Hostname: page-component-7c8c6479df-8mjnm Total loading time: 0 Render date: 2024-03-29T04:44:35.270Z Has data issue: false hasContentIssue false

De novo assembly and characterisation of the transcriptome of the Beringian pseudoscorpion

Published online by Cambridge University Press:  24 February 2021

Jacqueline E. Lebenzon*
Affiliation:
Department of Biology, University of Western Ontario, 1151 Richmond Street N, London, Ontario, N6A 3K7, Canada
Jantina Toxopeus
Affiliation:
Department of Biology, University of Western Ontario, 1151 Richmond Street N, London, Ontario, N6A 3K7, Canada
Susan E. Anthony
Affiliation:
Department of Biology, University of Western Ontario, 1151 Richmond Street N, London, Ontario, N6A 3K7, Canada
Brent J. Sinclair
Affiliation:
Department of Biology, University of Western Ontario, 1151 Richmond Street N, London, Ontario, N6A 3K7, Canada
*
*Corresponding author. Email: jlebenzo@uwo.ca

Abstract

Pseudoscorpions are microarthropods that are distributed from the equator to beyond the Arctic circle. Wyochernes asiaticus (Arachnida: Pseudoscorpiones: Chernetidae) is the northernmost species of pseudoscorpion and is broadly distributed in Beringia, an Arctic and sub-Arctic region that remained unglaciated during the last glacial maximum. Wyochernes asiaticus is anoxia tolerant and has moderate cold tolerance, but nothing is known about the molecular basis of their survival in Canadian polar environments. We de novo assembled and characterised the transcriptome of W. asiaticus collected from the Yukon Territory in northwestern Canada. We assembled an approximately 62.6-million base-pair transcriptome with a mean contig length of 1277, which was 76% complete, according to a benchmark universal single copy orthologue (BUSCO) analysis. We identified 1100 transcripts encoding proteins associated with stress tolerance in these pseudoscorpions, including heat shock proteins, antioxidants, ubiquitination and proteosomal proteins, and sirtuins. We also identified transcripts encoding putative venom proteins. We highlight eight transcripts with high sequence similarity to sequences of venom proteins (ctenitoxins and agatoxins) described from other pseudoscorpions. Our study yields the first transcriptome of a Beringian arthropod, providing important sequence information that will allow future investigation of how W. asiaticus survives in Canadian polar environments.

Type
Research Papers
Copyright
© The Author(s), 2021. Published by Cambridge University Press on behalf of the Entomological Society of Canada

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

Present address: Biology Department, St. Francis Xavier University, 2321 Notre Dame Avenue, Antigonish, Nova Scotia, B2G 2W5, Canada.

