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Posnien N, Hunnekuhl VS, Bucher G. Gene expression mapping of the neuroectoderm across phyla - conservation and divergence of early brain anlagen between insects and vertebrates. eLife 2023; 12:e92242. [PMID: 37750868 PMCID: PMC10522337 DOI: 10.7554/elife.92242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
Gene expression has been employed for homologizing body regions across bilateria. The molecular comparison of vertebrate and fly brains has led to a number of disputed homology hypotheses. Data from the fly Drosophila melanogaster have recently been complemented by extensive data from the red flour beetle Tribolium castaneum with its more insect-typical development. In this review, we revisit the molecular mapping of the neuroectoderm of insects and vertebrates to reconsider homology hypotheses. We claim that the protocerebrum is non-segmental and homologous to the vertebrate fore- and midbrain. The boundary between antennal and ocular regions correspond to the vertebrate mid-hindbrain boundary while the deutocerebrum represents the anterior-most ganglion with serial homology to the trunk. The insect head placode is shares common embryonic origin with the vertebrate adenohypophyseal placode. Intriguingly, vertebrate eyes develop from a different region compared to the insect compound eyes calling organ homology into question. Finally, we suggest a molecular re-definition of the classic concepts of archi- and prosocerebrum.
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Affiliation(s)
- Nico Posnien
- Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute, University GoettingenGöttingenGermany
| | - Vera S Hunnekuhl
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, University of GöttingenGöttingenGermany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, University of GöttingenGöttingenGermany
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Farnworth MS, Bucher G, Hartenstein V. Cover Image, Volume 530, Issue 13. J Comp Neurol 2022. [DOI: 10.1002/cne.25390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lehmann S, Atika B, Grossmann D, Schmitt-Engel C, Strohlein N, Majumdar U, Richter T, Weißkopf M, Ansari S, Teuscher M, Hakeemi MS, Li J, Weißbecker B, Klingler M, Bucher G, Wimmer EA. Phenotypic screen and transcriptomics approach complement each other in functional genomics of defensive stink gland physiology. BMC Genomics 2022; 23:608. [PMID: 35987630 PMCID: PMC9392906 DOI: 10.1186/s12864-022-08822-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/03/2022] [Indexed: 11/27/2022] Open
Abstract
Background Functional genomics uses unbiased systematic genome-wide gene disruption or analyzes natural variations such as gene expression profiles of different tissues from multicellular organisms to link gene functions to particular phenotypes. Functional genomics approaches are of particular importance to identify large sets of genes that are specifically important for a particular biological process beyond known candidate genes, or when the process has not been studied with genetic methods before. Results Here, we present a large set of genes whose disruption interferes with the function of the odoriferous defensive stink glands of the red flour beetle Tribolium castaneum. This gene set is the result of a large-scale systematic phenotypic screen using RNA interference applied in a genome-wide forward genetics manner. In this first-pass screen, 130 genes were identified, of which 69 genes could be confirmed to cause phenotypic changes in the glands upon knock-down, which vary from necrotic tissue and irregular reservoir size to irregular color or separation of the secreted gland compounds. Gene ontology analysis revealed that many of those genes are encoding enzymes (peptidases and cytochromes P450) as well as proteins involved in membrane trafficking with an enrichment in lysosome and mineral absorption pathways. The knock-down of 13 genes caused specifically a strong reduction of para-benzoquinones in the gland reservoirs, suggesting a specific function in the synthesis of these toxic compounds. Only 14 of the 69 confirmed gland genes are differentially overexpressed in stink gland tissue and thus could have been detected in a transcriptome-based analysis. However, only one out of eight genes identified by a transcriptomics approach known to cause phenotypic changes of the glands upon knock-down was recognized by this phenotypic screen, indicating the limitation of such a non-redundant first-pass screen. Conclusion Our results indicate the importance of combining diverse and independent methodologies to identify genes necessary for the function of a certain biological tissue, as the different approaches do not deliver redundant results but rather complement each other. The presented phenotypic screen together with a transcriptomics approach are now providing a set of close to hundred genes important for odoriferous defensive stink gland physiology in beetles. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08822-z.
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Klingler M, Bucher G. The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. EvoDevo 2022; 13:14. [PMID: 35854352 PMCID: PMC9295526 DOI: 10.1186/s13227-022-00201-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
The red flour beetle Tribolium castaneum has emerged as an important insect model system for a variety of topics. With respect to studying gene function, it is second only to the vinegar fly D. melanogaster. The RNAi response in T. castaneum is exceptionally strong and systemic, and it appears to target all cell types and processes. Uniquely for emerging model organisms, T. castaneum offers the opportunity of performing time- and cost-efficient large-scale RNAi screening, based on commercially available dsRNAs targeting all genes, which are simply injected into the body cavity. Well established transgenic and genome editing approaches are met by ease of husbandry and a relatively short generation time. Consequently, a number of transgenic tools like UAS/Gal4, Cre/Lox, imaging lines and enhancer trap lines are already available. T. castaneum has been a genetic experimental system for decades and now has become a workhorse for molecular and reverse genetics as well as in vivo imaging. Many aspects of development and general biology are more insect-typical in this beetle compared to D. melanogaster. Thus, studying beetle orthologs of well-described fly genes has allowed macro-evolutionary comparisons in developmental processes such as axis formation, body segmentation, and appendage, head and brain development. Transgenic approaches have opened new ways for in vivo imaging. Moreover, this emerging model system is the first choice for research on processes that are not represented in the fly, or are difficult to study there, e.g. extraembryonic tissues, cryptonephridial organs, stink gland function, or dsRNA-based pesticides.
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Affiliation(s)
- Martin Klingler
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Staudtstr. 5, 91058, Erlangen, Germany.
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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Farnworth MS, Bucher G, Hartenstein V. An atlas of the developing Tribolium castaneum brain reveals conservation in anatomy and divergence in timing to Drosophila melanogaster. J Comp Neurol 2022; 530:10.1002/cne.25335. [PMID: 35535818 PMCID: PMC9646932 DOI: 10.1002/cne.25335] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/11/2022]
Abstract
Insect brains are formed by conserved sets of neural lineages whose fibers form cohesive bundles with characteristic projection patterns. Within the brain neuropil, these bundles establish a system of fascicles constituting the macrocircuitry of the brain. The overall architecture of the neuropils and the macrocircuitry appear to be conserved. However, variation is observed, for example, in size, shape, and timing of development. Unfortunately, the developmental and genetic basis of this variation is poorly understood, although the rise of new genetically tractable model organisms such as the red flour beetle Tribolium castaneum allows the possibility to gain mechanistic insights. To facilitate such work, we present an atlas of the developing brain of T. castaneum, covering the first larval instar, the prepupal stage, and the adult, by combining wholemount immunohistochemical labeling of fiber bundles (acetylated tubulin) and neuropils (synapsin) with digital 3D reconstruction using the TrakEM2 software package. Upon comparing this anatomical dataset with the published work in Drosophila melanogaster, we confirm an overall high degree of conservation. Fiber tracts and neuropil fascicles, which can be visualized by global neuronal antibodies like antiacetylated tubulin in all invertebrate brains, create a rich anatomical framework to which individual neurons or other regions of interest can be referred to. The framework of a largely conserved pattern allowed us to describe differences between the two species with respect to parameters such as timing of neuron proliferation and maturation. These features likely reflect adaptive changes in developmental timing that govern the change from larval to adult brain.
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Affiliation(s)
- Max S Farnworth
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
- Evolution of Brains and Behaviour lab, School of Biological Sciences, University of Bristol, Bristol, UK
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California/Los Angeles, Los Angeles, USA
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Hakeemi MS, Ansari S, Teuscher M, Weißkopf M, Großmann D, Kessel T, Dönitz J, Siemanowski J, Wan X, Schultheis D, Frasch M, Roth S, Schoppmeier M, Klingler M, Bucher G. Screens in fly and beetle reveal vastly divergent gene sets required for developmental processes. BMC Biol 2022; 20:38. [PMID: 35135533 PMCID: PMC8827203 DOI: 10.1186/s12915-022-01231-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Most of the known genes required for developmental processes have been identified by genetic screens in a few well-studied model organisms, which have been considered representative of related species, and informative—to some degree—for human biology. The fruit fly Drosophila melanogaster is a prime model for insect genetics, and while conservation of many gene functions has been observed among bilaterian animals, a plethora of data show evolutionary divergence of gene function among more closely-related groups, such as within the insects. A quantification of conservation versus divergence of gene functions has been missing, without which it is unclear how representative data from model systems actually are. Results Here, we systematically compare the gene sets required for a number of homologous but divergent developmental processes between fly and beetle in order to quantify the difference of the gene sets. To that end, we expanded our RNAi screen in the red flour beetle Tribolium castaneum to cover more than half of the protein-coding genes. Then we compared the gene sets required for four different developmental processes between beetle and fly. We found that around 50% of the gene functions were identified in the screens of both species while for the rest, phenotypes were revealed only in fly (~ 10%) or beetle (~ 40%) reflecting both technical and biological differences. Accordingly, we were able to annotate novel developmental GO terms for 96 genes studied in this work. With this work, we publish the final dataset for the pupal injection screen of the iBeetle screen reaching a coverage of 87% (13,020 genes). Conclusions We conclude that the gene sets required for a homologous process diverge more than widely believed. Hence, the insights gained in flies may be less representative for insects or protostomes than previously thought, and work in complementary model systems is required to gain a comprehensive picture. The RNAi screening resources developed in this project, the expanding transgenic toolkit, and our large-scale functional data make T. castaneum an excellent model system in that endeavor. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01231-4.
