87 neuropeptide genes were identified, among which 84 genes were presented with complete open reading frames. The neuropeptide genes often had paralogs and paralogous genes showed different expression profiles in nine transcriptomes. Six crustacean hyperglycemic hormone/ion transport peptide-like (CHH/ITP) genes were predicted and CHH/ITP6 was expressed much higher than the others. Orcokinin 1 and orcokinin 2 genes were both expressed in brain at a similar level. But, interestingly, orcokinin 1 gene was ubiquitously expressed in appendages while orcokinin 2 gene was enriched in venom gland to an extreme extent. The expression profiling of neuropeptide genes offers clues for further functional investigation. Paralogous genes were also found to be clustered at scaffolds such as nine insulin-like peptide genes at three scaffolds and six pyrokinin genes at two scaffolds, indicating a result of local gene duplication. In contrast, the four C-type allatostatin family members were scattered at five scaffolds, different from their closely associated locations reported in many arthropod species including several spiders. The comprehensive inventory of P. pseudoannulata neuropeptides here expands our repository of chelicerate neuropeptides and further promotes our understanding of neuropeptide evolution and functions.
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Affiliation(s)
- Na Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Chenyang Han
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zewen Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China.
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Spider Venom: Components, Modes of Action, and Novel Strategies in Transcriptomic and Proteomic Analyses. Toxins (Basel) 2019; 11:toxins11100611. [PMID: 31652611 PMCID: PMC6832493 DOI: 10.3390/toxins11100611] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/18/2019] [Indexed: 12/19/2022] Open
Abstract
This review gives an overview on the development of research on spider venoms with a focus on structure and function of venom components and techniques of analysis. Major venom component groups are small molecular mass compounds, antimicrobial (also called cytolytic, or cationic) peptides (only in some spider families), cysteine-rich (neurotoxic) peptides, and enzymes and proteins. Cysteine-rich peptides are reviewed with respect to various structural motifs, their targets (ion channels, membrane receptors), nomenclature, and molecular binding. We further describe the latest findings concerning the maturation of antimicrobial, and cysteine-rich peptides that are in most known cases expressed as propeptide-containing precursors. Today, venom research, increasingly employs transcriptomic and mass spectrometric techniques. Pros and cons of venom gland transcriptome analysis with Sanger, 454, and Illumina sequencing are discussed and an overview on so far published transcriptome studies is given. In this respect, we also discuss the only recently described cross contamination arising from multiplexing in Illumina sequencing and its possible impacts on venom studies. High throughput mass spectrometric analysis of venom proteomes (bottom-up, top-down) are reviewed.
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27
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Drukewitz SH, von Reumont BM. The Significance of Comparative Genomics in Modern Evolutionary Venomics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Haney RA, Matte T, Forsyth FS, Garb JE. Alternative Transcription at Venom Genes and Its Role as a Complementary Mechanism for the Generation of Venom Complexity in the Common House Spider. Front Ecol Evol 2019; 7. [PMID: 31431897 PMCID: PMC6700725 DOI: 10.3389/fevo.2019.00085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The complex composition of venom, a proteinaceous secretion used by
diverse animal groups for predation or defense, is typically viewed as being
driven by gene duplication in conjunction with positive selection, leading to
large families of diversified toxins with selective venom gland expression. Yet,
the production of alternative transcripts at venom genes is often overlooked as
another potentially important process that could contribute proteins to venom,
and requires comprehensive datasets integrating genome and transcriptome
sequences together with proteomic characterization of venom to be fully
documented. In the common house spider, Parasteatoda
tepidariorum, we used RNA sequencing of four tissue types in
conjunction with the sequenced genome to provide a comprehensive transcriptome
annotation. We also used mass spectrometry to identify a minimum of 99 distinct
proteins in P tepidariorum venom, including at least 33
latrotoxins, pore-forming neurotoxins shared with the confamilial black widow.
We found that venom proteins are much more likely to come from multiple
transcript genes, whose transcripts produced distinct protein sequences. The
presence of multiple distinct proteins in venom from transcripts at individual
genes was confirmed for eight loci by mass spectrometry, and is possible at 21
others. Alternative transcripts from the same gene, whether encoding or not
encoding a protein found in venom, showed a range of expression patterns, but
were not necessarily restricted to the venom gland. However, approximately half
of venom protein encoding transcripts were found among the 1,318 transcripts
with strongly venom gland biased expression. Our findings revealed an important
role for alternative transcription in generating venom protein complexity and
expanded the traditional model of venom evolution.