Subject editor: Amanda Roe

References

Anthony, S.E., Buddle, C.M., and Sinclair, B.J. 2016. Thermal biology and immersion tolerance of the Beringian pseudoscorpion Wyochernes asiaticus . Polar Biology, 39: 13511355.CrossRefGoogle Scholar
Arnér, E.S. and Holmgren, A. 2000. Physiological functions of thioredoxin and thioredoxin reductase. European Journal of Biochemistry, 267: 61026109.CrossRefGoogle ScholarPubMed
Basha, E., O’Neill, H., and Vierling, E. 2012. Small heat shock proteins and α-crystallins: dynamic proteins with flexible functions. Trends in Biochemistry Science, 37: 106117.CrossRefGoogle ScholarPubMed
Becker, J. and Craig, E.A. 1994. Heat-shock proteins as molecular chaperones. European Journal of Biochemistry, 219: 1123.CrossRefGoogle ScholarPubMed
Benavides, L.R., Cosgrove, J.G., Harvey, M.S., and Giribet, G. 2019. Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones tree of life. Molecular Phylogenetics and Evolution, 139: 106509.CrossRefGoogle ScholarPubMed
Benoit, J.B., Lopez-Martinez, G., Phillips, Z.P., Patrick, K.R., and Denlinger, D.L. 2010. Heat shock proteins contribute to mosquito dehydration tolerance. Journal of Insect Physiology, 56: 151156.CrossRefGoogle ScholarPubMed
Block, W. and Convey, P. 1995. The biology, life cycle and ecophysiology of the Antarctic mite Alaskozetes antarcticus . Journal of Zoology, 236: 431449.CrossRefGoogle Scholar
Bowden, J. and Buddle, C. 2012. Life history of tundra-dwelling wolf spiders (Araneae: Lycosidae) from the Yukon Territory, Canada. Canadian Journal of Zoology, 90: 714721.CrossRefGoogle Scholar
Buddle, C.M. 2015. Life history and distribution of the Arctic pseudoscorpion, Wyochernes asiaticus (Chernetidae). Canadian Field Naturalist, 129: 134138.CrossRefGoogle Scholar
Cabezas-Cruz, A. and Valdés, J.J. 2014. Are ticks venomous animals? Frontiers in Zoology, 11: 47.CrossRefGoogle ScholarPubMed
Chang, G. and Kam, P. 1999. The physiological and pharmacological roles of cytochrome P450 isoenzymes. Anaesthesia, 54: 4250.CrossRefGoogle ScholarPubMed
Clark, M.S., Thorne, M.A., Purać, J., Burns, G., Hillyard, G., Popović, Ž.D., et al. 2009. Surviving the cold: molecular analyses of insect cryoprotective dehydration in the Arctic springtail Megaphorura arctica (Tullberg). BMC Genomics, 10: 328.CrossRefGoogle Scholar
Coulson, S.J. 2007. Terrestrial and freshwater invertebrate fauna of the High Arctic archipelago of Svalbard. Zootaxa, 1448: 4168.CrossRefGoogle Scholar
Dos Santos, W.F. and Coutinho-Netto, J. 2006. Effects of the Paratemnus elongatus pseudoscorpion venom in the uptake and binding of the L-glutamate and GABA from rat cerebral cortex. Journal of Biochemical and Molecular Toxicology, 20: 2734.CrossRefGoogle Scholar
Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32: 17921797.CrossRefGoogle ScholarPubMed
Emerich, B.L., Ferreira, R.C.M., Cordeiro, M.N., Borges, M.H., Pimenta, A.M.C., Figueiredo, S.G., et al. 2016. Ctenitoxin-PN1a, a peptide Phoneutria nigriventer spider venom, showed antinociceptive effect involving opioid and cannabinoid systems in rats. Toxins, 8: 106.CrossRefGoogle ScholarPubMed
Escoubas, P., De Weille, J.R., Lecoq, A., Diochot, S., Waldmann, R., Champigny, G., et al. 2000. Isolation of a tarantula toxin specific for a class of proton-gated Na+ channels. Journal of Biological Chemistry, 275: 2511625121.CrossRefGoogle ScholarPubMed
Gibson, A.K., Smith, Z., Fuqua, C., Clay, K., and Colbourne, J.K. 2013. Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum . BMC Genomics, 14: 135.CrossRefGoogle ScholarPubMed
Goldberg, A.L. 2003. Protein degradation and protection against misfolded or damaged proteins. Nature, 426: 895.CrossRefGoogle ScholarPubMed
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., et al. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology, 29: 644652.CrossRefGoogle ScholarPubMed
Grbić, M., Van Leeuwen, T., Clark, R.M., Rombauts, S., Rouzé, P., Grbić, V., et al. 2011. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature, 479: 487492.CrossRefGoogle ScholarPubMed
Grishin, E. 1999. Polypeptide neurotoxins from spider venoms. European Journal of Biochemistry, 264: 276280.CrossRefGoogle ScholarPubMed
Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M.B., Blood, P.D., Bowden, J., et al. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8: 14941512.CrossRefGoogle ScholarPubMed