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Affiliation(s)
- Muhammad Salim Hakeemi
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Salim Ansari
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Current address: Institute of Clinical Pharmacology, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Matthias Teuscher
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Matthias Weißkopf
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Daniela Großmann
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Current address: Department of Medical Bioinformatics, University Medical Center Göttingen, University of Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany
| | - Tobias Kessel
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.,Current address: Department of Insect Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
| | - Jürgen Dönitz
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Janna Siemanowski
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Current address: Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50924, Cologne, Germany
| | - Xuebin Wan
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Dorothea Schultheis
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.,Current address: Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Manfred Frasch
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Siegfried Roth
- Institute for Zoology/Developmental Biology, University of Cologne, Biocenter, Zülpicher Straße 47b, D-50674, Köln, Germany
| | - Michael Schoppmeier
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Martin Klingler
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach-Institut, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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Mehlhorn S, Hunnekuhl VS, Geibel S, Nauen R, Bucher G. Establishing RNAi for basic research and pest control and identification of the most efficient target genes for pest control: a brief guide. Front Zool 2021; 18:60. [PMID: 34863212 PMCID: PMC8643023 DOI: 10.1186/s12983-021-00444-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/04/2021] [Indexed: 11/14/2022] Open
Abstract
RNA interference (RNAi) has emerged as a powerful tool for knocking-down gene function in diverse taxa including arthropods for both basic biological research and application in pest control. The conservation of the RNAi mechanism in eukaryotes suggested that it should-in principle-be applicable to most arthropods. However, practical hurdles have been limiting the application in many taxa. For instance, species differ considerably with respect to efficiency of dsRNA uptake from the hemolymph or the gut. Here, we review some of the most frequently encountered technical obstacles when establishing RNAi and suggest a robust procedure for establishing this technique in insect species with special reference to pests. Finally, we present an approach to identify the most effective target genes for the potential control of agricultural and public health pests by RNAi.
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Affiliation(s)
- Sonja Mehlhorn
- Crop Science Division, Bayer AG, R&D, Pest Control, Alfred-Nobel-Straße 50, 40789, Monheim, Germany
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Vera S Hunnekuhl
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Sven Geibel
- Crop Science Division, Bayer AG, R&D, Pest Control, Alfred-Nobel-Straße 50, 40789, Monheim, Germany
| | - Ralf Nauen
- Crop Science Division, Bayer AG, R&D, Pest Control, Alfred-Nobel-Straße 50, 40789, Monheim, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.
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Beder T, Aromolaran O, Dönitz J, Tapanelli S, Adedeji E, Adebiyi E, Bucher G, Koenig R. Identifying essential genes across eukaryotes by machine learning. NAR Genom Bioinform 2021; 3:lqab110. [PMID: 34859210 PMCID: PMC8634067 DOI: 10.1093/nargab/lqab110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/09/2021] [Accepted: 11/29/2021] [Indexed: 02/07/2023] Open
Abstract
Identifying essential genes on a genome scale is resource intensive and has been performed for only a few eukaryotes. For less studied organisms essentiality might be predicted by gene homology. However, this approach cannot be applied to non-conserved genes. Additionally, divergent essentiality information is obtained from studying single cells or whole, multi-cellular organisms, and particularly when derived from human cell line screens and human population studies. We employed machine learning across six model eukaryotes and 60 381 genes, using 41 635 features derived from the sequence, gene function information and network topology. Within a leave-one-organism-out cross-validation, the classifiers showed high generalizability with an average accuracy close to 80% in the left-out species. As a case study, we applied the method to Tribolium castaneum and Bombyx mori and validated predictions experimentally yielding similar performances. Finally, using the classifier based on the studied model organisms enabled linking the essentiality information of human cell line screens and population studies.
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Affiliation(s)
- Thomas Beder
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
- Department of Internal Medicine II, University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Olufemi Aromolaran
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Jürgen Dönitz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Department of Medical Bioinformatics, University Medical Center Göttingen (UMG), 37099 Göttingen, Germany
| | - Sofia Tapanelli
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Eunice O Adedeji
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Ezekiel Adebiyi
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Rainer Koenig
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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Garcia-Perez NC, Bucher G, Buescher M. Shaking hands is a homeodomain transcription factor that controls axon outgrowth of central complex neurons in the insect model Tribolium. Development 2021; 148:272435. [PMID: 34415334 PMCID: PMC8543150 DOI: 10.1242/dev.199368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/09/2021] [Indexed: 01/22/2023]
Abstract
Gene regulatory mechanisms that specify subtype identity of central complex (CX) neurons are the subject of intense investigation. The CX is a compartment within the brain common to all insect species and functions as a ‘command center’ that directs motor actions. It is made up of several thousand neurons, with more than 60 morphologically distinct identities. Accordingly, transcriptional programs must effect the specification of at least as many neuronal subtypes. We demonstrate a role for the transcription factor Shaking hands (Skh) in the specification of embryonic CX neurons in Tribolium. The developmental dynamics of skh expression are characteristic of terminal selectors of subtype identity. In the embryonic brain, skh expression is restricted to a subset of neurons, many of which survive to adulthood and contribute to the mature CX. skh expression is maintained throughout the lifetime in at least some CX neurons. skh knockdown results in axon outgrowth defects, thus preventing the formation of an embryonic CX primordium. The previously unstudied Drosophila skh shows a similar embryonic expression pattern, suggesting that subtype specification of CX neurons may be conserved. Summary: A detailed examination of the developmental expression of the homeodomain transcription factor Shaking hands in Tribolium reveals a role in the formation of the central complex primordium.
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Affiliation(s)
- Natalia Carolina Garcia-Perez
- Johann Friedrich Blumenbach Institute of Zoology, GZMB, Department of Evolutionary Developmental Genetics, University of Goettingen, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
| | - Gregor Bucher
- Johann Friedrich Blumenbach Institute of Zoology, GZMB, Department of Evolutionary Developmental Genetics, University of Goettingen, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
| | - Marita Buescher
- Johann Friedrich Blumenbach Institute of Zoology, GZMB, Department of Evolutionary Developmental Genetics, University of Goettingen, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
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Mehlhorn S, Ulrich J, Baden CU, Buer B, Maiwald F, Lueke B, Geibel S, Bucher G, Nauen R. The mustard leaf beetle, Phaedon cochleariae, as a screening model for exogenous RNAi-based control of coleopteran pests. Pestic Biochem Physiol 2021; 176:104870. [PMID: 34119215 DOI: 10.1016/j.pestbp.2021.104870] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 05/28/2023]
Abstract
RNA interference (RNAi) is a promising, selective pest control technology based on the silencing of targeted genes mediated by the degradation of mRNA after the ingestion of double-stranded (ds) RNA. However, the identification of the best target genes remains a challenge, because large scale screening is only feasible in lab model systems and it remains unclear, to what degree such data can be transferred to pest species. Here, we report on our efforts to transfer target genes found in a lab model to the mustard leaf beetle, Phaedon cochleariae. The mustard leaf beetle can be reared easily and resource-efficient in large quantities all year round and is an established chrysomelid pest for higher throughput screening approaches in the crop protection industry. Mustard leaf beetle transcriptome sequencing and assembly revealed genes orthologous to those previously described as highly efficient RNAi targets in the model beetle Tribolium castaneum. First, we observed mortality after injection of dsRNA targeting the respective orthologous genes in 2nd instar mustard beetle larvae. Next, we adopted a robust, automated multi-well plate foliar RNAi screening procedure with 2nd instar larvae of the mustard leaf beetle to assess those genes. Indeed, foliar application and oral uptake of dsRNA targeting the same genes resulted in larval mortality as well. The most effective target genes with a strong (lethal) phenotype - at dsRNA doses as low as 300 ng/leaf disc (equal to 9.6 g/ha) - were srp54k, rop, αSNAP, rpn7 and rpt3. Rather limited effects were observed after application of dsRNA targeting cactus, shibire and PP-α, though they had previously been shown to be highly lethal in red flour beetle. Importantly, our experiments demonstrated that the overall efficacy pattern obtained after oral dsRNA application was well correlated with the results obtained after dsRNA injection. RT-qPCR confirmed significant target gene knock-down after normalization by employing three reference genes shown to be stably expressed across life stages. In summary, several RNAi targeted genes elicited a strong lethal phenotype and significant target gene knock-down after feeding, suggesting P. cochleariae as a potential coleopteran screening model for foliarly applied exogenous RNAi.
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Affiliation(s)
- Sonja Mehlhorn
- Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus von-Liebig-Weg 11, 37077 Göttingen, Germany; Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Julia Ulrich
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Christian U Baden
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Benjamin Buer
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Frank Maiwald
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Bettina Lueke
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Sven Geibel
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany.
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Buescher M, Oberhofer G, Garcia-Perez NC, Bucher G. A Protocol for Double Fluorescent In Situ Hybridization and Immunohistochemistry for the Study of Embryonic Brain Development in Tribolium castaneum. Methods Mol Biol 2020; 2047:219-232. [PMID: 31552657 DOI: 10.1007/978-1-4939-9732-9_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The red flour beetle, Tribolium castaneum, is an emerging model system well suited to the study of embryonic brain development and evolution (see Chapters 11 and 13 ). Brain genesis is driven by specific gene products whose expression underlies a tight spatiotemporal control. Therefore, the analysis of gene expression in time and space provides valuable insights into the molecular mechanisms that govern brain development. Since Tribolium-specific antibodies are scarce, fluorescent RNA in situ hybridization is the method of choice to determine the dynamics of individual gene expression. We have modified common RNA in situ protocols to facilitate the concomitant detection of two gene-specific expression patterns (double fluorescent RNA in situ). In addition, we describe a procedure which combines fluorescent single RNA in situ and immunostaining with gene-specific antibodies. Conventional in situ using RNA probes that are complementary to mature mRNAs often produce diffuse signals. We demonstrate that RNA in situ probes complementary to intronic gene sequences facilitate single cell resolution because the fluorescent signal is restricted to the nucleus. We believe our protocols can be adapted easily to suit the analysis of brain development in other insect species.
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Affiliation(s)
- Marita Buescher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Georg Oberhofer
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Natalia Carolina Garcia-Perez
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.