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Affiliation(s)
- Robert A Haney
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Taylor Matte
- Center for Regenerative Medicine, Boston University, Medical, Boston, MA, United States
| | - FitzAnthony S Forsyth
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
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29
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Dunbar JP, Sulpice R, Dugon MM. The kiss of (cell) death: can venom-induced immune response contribute to dermal necrosis following arthropod envenomations? Clin Toxicol (Phila) 2019; 57:677-685. [PMID: 30806093 DOI: 10.1080/15563650.2019.1578367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Introduction: Snakes, insects, arachnids and myriapods have been linked to necrosis following envenomation. However, the pathways involved in arthropod venom-induced necrosis remain a highly controversial topic among toxinologists, clinicians and the public. On the one hand, clinicians report on alleged envenomations based on symptoms and the victims' information. On the other hand, toxinologists and zoologists argue that symptoms are incompatible with the known venom activity of target species. This review draws from the literature on arthropod envenomations, snakebite, and inflammatory processes to suggest that envenomation by a range of organisms might trigger an intense inflammatory cascade that ultimately lead to necrosis. If confirmed, these processes would have important implications for the treatment of venom-induced necrosis. Objectives: To describe two inflammatory pathways of regulated necrosis, tumour necrosis factor (necroptosis) and Neutrophil Extracellular Traps (NETosis); to discuss existing knowledge about snake venom and arachnid-induced necrosis demonstrating the involvement of tumour necrosis factor and neutrophils in the development of tissue necrosis following envenomation and to contribute to the understanding of venom-induced necrosis by arthropods and provide clinicians with an insight into little known inflammatory processes which may occur post envenomation. Methods: ISI Web of Science databases were searched using the terms "spider bite necrosis", "arthropod envenomation necrosis", "venom necrosis", "venom immune response", "loxoscelism", "arachnidism", "necroptosis venom", "necroptosis dermatitis", "tumour necrosis factor TNF venom", "scorpionism", "scolopendrism", "centipede necrosis", "NETosis venom", "NETosis necrosis". Searches produced 1737 non-duplicate citations of which 74 were considered relevant to this manuscript. Non-peer-reviewed sources or absence of voucher material identifying the organism were excluded. What is necrosis? Necrosis is the breakdown of cell membrane integrity followed by inflowing extracellular fluid, organelle swelling and the release of proteolytic enzymes into the cytosol. Necrosis was historically considered an unregulated process; however, recent studies demonstrate that necrosis can also be a programmed event resulting from a controlled immune response (necroptosis). Tumour necrosis factor and the necroptosis pathway: Tumour necrosis factor is a pro-inflammatory cytokine involved in regulating immune response, inflammation and cell death/survival. The pro-inflammatory cytokine TNF-α participates in the development of necrosis after envenomation by vipers. Treatment with TNF-α-antibodies may significantly reduce the manifestation of necrosis. Neutrophil Extracellular Traps and the NETosis pathway: The process by which neutrophils discharge a mesh of DNA strands in the extracellular matrix to entangle ("trap") pathogens, preventing them from disseminating. Neutrophil Extracellular Traps have been recently described as important in venom-induced necrosis. Trapped venom accumulates at the bite site, resulting in significant localized necrosis. Arthropod venom driving necrosis: Insects, myriapods and arachnids can induce necrosis following envenomation. So far, the processes involved have only been investigated in two arachnids: Loxosceles spp. (recluse spiders) and Hemiscorpius lepturus (scorpion). Loxosceles venom contains phospholipases D which hydrolyse sphingomyelin, resulting in lysis of muscle fibers. Subsequently liberated ceramides act as intermediaries that regulate TNF-α and recruit neutrophils. Experiments show that immune-deficient mice injected with Loxosceles venom experience less venom-induced inflammatory response and survive longer than control mice. Necrosis following Hemiscorpius lepturus stings correlates with elevated concentrations of TNF-α. These observations suggest that necrosis may be indirectly triggered or worsened by pathways of regulated necrosis in addition to necrotic venom compounds. Conclusions: Envenomation often induce an intense inflammatory cascade, which under certain circumstances may produce necrotic lesions independently from direct venom activity. This could explain the inconsistent and circumstantial occurrence of necrosis following envenomation by a range of organisms. Future research should focus on identifying pathways to regulated necrosis following envenomation and determining more efficient ways to manage inflammation. We suggest that clinicians should consider the victim's immune response as an integral part of the envenomation syndrome.