Harvey, M.S. 2007. The smaller arachnid orders: diversity, descriptions and distributions from Linnaeus to the present (1758 to 2007). Zootaxa, 1668: 363380.CrossRefGoogle Scholar
Hopkins, D.M. 1982. Aspects of the paleogeography of Beringia during the late Pleistocene. In Paleoecology of Beringia. Edited by D.M. Hopkins, J.V. Matthews, and C.E. Schweger. Academic Press, Elsevier, Amsterdam, The Netherlands. Pp. 328.Google Scholar
Hughes, G.B. 2017. Taxonomy, systematics, and venom components of Neobisiid Pseudoscorpions (Pseudoscorpiones: Neobisiidae) [online]. PhD thesis. The University of Arizona, Tucson, Arizona, United States of America. Available from https://repository.arizona.edu/handle/10150/625632 [accessed 1 December 2020].Google Scholar
Huson, D.H., Auch, A.F., Qi, J., and Schuster, S.C. 2007. MEGAN analysis of metagenomic data, 17: 377386.Google ScholarPubMed
Jakob, U., Gaestel, M., Engel, K., and Buchner, J. 1993. Small heat shock proteins are molecular chaperones. Journal of Biological Chemistry, 268: 15171520.CrossRefGoogle ScholarPubMed
Joanisse, D.R. and Storey, K.B. 1998. Oxidative stress and antioxidants in stress and recovery of cold-hardy insects. Insect Biochemistry and Molecular Biology, 28: 2330.CrossRefGoogle Scholar
Joplin, K.H., Yocum, G.D., and Denlinger, D.L. 1990. Cold shock elicits expression of heat shock proteins in the flesh fly, Sarcophaga crassipalpis . Journal of Insect Physiology, 36: 825834.CrossRefGoogle Scholar
Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences, 8: 275282.Google ScholarPubMed
Kaiser, P. and Huang, L. 2005. Global approaches to understanding ubiquitination. Genome Biology, 6: 233.CrossRefGoogle ScholarPubMed
Kelley, J.L., Peyton, J.T., Fiston-Lavier, A.S., Teets, N.M., Yee, M.C., Johnston, J.S., et al. 2014. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature Communications, 5: 4611.CrossRefGoogle Scholar
King, G.F. and Hardy, M.C. 2013. Spider-venom peptides: structure, pharmacology, and potential for control of insect pests. Annual Reviews of Entomology, 58: 475496.CrossRefGoogle ScholarPubMed
Krämer, J., Pohl, H., and Predel, R. 2019. Venom collection and analysis in the pseudoscorpion Chelifer cancroides (Pseudoscorpiones: Cheliferidae). Toxicon, 162: 1523.CrossRefGoogle Scholar
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35: 15471549.CrossRefGoogle ScholarPubMed
Lalouette, L., Williams, C., Hervant, F., Sinclair, B.J., and Renault, D. 2011. Metabolic rate and oxidative stress in insects exposed to low-temperature thermal fluctuations. Comparative Biochemistry and Physiology A, 158: 229234.CrossRefGoogle ScholarPubMed
Li, R., Yan, Z., Wang, J., Song, Q., and Wang, Z. 2017. De novo characterization of venom apparatus transcriptome of Pardosa pseudoannulata and analysis of its gene expression in response to Bt protein. BMC Biotechnology, 17: 73.CrossRefGoogle ScholarPubMed
Lundy, P.M. and Frew, R. 1994. Effect of omega-agatoxin-IVA on autonomic neurotransmission. European Journal of Pharmacology, 261: 7984.CrossRefGoogle ScholarPubMed
Martin, M. 2011. Cutadapt removes adaptor sequences from high-throughput sequencing reads. EMBnet. Journal, 1: 1012.CrossRefGoogle Scholar
Meibers, H.E., Finch, G., Gregg, R.T., Glenn, S., Assani, K.D., Jennings, E.C., et al. 2019. Sex-and developmental-specific transcriptomic analyses of the Antarctic mite, Alaskozetes antarcticus, reveal transcriptional shifts underlying oribatid mite reproduction. Polar Biology, 42: 357370.CrossRefGoogle Scholar
Murienne, J., Harvey, M.S., and Giribet, G. 2008. First molecular phylogeny of the major clades of Pseudoscorpiones (Arthropoda: Chelicerata). Molecular Phylogenetics and Evolution, 49: 170184.CrossRefGoogle Scholar
Nogueiras, R., Habegger, K.M., Chaudhary, N., Finan, B., Banks, A.S., Dietrich, M.O., et al. 2012. Sirtuin 1 and sirtuin 3: physiological modulators of metabolism. Physiological Reviews, 92: 14791514.CrossRefGoogle Scholar
Pickering, A.M. and Davies, K.J. 2012. Degradation of damaged proteins: the main function of the 20S proteasome. Progress in Molecular Biology and Translational Science, 109: 227248.CrossRefGoogle ScholarPubMed
Posnien, N., Zeng, V., Schwager, E.E., Pechmann, M., Hilbrant, M., Keefe, J.D., et al. 2014. A comprehensive reference transcriptome resource for the common house spider Parasteatoda tepidariorum . PLOS One, 9: e104885. https://doi.org/10.1371/journal.pone.0104885.CrossRefGoogle ScholarPubMed