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12
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Mehlhorn SG, Geibel S, Bucher G, Nauen R. Profiling of RNAi sensitivity after foliar dsRNA exposure in different European populations of Colorado potato beetle reveals a robust response with minor variability. Pestic Biochem Physiol 2020; 166:104569. [PMID: 32448424 DOI: 10.1016/j.pestbp.2020.104569] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 05/10/2023]
Abstract
In recent years, substantial effort was spent on the exploration and implementation of RNAi technology using double-stranded RNA (dsRNA) for pest management purposes. However, only few studies investigated the geographical variation in RNAi sensitivity present in field-collected populations of the targeted insect pest. In this baseline study, 2nd instar larvae of 14 different European populations of Colorado potato beetle (CPB), Leptinotarsa decemlineata, collected from nine different countries were exposed to a foliarly applied diagnostic dose of dsactin (dsact) to test for possible variations in RNAi response. Only minor variability in RNAi sensitivity was observed between populations. However, the time necessary to trigger a dsRNA-mediated phenotypic response varied significantly among populations, indicated by significant differences in mortality figures obtained five days after treatment. An inbred German laboratory reference strain D01 and a Spanish field strain E02 showed almost 100% mortality after foliar exposure to 30 ng dsactin (equal to 0.96 g/ha), whereas another Spanish strain E01 was least responsive and showed only 30% mortality. Calculated LD50-values for foliarly applied dsact against strains D01 (most sensitive) and E01 (least sensitive) were 9.22 and 68.7 ng/leaf disc, respectively. The variability was not based on target gene sequence divergence or knock-down efficiency. Variability in expression of the core RNAi machinery genes dicer (dcr2a) and argonaute (ago2a) was observed but did not correlate with sensitivity. Interestingly, RT-qPCR data collected for all strains revealed a strong correlation between the expression level of dcr2a and ago2a (r 0.93) as well as ago2a and stauC (r 0.94), a recently described dsRNA binding protein in Coleopterans. Overall, this study demonstrates that sensitivity of CPB to sprayable RNAi slightly varies between strains but also shows that foliar RNAi as a control method works against all tested CPB populations collected across a broad geographic range in Europe. Thus, underpinning the potential of RNAi-based CPB control as a promising component in integrated pest management (IPM) and resistance management programs.
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Affiliation(s)
- Sonja G Mehlhorn
- Department of Evolutionary Developmental Genetics, Göttingen Center for Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany; Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Sven Geibel
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Göttingen Center for Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Pest Control, Alfred-Nobel-Str. 50, 40789 Monheim, Germany.
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13
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Schacht MI, Schomburg C, Bucher G. six3 acts upstream of foxQ2 in labrum and neural development in the spider Parasteatoda tepidariorum. Dev Genes Evol 2020; 230:95-104. [PMID: 32040712 PMCID: PMC7128001 DOI: 10.1007/s00427-020-00654-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/29/2020] [Indexed: 12/12/2022]
Abstract
Anterior patterning in animals is based on a gene regulatory network, which comprises highly conserved transcription factors like six3, pax6 and otx. More recently, foxQ2 was found to be an ancestral component of this network but its regulatory interactions showed evolutionary differences. In most animals, foxQ2 is a downstream target of six3 and knockdown leads to mild or no epidermal phenotypes. In contrast, in the red flour beetle Tribolium castaneum, foxQ2 gained a more prominent role in patterning leading to strong epidermal and brain phenotypes and being required for six3 expression. However, it has remained unclear which of these novel aspects were insect or arthropod specific. Here, we study expression and RNAi phenotype of the single foxQ2 ortholog of the spider Parasteatoda tepidariorum. We find early anterior expression similar to the one of insects. Further, we show an epidermal phenotype in the labrum similar to the insect phenotype. However, our data indicate that foxQ2 is positioned downstream of six3 like in other animals but unlike insects. Hence, the epidermal and neural pattering function of foxQ2 is ancestral for arthropods while the upstream role of foxQ2 may have evolved in the lineage leading to the insects.
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Affiliation(s)
- Magdalena Ines Schacht
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Christoph Schomburg
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
- Institut für Allgemeine Zoologie und Entwicklungsbiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 38, 35392, Giessen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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14
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Herndon N, Shelton J, Gerischer L, Ioannidis P, Ninova M, Dönitz J, Waterhouse RM, Liang C, Damm C, Siemanowski J, Kitzmann P, Ulrich J, Dippel S, Oberhofer G, Hu Y, Schwirz J, Schacht M, Lehmann S, Montino A, Posnien N, Gurska D, Horn T, Seibert J, Vargas Jentzsch IM, Panfilio KA, Li J, Wimmer EA, Stappert D, Roth S, Schröder R, Park Y, Schoppmeier M, Chung HR, Klingler M, Kittelmann S, Friedrich M, Chen R, Altincicek B, Vilcinskas A, Zdobnov E, Griffiths-Jones S, Ronshaugen M, Stanke M, Brown SJ, Bucher G. Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC Genomics 2020; 21:47. [PMID: 31937263 PMCID: PMC6961396 DOI: 10.1186/s12864-019-6394-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
Background The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.
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Affiliation(s)
- Nicolae Herndon
- Department of Computer Science, East Carolina University, Greenville, NC, 27858, USA
| | - Jennifer Shelton
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Lizzy Gerischer
- Institut für Mathematik und Informatik, Universität Greifswald, Greifswald, Germany
| | - Panos Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Maria Ninova
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Jürgen Dönitz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Carsten Damm
- Institut für Informatik, Fakultät für Mathematik und Informatik, Georg-August-Universität Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Janna Siemanowski
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Peter Kitzmann
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Julia Ulrich
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Stefan Dippel
- Göttinger Graduiertenschule fur Neurowissenschaften Biophysik und Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Georg Oberhofer
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Yonggang Hu
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Jonas Schwirz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Magdalena Schacht
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Sabrina Lehmann
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Alice Montino
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Nico Posnien
- Department of Developmental Biology, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Daniela Gurska
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Kristen A Panfilio
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Jianwei Li
- Department Developmental Biology, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Ernst A Wimmer
- Department of Developmental Biology, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Dominik Stappert
- Institute of Zoology: Developmental Biology, University of Cologne, Zülpicher Weg 47b, 50674, Cologne, Germany
| | - Siegfried Roth
- Institute of Zoology: Developmental Biology, University of Cologne, Zülpicher Weg 47b, 50674, Cologne, Germany
| | - Reinhard Schröder
- Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael Schoppmeier
- Department of Biology, Divison of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Ho-Ryun Chung
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnenstraße 63-73, 14195, Berlin, Germany
| | - Martin Klingler
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Sebastian Kittelmann
- Oxford Brookes University, Centre for Functional Genomics, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Markus Friedrich
- Department of Anatomy and Cell Biology, Wayne State University, Detroit, MI, 48202, USA
| | - Rui Chen
- Baylor College of Medicine, Houston, Texas, USA
| | - Boran Altincicek
- Institute of Crop Science and Resource Conservation (INRES-Phytomedicine), Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Evgeny Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Matthew Ronshaugen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Mario Stanke
- Institut für Mathematik und Informatik, Universität Greifswald, Greifswald, Germany.
| | - Sue J Brown
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Gregor Bucher
- Georg-August-Universität Göttingen, Göttingen, Germany.
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15
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Hunnekuhl VS, Siemanowski J, Farnworth MS, He B, Bucher G. Immunohistochemistry and Fluorescent Whole Mount RNA In Situ Hybridization in Larval and Adult Brains of Tribolium. Methods Mol Biol 2020; 2047:233-251. [PMID: 31552658 DOI: 10.1007/978-1-4939-9732-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Arthropod brains are fascinating structures that exhibit great complexity but also contain conserved elements that can be recognized between species. There is a long tradition of research in insect neuroanatomy, cell biology, and in studying the genetics of insect brain development. Recently, the beetle Tribolium castaneum has gained attention as a model for insect head and brain development, and many anterior patterning genes have so far been characterized in beetle embryos. The outcome of embryonic anterior development is the larval and, subsequently, the adult brain. A basic requirement to understand genetic cell type diversity within these structures is the ability to localize mRNA and protein of neural genes. Here we detail our protocols for RNA in situ hybridization in combination with immunohistochemistry, optimized for dissected brains of larval and adult beetles.
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Affiliation(s)
- Vera S Hunnekuhl
- Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Janna Siemanowski
- Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Max S Farnworth
- Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Bicheng He
- Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, Göttingen, Germany.
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16
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Farnworth MS, Eckermann KN, Ahmed HMM, Mühlen DS, He B, Bucher G. The Red Flour Beetle as Model for Comparative Neural Development: Genome Editing to Mark Neural Cells in Tribolium Brain Development. Methods Mol Biol 2020; 2047:191-217. [PMID: 31552656 DOI: 10.1007/978-1-4939-9732-9_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated) scientists working with Tribolium castaneum can now generate transgenic lines with site-specific insertions at their region of interest. We present two methods to generate in vivo imaging lines suitable for marking subsets of neurons with fluorescent proteins. The first method relies on homologous recombination and uses a 2A peptide to create a bicistronic mRNA. In such lines, the target and the marker proteins are not fused but produced at equal amounts. This work-intensive method is compared with creating gene-specific enhancer traps that do not rely on homologous recombination. These are faster to generate but reflect the expression of the target gene less precisely. Which method to choose, strongly depends on the aims of each research project and in turn impacts of how neural cells and their development are marked. We describe the necessary steps from designing constructs and guide RNAs to embryonic injection and making homozygous stocks.
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Affiliation(s)
- Max S Farnworth
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany. .,Göttingen Graduate Center for Molecular Biosciences, Neurosciences and Biophysics, Göttingen, Germany.
| | - Kolja N Eckermann
- Göttingen Graduate Center for Molecular Biosciences, Neurosciences and Biophysics, Göttingen, Germany.,Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Hassan M M Ahmed
- Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.,Department of Crop Protection, Faculty of Agriculture, University of Khartoum, Khartoum-North, Khartoum, Sudan
| | - Dominik S Mühlen
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.,Göttingen Graduate Center for Molecular Biosciences, Neurosciences and Biophysics, Göttingen, Germany
| | - Bicheng He
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.