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Affiliation(s)
- John P Dunbar
- a Venom Systems and Proteomics Lab, School of Natural Sciences , Ryan Institute, National University of Ireland Galway , Galway , Ireland
| | - Ronan Sulpice
- b Plant Systems Biology Laboratory , Plant AgriBiosciences Research Centre, School of Natural Science, Ryan Institute, National University of Ireland Galway , Galway , Ireland
| | - Michel M Dugon
- a Venom Systems and Proteomics Lab, School of Natural Sciences , Ryan Institute, National University of Ireland Galway , Galway , Ireland
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30
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Arthropod venoms: Biochemistry, ecology and evolution. Toxicon 2018; 158:84-103. [PMID: 30529476 DOI: 10.1016/j.toxicon.2018.11.433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.
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Vizueta J, Rozas J, Sánchez-Gracia A. Comparative Genomics Reveals Thousands of Novel Chemosensory Genes and Massive Changes in Chemoreceptor Repertories across Chelicerates. Genome Biol Evol 2018; 10:1221-1236. [PMID: 29788250 PMCID: PMC5952958 DOI: 10.1093/gbe/evy081] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 12/15/2022] Open
Abstract
Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability of a number of chelicerate genomes constitutes a great opportunity to better characterize gene families involved in this important function in a lineage that emerged and colonized land independently of insects. At the same time, that offers new opportunities and challenges for the study of this interesting animal branch in many translational research areas. Here, we have performed a comprehensive comparative genomics study that explicitly considers the high fragmentation of available draft genomes and that for the first time included complete genome data that cover most of the chelicerate diversity. Our exhaustive searches exposed thousands of previously uncharacterized chemosensory sequences, most of them encoding members of the gustatory and ionotropic receptor families. The phylogenetic and gene turnover analyses of these sequences indicated that the whole-genome duplication events proposed for this subphylum would not explain the differences in the number of chemoreceptors observed across species. A constant and prolonged gene birth and death process, altered by episodic bursts of gene duplication yielding lineage-specific expansions, has contributed significantly to the extant chemosensory diversity in this group of animals. This study also provides valuable insights into the origin and functional diversification of other relevant chemosensory gene families different from receptors, such as odorant-binding proteins and other related molecules.
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Affiliation(s)
- Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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32
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Guiding recombinant antivenom development by omics technologies. N Biotechnol 2018; 45:19-27. [DOI: 10.1016/j.nbt.2017.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/16/2017] [Indexed: 11/23/2022]
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von Reumont BM. Studying Smaller and Neglected Organisms in Modern Evolutionary Venomics Implementing RNASeq (Transcriptomics)-A Critical Guide. Toxins (Basel) 2018; 10:toxins10070292. [PMID: 30012955 PMCID: PMC6070909 DOI: 10.3390/toxins10070292] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/06/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022] Open
Abstract
Venoms are evolutionary key adaptations that species employ for defense, predation or competition. However, the processes and forces that drive the evolution of venoms and their toxin components remain in many aspects understudied. In particular, the venoms of many smaller, neglected (mostly invertebrate) organisms are not characterized in detail, especially with modern methods. For the majority of these taxa, even their biology is only vaguely known. Modern evolutionary venomics addresses the question of how venoms evolve by applying a plethora of -omics methods. These recently became so sensitive and enhanced that smaller, neglected organisms are now more easily accessible to comparatively study their venoms. More knowledge about these taxa is essential to better understand venom evolution in general. The methodological core pillars of integrative evolutionary venomics are genomics, transcriptomics and proteomics, which are complemented by functional morphology and the field of protein synthesis and activity tests. This manuscript focuses on transcriptomics (or RNASeq) as one toolbox to describe venom evolution in smaller, neglected taxa. It provides a hands-on guide that discusses a generalized RNASeq workflow, which can be adapted, accordingly, to respective projects. For neglected and small taxa, generalized recommendations are difficult to give and conclusions need to be made individually from case to case. In the context of evolutionary venomics, this overview highlights critical points, but also promises of RNASeq analyses. Methodologically, these concern the impact of read processing, possible improvements by perfoming multiple and merged assemblies, and adequate quantification of expressed transcripts. Readers are guided to reappraise their hypotheses on venom evolution in smaller organisms and how robustly these are testable with the current transcriptomics toolbox. The complementary approach that combines particular proteomics but also genomics with transcriptomics is discussed as well. As recently shown, comparative proteomics is, for example, most important in preventing false positive identifications of possible toxin transcripts. Finally, future directions in transcriptomics, such as applying 3rd generation sequencing strategies to overcome difficulties by short read assemblies, are briefly addressed.