Purać, J., Burns, G., Thorne, M.A.S., Grubor-Lajšić, G., Worland, M.R., and Clark, M.S. 2008. Cold hardening processes in the Antarctic springtail, Cryptopygus antarcticus: clues from a microarray. Journal of Insect Physiology, 54: 13561362.CrossRefGoogle ScholarPubMed
Quintero-Hernández, V., Ortiz, E., Rendón-Anaya, M., Schwartz, E., Becerril, B., Corzo, G., and Possani, L. 2011. Scorpion and spider venom peptides: gene cloning and peptide expression. Toxicon, 58: 644663.CrossRefGoogle ScholarPubMed
Rinehart, J.P., Hayward, S.A., Elnitsky, M.A., Sandro, L.H., Lee, R.E., and Denlinger, D.L. 2006. Continuous up-regulation of heat shock proteins in larvae, but not adults, of a polar insect. Proceedings of the National Academy of Sciences, 103: 1422314227.CrossRefGoogle Scholar
Rosendale, A.J., Romick-Rosendale, L.E., Watanabe, M., Dunlevy, M.E., and Benoit, J.B. 2016. Mechanistic underpinnings of dehydration stress in the American dog tick revealed through RNA-Seq and metabolomics. Journal of Experimental Biology, 219: 18081819.CrossRefGoogle ScholarPubMed
Sang, W., Ma, W.H., Qiu, L., Zhu, Z.H., and Lei, C.L. 2012. The involvement of heat shock protein and cytochrome P450 genes in response to UV-A exposure in the beetle Tribolium castaneum . Journal of Insect Physiology, 58: 830836.CrossRefGoogle ScholarPubMed
Santibáñez-López, C., Ontano, A., Harvey, M., and Sharma, P. 2018. Transcriptomic analysis of pseudoscorpion venom reveals a unique cocktail dominated by enzymes and protease inhibitors. Toxins, 10: 207.CrossRefGoogle ScholarPubMed
Semenza, G.L. 2007. Hypoxia-inducible factor 1 (HIF-1) pathway. Science Signalling, 407: cm8. http://doi.org.10.1126/stke.4072007cm8.Google Scholar
Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., and Zdobnov, E.M. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31: 32103212.CrossRefGoogle ScholarPubMed
Sorger, P.K. 1991. Heat shock factor and the heat shock response. Cell, 65: 363366.CrossRefGoogle ScholarPubMed
Stanton-Geddes, J., Nguyen, A., Chick, L., Vincent, J., Vangala, M., Dunn, R.R., et al. 2016. Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species. BMC Genomics, 17: 171.CrossRefGoogle ScholarPubMed
Teets, N.M. and Denlinger, D.L. 2013. Autophagy in Antarctica: combating dehydration stress in the world’s southernmost insect. Autophagy, 9: 629631.CrossRefGoogle ScholarPubMed
Teets, N.M., Peyton, J.T., Ragland, G.J., Colinet, H., Renault, D., Hahn, D.A., and Denlinger, D.L. 2012. Combined transcriptomic and metabolomic approach uncovers molecular mechanisms of cold tolerance in a temperate flesh fly. Physiological Genomics, 44: 764777.CrossRefGoogle Scholar
Torson, A.S., Yocum, G.D., Rinehart, J.P., Nash, S.A., and Bowsher, J.H. 2019. Fluctuating thermal regimes prevent chill injury but do not change patterns of oxidative stress in the alfalfa leafcutting bee, Megachile rotundata . Journal of Insect Physiology, 118: 103935.CrossRefGoogle Scholar
Toxopeus, J., Des Marteaux, L.E., and Sinclair, B.J. 2019. How crickets become freeze tolerant: the transcriptomic underpinnings of acclimation in Gryllus veletis . Comparative Biochemistry and Physiology, Part D: Genomics and Proteomics, 29: 5566.Google ScholarPubMed
Verdin, E., Hirschey, M.D., Finley, L.W., and Haigis, M.C. 2010. Sirtuin regulation of mitochondria: energy production, apoptosis, and signaling. Trends in Biochemical Sciences, 35: 669675.CrossRefGoogle ScholarPubMed
Walker, D.W. and Benzer, S. 2004. Mitochondrial “swirls” induced by oxygen stress and in the Drosophila mutant hyperswirl. Proceedings of the National Academy of Sciences, 101: 1029010295.CrossRefGoogle ScholarPubMed
Wu, Y.T., Wu, S.B., and Wei, Y.H. 2014. Roles of sirtuins in the regulation of antioxidant defense and bioenergetic function of mitochondria under oxidative stress. Free Radical Research, 48: 10701084.CrossRefGoogle ScholarPubMed
Zhu, M., Zhang, W., Liu, F., Chen, X., Li, H., and Xu, B. 2016. Characterization of an Apis cerana cerana cytochrome P450 gene (AccCYP336A1) and its roles in oxidative stresses responses. Gene, 584: 120128.CrossRefGoogle ScholarPubMed
Supplementary material: PDF

Lebenzon et al. supplementary material

Lebenzon et al. supplementary material 1

Download Lebenzon et al. supplementary material(PDF)
PDF 450.3 KB
Supplementary material: File

Lebenzon et al. supplementary material

Lebenzon et al. supplementary material 2

Download Lebenzon et al. supplementary material(File)
File 7.4 MB