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17
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He B, Buescher M, Farnworth MS, Strobl F, Stelzer EHK, Koniszewski NDB, Muehlen D, Bucher G. An ancestral apical brain region contributes to the central complex under the control of foxQ2 in the beetle Tribolium. eLife 2019; 8:e49065. [PMID: 31625505 PMCID: PMC6837843 DOI: 10.7554/elife.49065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/17/2019] [Indexed: 12/11/2022] Open
Abstract
The genetic control of anterior brain development is highly conserved throughout animals. For instance, a conserved anterior gene regulatory network specifies the ancestral neuroendocrine center of animals and the apical organ of marine organisms. However, its contribution to the brain in non-marine animals has remained elusive. Here, we study the function of the Tc-foxQ2 forkhead transcription factor, a key regulator of the anterior gene regulatory network of insects. We characterized four distinct types of Tc-foxQ2 positive neural progenitor cells based on differential co-expression with Tc-six3/optix, Tc-six4, Tc-chx/vsx, Tc-nkx2.1/scro, Tc-ey, Tc-rx and Tc-fez1. An enhancer trap line built by genome editing marked Tc-foxQ2 positive neurons, which projected through the primary brain commissure and later through a subset of commissural fascicles. Eventually, they contributed to the central complex. Strikingly, in Tc-foxQ2 RNAi knock-down embryos the primary brain commissure did not split and subsequent development of midline brain structures stalled. Our work establishes foxQ2 as a key regulator of brain midline structures, which distinguish the protocerebrum from segmental ganglia. Unexpectedly, our data suggest that the central complex evolved by integrating neural cells from an ancestral anterior neuroendocrine center.
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Affiliation(s)
- Bicheng He
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Marita Buescher
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Max Stephen Farnworth
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
- Göttingen Graduate Center for Molecular BiosciencesNeurosciences and BiophysicsGöttingenGermany
| | - Frederic Strobl
- Buchmann Institute for Molecular Life Sciences (BMLS)Goethe UniversityFrankfurtGermany
| | - Ernst HK Stelzer
- Buchmann Institute for Molecular Life Sciences (BMLS)Goethe UniversityFrankfurtGermany
| | - Nikolaus DB Koniszewski
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Dominik Muehlen
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Gregor Bucher
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
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18
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Dönitz J, Gerischer L, Hahnke S, Pfeiffer S, Bucher G. Expanded and updated data and a query pipeline for iBeetle-Base. Nucleic Acids Res 2019; 46:D831-D835. [PMID: 29069517 PMCID: PMC5753255 DOI: 10.1093/nar/gkx984] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022] Open
Abstract
The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/.
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Affiliation(s)
- Jürgen Dönitz
- Dpt. of Evolutionary Developmental Genetics, Georg August University of Göttingen, 37077 Göttingen, Germany.,Institute of Bioinformatics, University Medical Center Göttingen (UMG) Georg August University, 37077 Göttingen, Germany
| | - Lizzy Gerischer
- Institute for Mathematics and Computer Science, Ernst Moritz Arndt University, 17487 Greifswald, Germany
| | - Stefan Hahnke
- Dpt. of Evolutionary Developmental Genetics, Georg August University of Göttingen, 37077 Göttingen, Germany
| | - Stefan Pfeiffer
- Dpt. of Evolutionary Developmental Genetics, Georg August University of Göttingen, 37077 Göttingen, Germany
| | - Gregor Bucher
- Dpt. of Evolutionary Developmental Genetics, Georg August University of Göttingen, 37077 Göttingen, Germany
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19
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Hu Y, Schmitt-Engel C, Schwirz J, Stroehlein N, Richter T, Majumdar U, Bucher G. A morphological novelty evolved by co-option of a reduced gene regulatory network and gene recruitment in a beetle. Proc Biol Sci 2018; 285:rspb.2018.1373. [PMID: 30135167 DOI: 10.1098/rspb.2018.1373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/25/2018] [Indexed: 12/18/2022] Open
Abstract
The mechanisms underlying the evolution of morphological novelties have remained enigmatic but co-option of existing gene regulatory networks (GRNs), recruitment of genes and the evolution of orphan genes have all been suggested to contribute. Here, we study a morphological novelty of beetle pupae called gin-trap. By combining the classical candidate gene approach with unbiased screening in the beetle Tribolium castaneum, we find that 70% of the tested components of the wing network were required for gin-trap development. However, many downstream and even upstream components were not included in the co-opted network. Only one gene was recruited from another biological context, but it was essential for the anteroposterior symmetry of the gin-traps, which represents a gin-trap-unique morphological innovation. Our data highlight the importance of co-option and modification of GRNs. The recruitment of single genes may not be frequent in the evolution of morphological novelties, but may be essential for subsequent diversification of the novelties. Finally, after having screened about 28% of annotated genes in the Tribolium genome to identify the genes required for gin-trap development, we found none of them are orphan genes, suggesting that orphan genes may have played only a minor, if any, role in the evolution of gin-traps.
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Affiliation(s)
- Yonggang Hu
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Christian Schmitt-Engel
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Jonas Schwirz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Nadi Stroehlein
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Tobias Richter
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Upalparna Majumdar
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
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20
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017. [PMID: 28756775 DOI: 10.1186/s12915-017-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. RESULTS We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. CONCLUSIONS Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
- Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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21
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017; 15:62. [PMID: 28756775 PMCID: PMC5535294 DOI: 10.1186/s12915-017-0399-x] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.,Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark.,Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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Kitzmann P, Weißkopf M, Schacht MI, Bucher G. A key role for foxQ2 in anterior head and central brain patterning in insects. Development 2017; 144:2969-2981. [PMID: 28811313 PMCID: PMC5592812 DOI: 10.1242/dev.147637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 07/05/2017] [Indexed: 01/14/2023]
Abstract
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the red flour beetle Tribolium castaneum ortholog of foxQ2 (Tc-foxQ2) as a novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression. Surprisingly, Tc-foxQ2 and Tc-six3 mutually activate each other, forming a novel regulatory module at the top of the aGRN. Comparisons of our results with those of sea urchins and cnidarians suggest that foxQ2 has acquired more upstream functions in the aGRN during protostome evolution. Our findings expand the knowledge on foxQ2 gene function to include essential roles in epidermal development and central brain patterning.
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Affiliation(s)
- Peter Kitzmann
- Department of Evolutionary Developmental Genetics, GZMB, Universität Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Matthias Weißkopf
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstraße 5, 91058 Erlangen, Germany
| | - Magdalena Ines Schacht
- Department of Evolutionary Developmental Genetics, GZMB, Universität Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, Universität Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
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Hahn N, Knorr DY, Liebig J, Wüstefeld L, Peters K, Büscher M, Bucher G, Ehrenreich H, Heinrich R. The Insect Ortholog of the Human Orphan Cytokine Receptor CRLF3 Is a Neuroprotective Erythropoietin Receptor. Front Mol Neurosci 2017; 10:223. [PMID: 28769759 PMCID: PMC5509957 DOI: 10.3389/fnmol.2017.00223] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/28/2017] [Indexed: 12/26/2022] Open
Abstract
The cytokine erythropoietin (Epo) mediates various cell homeostatic responses to environmental challenges and pathological insults. While stimulation of vertebrate erythrocyte production is mediated by homodimeric “classical” Epo receptors, alternative receptors are involved in neuroprotection. However, their identity remains enigmatic due to complex cytokine ligand and receptor interactions and conflicting experimental results. Besides the classical Epo receptor, the family of type I cytokine receptors also includes the poorly characterized orphan cytokine receptor-like factor 3 (CRLF3) present in vertebrates including human and various insect species. By making use of the more simple genetic makeup of insect model systems, we studied whether CRLF3 is a neuroprotective Epo receptor in animals. We identified a single ortholog of CRLF3 in the beetle Tribolium castaneum, and established protocols for primary neuronal cell cultures from Tribolium brains and efficient in vitro RNA interference. Recombinant human Epo as well as the non-erythropoietic Epo splice variant EV-3 increased the survival of serum-deprived brain neurons, confirming the previously described neuroprotective effect of Epo in insects. Moreover, Epo completely prevented hypoxia-induced apoptotic cell death of primary neuronal cultures. Knockdown of CRLF3 expression by RNA interference with two different double stranded RNA (dsRNA) fragments abolished the neuroprotective effect of Epo, indicating that CRLF3 is a crucial component of the insect Epo-responsive receptor. This suggests that a common urbilaterian ancestor of the orphan human and insect cytokine receptor CRLF3 served as a neuroprotective receptor for an Epo-like cytokine. Our work also suggests that vertebrate CRLF3, like its insect ortholog, might represent a tissue protection-mediating receptor.