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Affiliation(s)
- Björn Marcus von Reumont
- Justus Liebig University of Giessen, Institute for Insect Biotechnology, Heinrich Buff Ring 58, 35392 Giessen, Germany.
- Natural History Museum, Department of Life Sciences, Cromwell Rd, London SW75BD, UK.
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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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Garb JE, Sharma PP, Ayoub NA. Recent progress and prospects for advancing arachnid genomics. CURRENT OPINION IN INSECT SCIENCE 2018; 25:51-57. [PMID: 29602362 PMCID: PMC6658092 DOI: 10.1016/j.cois.2017.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/10/2017] [Indexed: 06/08/2023]
Abstract
Arachnids exhibit tremendous species richness and adaptations of biomedical, industrial, and agricultural importance. Yet genomic resources for arachnids are limited, with the first few spider and scorpion genomes becoming accessible in the last four years. We review key insights from these genome projects, and recommend additional genomes for sequencing, emphasizing taxa of greatest value to the scientific community. We suggest greater sampling of spiders whose genomes are understudied but hold important protein recipes for silk and venom production. We further recommend arachnid genomes to address significant evolutionary topics, including the phenotypic impact of genome duplications. A barrier to high-quality arachnid genomes are assemblies based solely on short-read data, which may be overcome by long-range sequencing and other emerging methods.
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Affiliation(s)
- Jessica E Garb
- Department of Biological Sciences, 198 Riverside Street, Olsen Hall 414, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Prashant P Sharma
- Department of Integrative Biology, 352 Birge Hall, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, USA
| | - Nadia A Ayoub
- Department of Biology, 204 West Washington Street, Howe Hall, Washington and Lee University, Lexington, VA 24450, USA
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Li R, Yan Z, Wang J, Song Q, Wang Z. De novo characterization of venom apparatus transcriptome of Pardosa pseudoannulata and analysis of its gene expression in response to Bt protein. BMC Biotechnol 2017; 17:73. [PMID: 29115956 PMCID: PMC5678584 DOI: 10.1186/s12896-017-0392-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/30/2017] [Indexed: 12/20/2022] Open
Abstract
Background Pardosa pseudoannulata is a prevailing spider species, and has been regarded as an important bio-control agent of insect pests in farmland of China. However, the available genomic and transcriptomic databases of P. pseudoannulata and their venom are limited, which severely hampers functional genomic analysis of P. pseudoannulata. Recently high-throughput sequencing technology has been proved to be an efficient tool for profiling the transcriptome of relevant non-target organisms exposed to Bacillus thuringiensis (Bt) protein through food webs. Results In this study, the transcriptome of the venom apparatus was analyzed. A total of 113,358 non-redundant unigenes were yielded, among which 34,041 unigenes with complete or various length encoding regions were assigned biological function annotations and annotated with gene ontology and karyotic orthologous group terms. In addition, 3726 unigenes involved in response to stimulus and 720 unigenes associated with immune-response pathways were identified. Furthermore, we investigated transcriptomic changes in the venom apparatus using tag-based DGE technique. A total of 1724 differentially expressed genes (DEGs) were detected, while 75 and 372 DEGs were functionally annotated with KEGG pathways and GO terms, respectively. qPCR analyses were performed to verify the DEGs directly or indirectly related to immune and stress responses, including genes encoding heat shock protein, toll-like receptor, GST and NADH dehydrogenase. Conclusion This is the first study conducted to specifically investigate the venom apparatus of P. pseudoannulata in response to Bt protein exposure through tritrophic chain. A substantial fraction of transcript sequences was generated by high-throughput sequencing of the venom apparatus of P. pseudoannulata. Then a comparative transcriptome analysis showing a large number of candidate genes involved in immune response were identified by the tag-based DGE technology. This transcriptome dataset will provide a comprehensive sequence resource for furture molecular genetic research of the venom apparatus of P. pseudoannulata. Electronic supplementary material The online version of this article (10.1186/s12896-017-0392-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong Li
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China.,Department of Biosciences, Hunan University of Arts and Science, Changde, 415000, China
| | - Zhenzhen Yan
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China
| | - Juan Wang
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Zhi Wang
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China.
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