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Affiliation(s)
- Nina Hahn
- Department of Cellular Neurobiology, Institute for Zoology, Georg-August-University GoettingenGoettingen, Germany
| | - Debbra Y Knorr
- Department of Cellular Neurobiology, Institute for Zoology, Georg-August-University GoettingenGoettingen, Germany
| | - Johannes Liebig
- Department of Cellular Neurobiology, Institute for Zoology, Georg-August-University GoettingenGoettingen, Germany
| | - Liane Wüstefeld
- Clinical Neuroscience, Max Planck Institute of Experimental MedicineGoettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB)Goettingen, Germany
| | - Karsten Peters
- Department of Cellular Neurobiology, Institute for Zoology, Georg-August-University GoettingenGoettingen, Germany
| | - Marita Büscher
- Department of Evolutionary Developmental Biology, Institute for Zoology, Georg-August-University GoettingenGoettingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Biology, Institute for Zoology, Georg-August-University GoettingenGoettingen, Germany
| | - Hannelore Ehrenreich
- Clinical Neuroscience, Max Planck Institute of Experimental MedicineGoettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB)Goettingen, Germany
| | - Ralf Heinrich
- Department of Cellular Neurobiology, Institute for Zoology, Georg-August-University GoettingenGoettingen, Germany
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Koniszewski NDB, Kollmann M, Bigham M, Farnworth M, He B, Büscher M, Hütteroth W, Binzer M, Schachtner J, Bucher G. The insect central complex as model for heterochronic brain development-background, concepts, and tools. Dev Genes Evol 2016; 226:209-19. [PMID: 27056385 PMCID: PMC4896989 DOI: 10.1007/s00427-016-0542-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/17/2016] [Indexed: 11/28/2022]
Abstract
The adult insect brain is composed of neuropils present in most taxa. However, the relative size, shape, and developmental timing differ between species. This diversity of adult insect brain morphology has been extensively described while the genetic mechanisms of brain development are studied predominantly in Drosophila melanogaster. However, it has remained enigmatic what cellular and genetic mechanisms underlie the evolution of neuropil diversity or heterochronic development. In this perspective paper, we propose a novel approach to study these questions. We suggest using genome editing to mark homologous neural cells in the fly D. melanogaster, the beetle Tribolium castaneum, and the Mediterranean field cricket Gryllus bimaculatus to investigate developmental differences leading to brain diversification. One interesting aspect is the heterochrony observed in central complex development. Ancestrally, the central complex is formed during embryogenesis (as in Gryllus) but in Drosophila, it arises during late larval and metamorphic stages. In Tribolium, it forms partially during embryogenesis. Finally, we present tools for brain research in Tribolium including 3D reconstruction and immunohistochemistry data of first instar brains and the generation of transgenic brain imaging lines. Further, we characterize reporter lines labeling the mushroom bodies and reflecting the expression of the neuroblast marker gene Tc-asense, respectively.
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Affiliation(s)
- Nikolaus Dieter Bernhard Koniszewski
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, CNMPB, Georg-August-University Göttingen, Göttingen Campus, Göttingen, Germany.,Institute of Medical Microbiology, Otto-von-Guericke-University, Magdeburg, Germany
| | - Martin Kollmann
- Department of Biology, Animal Physiology, Philipps-University, Marburg, Germany
| | - Mahdiyeh Bigham
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, CNMPB, Georg-August-University Göttingen, Göttingen Campus, Göttingen, Germany
| | - Max Farnworth
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, CNMPB, Georg-August-University Göttingen, Göttingen Campus, Göttingen, Germany
| | - Bicheng He
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, CNMPB, Georg-August-University Göttingen, Göttingen Campus, Göttingen, Germany
| | - Marita Büscher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, CNMPB, Georg-August-University Göttingen, Göttingen Campus, Göttingen, Germany
| | - Wolf Hütteroth
- Department of Biology, Animal Physiology, Philipps-University, Marburg, Germany.,Department of Biology, Neurobiology, University of Konstanz, Constance, Germany
| | - Marlene Binzer
- Department of Biology, Animal Physiology, Philipps-University, Marburg, Germany
| | - Joachim Schachtner
- Department of Biology, Animal Physiology, Philipps-University, Marburg, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, CNMPB, Georg-August-University Göttingen, Göttingen Campus, Göttingen, Germany.
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Oberhofer G, Grossmann D, Siemanowski JL, Beissbarth T, Bucher G. Wnt/β-catenin signaling integrates patterning and metabolism of the insect growth zone. Development 2014; 141:4740-50. [PMID: 25395458 PMCID: PMC4299277 DOI: 10.1242/dev.112797] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Wnt/β-catenin and hedgehog (Hh) signaling are essential for transmitting signals across cell membranes in animal embryos. Early patterning of the principal insect model, Drosophila melanogaster, occurs in the syncytial blastoderm, where diffusion of transcription factors obviates the need for signaling pathways. However, in the cellularized growth zone of typical short germ insect embryos, signaling pathways are predicted to play a more fundamental role. Indeed, the Wnt/β-catenin pathway is required for posterior elongation in most arthropods, although which target genes are activated in this context remains elusive. Here, we use the short germ beetle Tribolium castaneum to investigate two Wnt and Hh signaling centers located in the head anlagen and in the growth zone of early embryos. We find that Wnt/β-catenin signaling acts upstream of Hh in the growth zone, whereas the opposite interaction occurs in the head. We determine the target gene sets of the Wnt/β-catenin and Hh pathways and find that the growth zone signaling center activates a much greater number of genes and that the Wnt and Hh target gene sets are essentially non-overlapping. The Wnt pathway activates key genes of all three germ layers, including pair-rule genes, and Tc-caudal and Tc-twist. Furthermore, the Wnt pathway is required for hindgut development and we identify Tc-senseless as a novel hindgut patterning gene required in the early growth zone. At the same time, Wnt acts on growth zone metabolism and cell division, thereby integrating growth with patterning. Posterior Hh signaling activates several genes potentially involved in a proteinase cascade of unknown function.
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Affiliation(s)
- Georg Oberhofer
- Department of Evolutionary Developmental Biology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg-August-University, Justus von Liebig Weg 11, Göttingen D-37077, Germany
| | - Daniela Grossmann
- Department of Evolutionary Developmental Biology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg-August-University, Justus von Liebig Weg 11, Göttingen D-37077, Germany
| | - Janna L Siemanowski
- Department of Evolutionary Developmental Biology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg-August-University, Justus von Liebig Weg 11, Göttingen D-37077, Germany
| | - Tim Beissbarth
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, Göttingen D-37073, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Biology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg-August-University, Justus von Liebig Weg 11, Göttingen D-37077, Germany
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Dönitz J, Schmitt-Engel C, Grossmann D, Gerischer L, Tech M, Schoppmeier M, Klingler M, Bucher G. iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum. Nucleic Acids Res 2014; 43:D720-5. [PMID: 25378303 PMCID: PMC4383896 DOI: 10.1093/nar/gku1054] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The iBeetle-Base (http://ibeetle-base.uni-goettingen.de) makes available annotations of RNAi phenotypes, which were gathered in a large scale RNAi screen in the red flour beetle Tribolium castaneum (iBeetle screen). In addition, it provides access to sequence information and links for all Tribolium castaneum genes. The iBeetle-Base contains the annotations of phenotypes of several thousands of genes knocked down during embryonic and metamorphic epidermis and muscle development in addition to phenotypes linked to oogenesis and stink gland biology. The phenotypes are described according to the EQM (entity, quality, modifier) system using controlled vocabularies and the Tribolium morphological ontology (TrOn). Furthermore, images linked to the respective annotations are provided. The data are searchable either for specific phenotypes using a complex ‘search for morphological defects’ or a ‘quick search’ for gene names and IDs. The red flour beetle Tribolium castaneum has become an important model system for insect functional genetics and is a representative of the most species rich taxon, the Coleoptera, which comprise several devastating pests. It is used for studying insect typical development, the evolution of development and for research on metabolism and pest control. Besides Drosophila, Tribolium is the first insect model organism where large scale unbiased screens have been performed.
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Affiliation(s)
- Jürgen Dönitz
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, GZMB, Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, 37075 Göttingen, Germany
| | - Christian Schmitt-Engel
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, GZMB, Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, 37075 Göttingen, Germany Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Daniela Grossmann
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, GZMB, Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, 37075 Göttingen, Germany
| | - Lizzy Gerischer
- Institute for Mathematics and Computer Science, Ernst Moritz Arndt University, 17487 Greifswald, Germany
| | - Maike Tech
- Institute of Microbiology and Genetics, Department of Bioinformatics, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Michael Schoppmeier
- Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Martin Klingler
- Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, GZMB, Department of Evolutionary Developmental Genetics, Georg-August-University Göttingen, 37075 Göttingen, Germany
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Dönitz J, Grossmann D, Schild I, Schmitt-Engel C, Bradler S, Prpic NM, Bucher G. TrOn: an anatomical ontology for the beetle Tribolium castaneum. PLoS One 2013; 8:e70695. [PMID: 23936240 PMCID: PMC3728323 DOI: 10.1371/journal.pone.0070695] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022] Open
Abstract
In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera), is an emerging model organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated the Tribolium Ontology (TrOn), which describes the morphology of the red flour beetle. The content of this ontology comprises so far most external morphological structures as well as some internal ones. All modeled structures are consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast, downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage. Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine the characteristics of generic and concrete terms with features of both. These annotation principles take into account the changing morphology of the beetle during development and provide generic terms to be used in applications or for cross linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi) screen. The ontology is available for download at http://ibeetle-base.uni-goettingen.de.
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Affiliation(s)
- Jürgen Dönitz
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany.
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Peel AD, Schanda J, Grossmann D, Ruge F, Oberhofer G, Gilles AF, Schinko JB, Klingler M, Bucher G. Tc-knirps plays different roles in the specification of antennal and mandibular parasegment boundaries and is regulated by a pair-rule gene in the beetle Tribolium castaneum. BMC Dev Biol 2013; 13:25. [PMID: 23777260 PMCID: PMC3698154 DOI: 10.1186/1471-213x-13-25] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/12/2013] [Indexed: 01/03/2023]
Abstract
Background The Drosophila larval head is evolutionarily derived at the genetic and morphological level. In the beetle Tribolium castaneum, development of the larval head more closely resembles the ancestral arthropod condition. Unlike in Drosophila, a knirps homologue (Tc-kni) is required for development of the antennae and mandibles. However, published Tc-kni data are restricted to cuticle phenotypes and Tc-even-skipped and Tc-wingless stainings in knockdown embryos. Hence, it has remained unclear whether the entire antennal and mandibular segments depend on Tc-kni function, and whether the intervening intercalary segment is formed completely. We address these questions with a detailed examination of Tc-kni function. Results By examining the expression of marker genes in RNAi embryos, we show that Tc-kni is required only for the formation of the posterior parts of the antennal and mandibular segments (i.e. the parasegmental boundaries). Moreover, we find that the role of Tc-kni is distinct in these segments: Tc-kni is required for the initiation of the antennal parasegment boundary, but only for the maintenance of the mandibular parasegmental boundary. Surprisingly, Tc-kni controls the timing of expression of the Hox gene Tc-labial in the intercalary segment, although this segment does form in the absence of Tc-kni function. Unexpectedly, we find that the pair-rule gene Tc-even-skipped helps set the posterior boundary of Tc-kni expression in the mandible. Using the mutant antennaless, a likely regulatory Null mutation at the Tc-kni locus, we provide evidence that our RNAi studies represent a Null situation. Conclusions Tc-kni is required for the initiation of the antennal and the maintenance of the mandibular parasegmental boundaries. Tc-kni is not required for specification of the anterior regions of these segments, nor the intervening intercalary segment, confirming that Tc-kni is not a canonical ‘gap-gene’. Our finding that a gap gene orthologue is regulated by a pair rule gene adds to the view that the segmentation gene hierarchies differ between Tribolium and Drosophila upstream of the pair rule gene level. In Tribolium, as in Drosophila, head and trunk segmentation gene networks cooperate to pattern the mandibular segment, albeit involving Tc-kni as novel component.
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Affiliation(s)
- Andrew D Peel
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FoRTH), Nikolaou Plastira 100, GR-70013, Heraklion, Crete, Greece
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Abstract
Early embryonic stages differ significantly among related animal taxa while subsequent development converges at the conserved phylotypic stage before again diverging. Although this phenomenon has long been observed, its underlying genetic mechanisms remain enigmatic. The dipteran Drosophila melanogaster develops as a long germ embryo where the head anlagen form a cap at the anterior pole of the blastoderm. Consequently, the anterior and terminal maternal systems give crucial input for head patterning. However, in the short germ beetle Tribolium castaneum, as in most insects, the head anlagen is located at a ventral position distant from the anterior pole of the blastoderm. In line with these divergent embryonic anlagen, several differences in the axis formation between the insects have been discovered. We now ask to what extent patterning and morphogenesis of the anterior median region (AMR) of the head, including clypeolabral and stomodeal anlagen, differ among these insects. Unexpectedly, we find that Tc-huckebein is not a terminal gap gene and, unlike its Drosophila ortholog, is not involved in Tribolium head development. Instead, Tc-six3 acts upstream of Tc-crocodile and Tc-cap'n'collar to pattern posterior and anterior parts of the AMR, respectively. We further find that instead of huckebein, Tc-crocodile is required for stomodeum development by activating Tc-forkhead. Finally, a morphogenetic movement not found in Drosophila shapes the embryonic head of Tribolium. Apparently, with anterior displacement of the head anlagen during long germ evolution of Drosophila, the ancestral regulation by the bilaterian anterior control gene six3 was replaced by the anterior and terminal maternal systems, which were further elaborated by adding bicoid, tailless and huckebein as anterior regionalization genes.
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Affiliation(s)
- Sebastian Kittelmann
- Department of Evolutionary Genetics, Göttingen Center of Molecular Biology, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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Posnien N, Koniszewski NDB, Hein HJ, Bucher G. Candidate gene screen in the red flour beetle Tribolium reveals six3 as ancient regulator of anterior median head and central complex development. PLoS Genet 2011; 7:e1002416. [PMID: 22216011 PMCID: PMC3245309 DOI: 10.1371/journal.pgen.1002416] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/13/2011] [Indexed: 11/19/2022] Open
Abstract
Several highly conserved genes play a role in anterior neural plate patterning of vertebrates and in head and brain patterning of insects. However, head involution in Drosophila has impeded a systematic identification of genes required for insect head formation. Therefore, we use the red flour beetle Tribolium castaneum in order to comprehensively test the function of orthologs of vertebrate neural plate patterning genes for a function in insect head development. RNAi analysis reveals that most of these genes are indeed required for insect head capsule patterning, and we also identified several genes that had not been implicated in this process before. Furthermore, we show that Tc-six3/optix acts upstream of Tc-wingless, Tc-orthodenticle1, and Tc-eyeless to control anterior median development. Finally, we demonstrate that Tc-six3/optix is the first gene known to be required for the embryonic formation of the central complex, a midline-spanning brain part connected to the neuroendocrine pars intercerebralis. These functions are very likely conserved among bilaterians since vertebrate six3 is required for neuroendocrine and median brain development with certain mutations leading to holoprosencephaly.
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Affiliation(s)
- Nico Posnien
- Center for Molecular Physiology of the Brain (CMPB), Göttingen Center of Molecular Biology, Caspari-Haus, Georg-August-University Göttingen, Göttingen, Germany
- School of Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Nikolaus Dieter Bernhard Koniszewski
- Center for Molecular Physiology of the Brain (CMPB), Göttingen Center of Molecular Biology, Caspari-Haus, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Gregor Bucher
- Center for Molecular Physiology of the Brain (CMPB), Göttingen Center of Molecular Biology, Caspari-Haus, Georg-August-University Göttingen, Göttingen, Germany
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Zehnder S, Schwaller P, von Arx U, Bucher G, Neuenschwander B. Micro structuring of transparent materials with NIR ns-laser pulses. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.phpro.2011.03.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Steinmetz PR, Urbach R, Posnien N, Eriksson J, Kostyuchenko RP, Brena C, Guy K, Akam M, Bucher G, Arendt D. Six3 demarcates the anterior-most developing brain region in bilaterian animals. EvoDevo 2010; 1:14. [PMID: 21190549 PMCID: PMC3025827 DOI: 10.1186/2041-9139-1-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 12/29/2010] [Indexed: 12/30/2023] Open
Abstract
Background The heads of annelids (earthworms, polychaetes, and others) and arthropods (insects, myriapods, spiders, and others) and the arthropod-related onychophorans (velvet worms) show similar brain architecture and for this reason have long been considered homologous. However, this view is challenged by the 'new phylogeny' placing arthropods and annelids into distinct superphyla, Ecdysozoa and Lophotrochozoa, together with many other phyla lacking elaborate heads or brains. To compare the organisation of annelid and arthropod heads and brains at the molecular level, we investigated head regionalisation genes in various groups. Regionalisation genes subdivide developing animals into molecular regions and can be used to align head regions between remote animal phyla. Results We find that in the marine annelid Platynereis dumerilii, expression of the homeobox gene six3 defines the apical region of the larval body, peripherally overlapping the equatorial otx+ expression. The six3+ and otx+ regions thus define the developing head in anterior-to-posterior sequence. In another annelid, the earthworm Pristina, as well as in the onychophoran Euperipatoides, the centipede Strigamia and the insects Tribolium and Drosophila, a six3/optix+ region likewise demarcates the tip of the developing animal, followed by a more posterior otx/otd+ region. Identification of six3+ head neuroectoderm in Drosophila reveals that this region gives rise to median neurosecretory brain parts, as is also the case in annelids. In insects, onychophorans and Platynereis, the otx+ region instead harbours the eye anlagen, which thus occupy a more posterior position. Conclusions These observations indicate that the annelid, onychophoran and arthropod head develops from a conserved anterior-posterior sequence of six3+ and otx+ regions. The six3+ anterior pole of the arthropod head and brain accordingly lies in an anterior-median embryonic region and, in consequence, the optic lobes do not represent the tip of the neuraxis. These results support the hypothesis that the last common ancestor of annelids and arthropods already possessed neurosecretory centres in the most anterior region of the brain. In light of its broad evolutionary conservation in protostomes and, as previously shown, in deuterostomes, the six3-otx head patterning system may be universal to bilaterian animals.
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Affiliation(s)
- Patrick Rh Steinmetz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany.,University of Vienna, Department for Molecular Evolution and Development, Althanstrasse 14, A-1090 Vienna, Austria
| | - Rolf Urbach
- Johannes Gutenberg-Universität Mainz, Institut für Genetik, J.-J.-Becher-Weg 32, 55128 Mainz, Germany
| | - Nico Posnien
- Johann-Friedrich-Blumenbach-Institute of Zoology, Anthropology and Developmental Biology, DFG Research Centre for Molecular Physiology of the Brain (CMPB), Georg August University, von-Liebig-Weg-11, 37077 Göttingen, Germany.,Vetmeduni Vienna, Institute of Population Genetics, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Joakim Eriksson
- University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK.,Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK
| | - Roman P Kostyuchenko
- Department of Embryology, State University of St. Petersburg, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Carlo Brena
- University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK
| | - Keren Guy
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Michael Akam
- University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK
| | - Gregor Bucher
- Johann-Friedrich-Blumenbach-Institute of Zoology, Anthropology and Developmental Biology, DFG Research Centre for Molecular Physiology of the Brain (CMPB), Georg August University, von-Liebig-Weg-11, 37077 Göttingen, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
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Posnien N, Schinko JB, Kittelmann S, Bucher G. Genetics, development and composition of the insect head--a beetle's view. Arthropod Struct Dev 2010; 39:399-410. [PMID: 20800703 DOI: 10.1016/j.asd.2010.08.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 08/08/2010] [Accepted: 08/15/2010] [Indexed: 05/29/2023]
Abstract
Many questions regarding evolution and ontogeny of the insect head remain open. Likewise, the genetic basis of insect head development is poorly understood. Recently, the investigation of gene expression data and the analysis of patterning gene function have revived interest in insect head development. Here, we argue that the red flour beetle Tribolium castaneum is a well suited model organism to spearhead research with respect to the genetic control of insect head development. We review recent molecular data and discuss its bearing on early development and morphogenesis of the head. We present a novel hypothesis on the ontogenetic origin of insect head sutures and review recent insights into the question on the origin of the labrum. Further, we argue that the study of developmental genes may identify the elusive anterior non-segmental region and present some evidence in favor of its existence. With respect to the question of evolution of patterning we show that the head Anlagen of the fruit fly Drosophila melanogaster and Tribolium differ considerably and we review profound differences of their genetic regulation. Finally, we discuss which insect model species might help us to answer the open questions concerning the genetic regulation of head development and its evolution.
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Affiliation(s)
- Nico Posnien
- Institute for Population Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, Vienna, Austria
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Posnien N, Koniszewski N, Bucher G. Insect Tc-six4 marks a unit with similarity to vertebrate placodes. Dev Biol 2010; 350:208-16. [PMID: 21034730 DOI: 10.1016/j.ydbio.2010.10.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 10/18/2010] [Accepted: 10/19/2010] [Indexed: 11/20/2022]
Abstract
Cranial placodes are specialized ectodermal regions in the developing vertebrate head that give rise to both neural and non-neural cell types of the neuroendocrine system and the sense organs of the visual, olfactory and acoustic systems. The cranial placodes develop from a panplacodal region which is specifically marked by genes of the eyes absent/eya and two "six homeobox" family members (sine oculis/six1 and six4). It had been believed that cranial placodes are evolutionary novelties of vertebrates. However, data from non-vertebrate chordates suggest that placode-like structures evolved in the chordate ancestor already. Here, we identify a morphological structure in the embryonic head of the beetle Tribolium castaneum with placode-like features. It is marked by the orthologs of the panplacodal markers Tc-six4, Tc-eya and Tc-sine oculis/six1 (Tc-six1) and expresses several genes known to be involved in adenohypophyseal placode development in vertebrates. Moreover, it contributes to both epidermal and neural tissues. We identify Tc-six4 as a specific marker for this structure that we term the insect head placode. Finally, we reveal the regulatory gene network of the panplacodal genes Tc-six4, Tc-eya and Tc-six1 and identify them as head epidermis patterning genes. Our finding of a placode-like structure in an insect suggests that a placode precursor was already present in the last common ancestor of bilaterian animals.
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Affiliation(s)
- Nico Posnien
- Center of Molecular Brain Physiology, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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Schinko J, Posnien N, Kittelmann S, Koniszewski N, Bucher G. Single and double whole-mount in situ hybridization in red flour beetle (Tribolium) embryos. Cold Spring Harb Protoc 2010; 2009:pdb.prot5258. [PMID: 20147234 DOI: 10.1101/pdb.prot5258] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Johannes Schinko
- Johann-Friedrich-Blumenbach Institute, Department of Developmental Biology, Georg-August-University Göttingen, 37077 Göttingen, Germany
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Schinko JB, Weber M, Viktorinova I, Kiupakis A, Averof M, Klingler M, Wimmer EA, Bucher G. Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters. BMC Dev Biol 2010; 10:53. [PMID: 20482875 PMCID: PMC2882914 DOI: 10.1186/1471-213x-10-53] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 05/19/2010] [Indexed: 12/05/2022]
Abstract
Background The red flour beetle Tribolium castaneum has developed into an insect model system second only to Drosophila. Moreover, as a coleopteran it represents the most species-rich metazoan taxon which also includes many pest species. The genetic toolbox for Tribolium research has expanded in the past years but spatio-temporally controlled misexpression of genes has not been possible so far. Results Here we report the establishment of the GAL4/UAS binary expression system in Tribolium castaneum. Both GAL4Δ and GAL4VP16 driven by the endogenous heat shock inducible promoter of the Tribolium hsp68 gene are efficient in activating reporter gene expression under the control of the Upstream Activating Sequence (UAS). UAS driven ubiquitous tGFP fluorescence was observed in embryos within four hours after activation while in-situ hybridization against tGFP revealed expression already after two hours. The response is quick in relation to the duration of embryonic development in Tribolium - 72 hours with segmentation being completed after 24 hours - which makes the study of early embryonic processes possible using this system. By comparing the efficiency of constructs based on Tribolium, Drosophila, and artificial core promoters, respectively, we find that the use of endogenous core promoters is essential for high-level expression of transgenic constructs. Conclusions With the established GAL4/UAS binary expression system, ectopic misexpression approaches are now feasible in Tribolium. Our results support the contention that high-level transgene expression usually requires endogenous regulatory sequences, including endogenous core promoters in Tribolium and probably also other model systems.
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Affiliation(s)
- Johannes B Schinko
- Ernst Caspari Haus, Georg-August-University Göttingen, Justus-von-Liebig-Weg11, 37077 Göttingen, Germany
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Posnien N, Bucher G. Formation of the insect head involves lateral contribution of the intercalary segment, which depends on Tc-labial function. Dev Biol 2009; 338:107-16. [PMID: 19913530 DOI: 10.1016/j.ydbio.2009.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 10/20/2009] [Accepted: 11/06/2009] [Indexed: 10/20/2022]
Abstract
The insect head is composed of several segments. During embryonic development, the segments fuse to form a rigid head capsule where obvious segmental boundaries are lacking. Hence, the assignment of regions of the insect head to specific segments is hampered, especially with respect to dorsal (vertex) and lateral (gena) parts. We show that upon Tribolium labial (Tc-lab) knock down, the intercalary segment is deleted but not transformed. Furthermore, we find that the intercalary segment contributes to lateral parts of the head cuticle in Tribolium. Based on several additional mutant and RNAi phenotypes that interfere with gnathal segment development, we show that these segments do not contribute to the dorsal head capsule apart from the dorsal ridge. Opposing the classical view but in line with findings in the vinegar fly Drosophila melanogaster and the milkweed bug Oncopeltus fasciatus, we propose a "bend and zipper" model for insect head capsule formation.
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Affiliation(s)
- Nico Posnien
- Department of Developmental Biology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg-August-University, 37077 Göttingen, Germany
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Trauner J, Schinko J, Lorenzen MD, Shippy TD, Wimmer EA, Beeman RW, Klingler M, Bucher G, Brown SJ. Large-scale insertional mutagenesis of a coleopteran stored grain pest, the red flour beetle Tribolium castaneum, identifies embryonic lethal mutations and enhancer traps. BMC Biol 2009; 7:73. [PMID: 19891766 PMCID: PMC2779179 DOI: 10.1186/1741-7007-7-73] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 11/05/2009] [Indexed: 11/26/2022] Open
Abstract
Background Given its sequenced genome and efficient systemic RNA interference response, the red flour beetle Tribolium castaneum is a model organism well suited for reverse genetics. Even so, there is a pressing need for forward genetic analysis to escape the bias inherent in candidate gene approaches. Results To produce easy-to-maintain insertional mutations and to obtain fluorescent marker lines to aid phenotypic analysis, we undertook a large-scale transposon mutagenesis screen. In this screen, we produced more than 6,500 new piggyBac insertions. Of these, 421 proved to be recessive lethal, 75 were semi-lethal, and eight indicated recessive sterility, while 505 showed new enhancer-trap patterns. Insertion junctions were determined for 403 lines and often appeared to be located within transcription units. Insertion sites appeared to be randomly distributed throughout the genome, with the exception of a preference for reinsertion near the donor site. Conclusion A large collection of enhancer-trap and embryonic lethal beetle lines has been made available to the research community and will foster investigations into diverse fields of insect biology, pest control, and evolution. Because the genetic elements used in this screen are species-nonspecific, and because the crossing scheme does not depend on balancer chromosomes, the methods presented herein should be broadly applicable for many insect species.
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Affiliation(s)
- Jochen Trauner
- 1Department of Biology, Developmental Biology, Friedrich-Alexander-University Erlangen, Erlangen, Germany.
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Yang X, Weber M, ZarinKamar N, Posnien N, Friedrich F, Wigand B, Beutel R, Damen WG, Bucher G, Klingler M, Friedrich M. Probing the Drosophila retinal determination gene network in Tribolium (II): The Pax6 genes eyeless and twin of eyeless. Dev Biol 2009; 333:215-27. [DOI: 10.1016/j.ydbio.2009.06.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 05/18/2009] [Accepted: 06/07/2009] [Indexed: 11/15/2022]
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Abstract
INTRODUCTIONTribolium castaneum is exceptionally amenable to gene knockdown by RNA interference (RNAi) which, in this insect, is systemic (spreading throughout the organism and to the next generation), highly penetrant, and able to phenocopy genetic null phenotypes. Hence, any gene function can be knocked down at any stage in (apparently) all tissues upon injection of double-stranded RNA (dsRNA). The RNAi effect is elicited both in the injected animal and, if female pupae or adults have been injected, transferred to the offspring. Embryonic RNAi (eRNAi) usually generates the strongest phenotypes in the injected individual, but suffers from elevated lethality caused by injection injury. Pupal RNAi (pRNAi), in which female pupae are injected and phenotypes scored in the offspring, is the easiest to perform. However, in some cases, the knockdown of a gene leads to sterility of the injected female. This problem can be circumvented in many cases by injecting adult females (aRNAi) or using eRNAi. In order to interfere with processes during metamorphosis, injection into last-stage larvae is used (lRNAi). Up to two genes in a single experiment have been successfully knocked down via RNAi. The inclusion of more than two genes usually leads to a dilution effect, which lowers phenotypic strength. This protocol describes the production of dsRNA from a polymerase chain reaction (PCR) template, injection procedures for each Tribolium life stage, and important controls for effective analysis.
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Affiliation(s)
- Nico Posnien
- Johann-Friedrich-Blumenbach Institute, Department of Developmental Biology, Georg-August-University Göttingen, 37077 Göttingen, Germany
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Brown SJ, Shippy TD, Miller S, Bolognesi R, Beeman RW, Lorenzen MD, Bucher G, Wimmer EA, Klingler M. The red flour beetle, Tribolium castaneum (Coleoptera): a model for studies of development and pest biology. Cold Spring Harb Protoc 2009; 2009:pdb.emo126. [PMID: 20147228 DOI: 10.1101/pdb.emo126] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
INTRODUCTIONTribolium castaneum is a small, low-maintenance beetle that has emerged as a sophisticated model system for studying the evolution of development and that complements (in some cases, even rivals) Drosophila for functional genetic analysis of basic biological questions. Although Tribolium and Drosophila are both holometabolous insects, they differ fundamentally in larval and adult morphology. Even generally conserved developmental features, such as body segmentation, are achieved by quite different means. Thus, comparison of developmental mechanisms between these two insects can address many interesting questions concerning the evolution of morphology and other characters. Genetic tools available for Tribolium include genetic maps for visible and molecular markers, chromosomal rearrangements that enable lethal mutations to be balanced in true-breeding stocks, transposon-based transformation systems, a completed and annotated genome sequence, and systemic RNA interference (RNAi), which makes it possible to knock down any given gene and even particular splice variants in the offspring or in any tissue of the injected animal. Inactivating gene functions at various developmental stages provides new opportunities to investigate post-embryonic development, as well as larval and adult physiology, including hormonal control, host-parasite interactions, and pesticide resistance.
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Affiliation(s)
- Susan J Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
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Witek A, Herlyn H, Meyer A, Boell L, Bucher G, Hankeln T. EST based phylogenomics of Syndermata questions monophyly of Eurotatoria. BMC Evol Biol 2008; 8:345. [PMID: 19113997 PMCID: PMC2654452 DOI: 10.1186/1471-2148-8-345] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 12/29/2008] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The metazoan taxon Syndermata comprising Rotifera (in the classical sense of Monogononta+Bdelloidea+Seisonidea) and Acanthocephala has raised several hypotheses connected to the phylogeny of these animal groups and the included subtaxa. While the monophyletic origin of Syndermata and Acanthocephala is well established based on morphological and molecular data, the phylogenetic position of Syndermata within Spiralia, the monophyletic origin of Monogononta, Bdelloidea, and Seisonidea and the acanthocephalan sister group are still a matter of debate. The comparison of the alternative hypotheses suggests that testing the phylogenetic validity of Eurotatoria (Monogononta+Bdelloidea) is the key to unravel the phylogenetic relations within Syndermata. The syndermatan phylogeny in turn is a prerequisite for reconstructing the evolution of the acanthocephalan endoparasitism. RESULTS Here we present our results from a phylogenomic approach studying i) the phylogenetic position of Syndermata within Spiralia, ii) the monophyletic origin of monogononts and bdelloids and iii) the phylogenetic relations of the latter two taxa to acanthocephalans. For this analysis we have generated EST libraries of Pomphorhynchus laevis, Echinorhynchus truttae (Acanthocephala) and Brachionus plicatilis (Monogononta). By extending these data with database entries of B. plicatilis, Philodina roseola (Bdelloidea) and 25 additional metazoan species, we conducted phylogenetic reconstructions based on 79 ribosomal proteins using maximum likelihood and bayesian approaches. Our findings suggest that the phylogenetic position of Syndermata within Spiralia is close to Platyhelminthes, that Eurotatoria are not monophyletic and that bdelloids are more closely related to acanthocephalans than monogononts. CONCLUSION Mapping morphological character evolution onto molecular phylogeny suggests the (partial or complete) reduction of the corona and the emergence of a retractable anterior end (rostrum, proboscis) before the separation of Acanthocephala. In particular, the evolution of a rostrum might have been a key event leading to the later evolution of the acanthocephalan endoparasitism, given the enormous relevance of the proboscis for anchoring of the adults to the definitive hosts' intestinal wall.
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Affiliation(s)
- Alexander Witek
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, J. J.-Becherweg 32, D-55099 Mainz, Germany
| | - Holger Herlyn
- Institute of Anthropology, Johannes Gutenberg-University Mainz, Colonel-Kleinmann-Weg 2, D-55099 Mainz, Germany
| | - Achim Meyer
- Institute of Zoology, Johannes Gutenberg-University Mainz, Müllerweg 6, D-55099 Mainz, Germany
| | - Louis Boell
- Johann Friedrich Blumenbach Institute of Anthropology and Zoology, Georg-August-University Göttingen, J. v. Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Gregor Bucher
- Johann Friedrich Blumenbach Institute of Anthropology and Zoology, Georg-August-University Göttingen, J. v. Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, J. J.-Becherweg 32, D-55099 Mainz, Germany
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Cerny AC, Grossmann D, Bucher G, Klingler M. The Tribolium ortholog of knirps and knirps-related is crucial for head segmentation but plays a minor role during abdominal patterning. Dev Biol 2008; 321:284-94. [DOI: 10.1016/j.ydbio.2008.05.527] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Revised: 05/08/2008] [Accepted: 05/09/2008] [Indexed: 12/01/2022]
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Boell LA, Bucher G. Whole-mount in situ hybridization in the rotifer Brachionus plicatilis representing a basal branch of lophotrochozoans. Dev Genes Evol 2008; 218:445-51. [PMID: 18594859 PMCID: PMC2490725 DOI: 10.1007/s00427-008-0234-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 06/10/2008] [Indexed: 12/02/2022]
Abstract
In order to broaden the comparative scope of evolutionary developmental biology and to refine our picture of animal macroevolution, it is necessary to establish new model organisms, especially from previously underrepresented groups, like the Lophotrochozoa. We have established the culture and protocols for molecular developmental biology in the rotifer species Brachionus plicatilis Müller (Rotifera, Monogononta). Rotifers are nonsegmented animals with enigmatic basal position within the lophotrochozoans and marked by several evolutionary novelties like the wheel organ (corona), the median eye, and the nonpaired posterior foot. The expression of Bp-Pax-6 is shown using whole-mount in situ hybridization. The inexpensive easy culture and experimental tractability of Brachionus as well as the range of interesting questions to which it holds the key make it a promising addition to the “zoo” of evo-devo model organisms.
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Affiliation(s)
- Louis A Boell
- Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Strasse 2, 24306, Plön, Germany
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Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJP, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DEK, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HMG, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJP, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KKO, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G. The genome of the model beetle and pest Tribolium castaneum. Nature 2008; 452:949-55. [PMID: 18362917 DOI: 10.1038/nature06784] [Citation(s) in RCA: 976] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 02/06/2008] [Indexed: 02/08/2023]
Abstract
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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Affiliation(s)
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- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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Schinko JB, Kreuzer N, Offen N, Posnien N, Wimmer EA, Bucher G. Divergent functions of orthodenticle, empty spiracles and buttonhead in early head patterning of the beetle Tribolium castaneum (Coleoptera). Dev Biol 2008; 317:600-13. [PMID: 18407258 DOI: 10.1016/j.ydbio.2008.03.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 03/03/2008] [Accepted: 03/04/2008] [Indexed: 01/08/2023]
Abstract
The head gap genes orthodenticle (otd), empty spiracles (ems) and buttonhead (btd) are required for metamerization and segment specification in Drosophila. We asked whether the function of their orthologs is conserved in the red flour beetle Tribolium castaneum which in contrast to Drosophila develops its larval head in a way typical for insects. We find that depending on dsRNA injection time, two functions of Tc-orthodenticle1 (Tc-otd1) can be identified. The early regionalization function affects all segments formed during the blastoderm stage while the later head patterning function is similar to Drosophila. In contrast, both expression and function of Tc-empty spiracles (Tc-ems) are restricted to the posterior part of the ocular and the anterior part of the antennal segment and Tc-buttonhead (Tc-btd) is not required for head cuticle formation at all. We conclude that the gap gene like roles of ems and btd are not conserved while at least the head patterning function of otd appears to be similar in fly and beetle. Hence, the ancestral mode of insect head segmentation remains to be discovered. With this work, we establish Tribolium as a model system for arthropod head development that does not suffer from the Drosophila specific problems like head involution and strongly reduced head structures.
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Affiliation(s)
- Johannes B Schinko
- Department of Developmental Biology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg-August-University Göttingen, Germany
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Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D, Bucher G. Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium. Genome Biol 2008; 9:R10. [PMID: 18201385 PMCID: PMC2395250 DOI: 10.1186/gb-2008-9-1-r10] [Citation(s) in RCA: 396] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 11/13/2007] [Accepted: 01/17/2008] [Indexed: 12/13/2022] Open
Abstract
Tribolium resembles C. elegans in showing a robust systemic RNAi response, but does not have C. elegans-type RNAi mechanisms; insect systemic RNAi probably uses a different mechanism. Background RNA interference (RNAi) is a highly conserved cellular mechanism. In some organisms, such as Caenorhabditis elegans, the RNAi response can be transmitted systemically. Some insects also exhibit a systemic RNAi response. However, Drosophila, the leading insect model organism, does not show a robust systemic RNAi response, necessitating another model system to study the molecular mechanism of systemic RNAi in insects. Results We used Tribolium, which exhibits robust systemic RNAi, as an alternative model system. We have identified the core RNAi genes, as well as genes potentially involved in systemic RNAi, from the Tribolium genome. Both phylogenetic and functional analyses suggest that Tribolium has a somewhat larger inventory of core component genes than Drosophila, perhaps allowing a more sensitive response to double-stranded RNA (dsRNA). We also identified three Tribolium homologs of C. elegans sid-1, which encodes a possible dsRNA channel. However, detailed sequence analysis has revealed that these Tribolium homologs share more identity with another C. elegans gene, tag-130. We analyzed tag-130 mutants, and found that this gene does not have a function in systemic RNAi in C. elegans. Likewise, the Tribolium sid-like genes do not seem to be required for systemic RNAi. These results suggest that insect sid-1-like genes have a different function than dsRNA uptake. Moreover, Tribolium lacks homologs of several genes important for RNAi in C. elegans. Conclusion Although both Tribolium and C. elegans show a robust systemic RNAi response, our genome-wide survey reveals significant differences between the RNAi mechanisms of these organisms. Thus, insects may use an alternative mechanism for the systemic RNAi response. Understanding this process would assist with rendering other insects amenable to systemic RNAi, and may influence pest control approaches.
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Affiliation(s)
- Yoshinori Tomoyasu
- Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA.
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