1
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Benvenuto G, Leone S, Astoricchio E, Bormke S, Jasek S, D'Aniello E, Kittelmann M, McDonald K, Hartenstein V, Baena V, Escrivà H, Bertrand S, Schierwater B, Burkhardt P, Ruiz-Trillo I, Jékely G, Ullrich-Lüter J, Lüter C, D'Aniello S, Arnone MI, Ferraro F. Evolution of the ribbon-like organization of the Golgi apparatus in animal cells. Cell Rep 2024; 43:113791. [PMID: 38428420 DOI: 10.1016/j.celrep.2024.113791] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024] Open
Abstract
The "ribbon," a structural arrangement in which Golgi stacks connect to each other, is considered to be restricted to vertebrate cells. Although ribbon disruption is linked to various human pathologies, its functional role in cellular processes remains unclear. In this study, we investigate the evolutionary origin of the Golgi ribbon. We observe a ribbon-like architecture in the cells of several metazoan taxa suggesting its early emergence in animal evolution predating the appearance of vertebrates. Supported by AlphaFold2 modeling, we propose that the evolution of Golgi reassembly and stacking protein (GRASP) binding by golgin tethers may have driven the joining of Golgi stacks resulting in the ribbon-like configuration. Additionally, we find that Golgi ribbon assembly is a shared developmental feature of deuterostomes, implying a role in embryogenesis. Overall, our study points to the functional significance of the Golgi ribbon beyond vertebrates and underscores the need for further investigations to unravel its elusive biological roles.
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Affiliation(s)
- Giovanna Benvenuto
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Serena Leone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Emanuele Astoricchio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | | | - Sanja Jasek
- Living Systems Institute, University of Exeter, Exeter, UK; Heidelberg University, Centre for Organismal Studies (COS), Heidelberg, Germany
| | - Enrico D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Maike Kittelmann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Kent McDonald
- Electron Microscope Lab, University of California Berkeley, Berkeley, CA, USA
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Valentina Baena
- Department of Cell Biology, UConn Health, Farmington, CT, USA
| | - Héctor Escrivà
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, France
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-Mer, France
| | - Bernd Schierwater
- Institute of Ecology and Evolution, Hannover University of Veterinary Medicine Foundation, Hannover, Germany
| | | | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Exeter, UK; Heidelberg University, Centre for Organismal Studies (COS), Heidelberg, Germany
| | | | | | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy
| | - Francesco Ferraro
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn (SZN), Naples, Italy.
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2
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Najle SR, Grau-Bové X, Elek A, Navarrete C, Cianferoni D, Chiva C, Cañas-Armenteros D, Mallabiabarrena A, Kamm K, Sabidó E, Gruber-Vodicka H, Schierwater B, Serrano L, Sebé-Pedrós A. Stepwise emergence of the neuronal gene expression program in early animal evolution. Cell 2023; 186:4676-4693.e29. [PMID: 37729907 PMCID: PMC10580291 DOI: 10.1016/j.cell.2023.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/13/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
The assembly of the neuronal and other major cell type programs occurred early in animal evolution. We can reconstruct this process by studying non-bilaterians like placozoans. These small disc-shaped animals not only have nine morphologically described cell types and no neurons but also show coordinated behaviors triggered by peptide-secreting cells. We investigated possible neuronal affinities of these peptidergic cells using phylogenetics, chromatin profiling, and comparative single-cell genomics in four placozoans. We found conserved cell type expression programs across placozoans, including populations of transdifferentiating and cycling cells, suggestive of active cell type homeostasis. We also uncovered fourteen peptidergic cell types expressing neuronal-associated components like the pre-synaptic scaffold that derive from progenitor cells with neurogenesis signatures. In contrast, earlier-branching animals like sponges and ctenophores lacked this conserved expression. Our findings indicate that key neuronal developmental and effector gene modules evolved before the advent of cnidarian/bilaterian neurons in the context of paracrine cell signaling.
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Affiliation(s)
- Sebastián R Najle
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Chiva
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Didac Cañas-Armenteros
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Arrate Mallabiabarrena
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Bremen, Germany; Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany; American Museum of Natural History, Richard Gilder Graduate School, NY, USA
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain.
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3
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Tessler M, Galen SC, DeSalle R, Schierwater B. Let’s end taxonomic blank slates with molecular morphology. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016412] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved.
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4
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Tessler M, Neumann JS, Kamm K, Osigus HJ, Eshel G, Narechania A, Burns JA, DeSalle R, Schierwater B. Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Placozoa is an ancient phylum of extraordinarily unusual animals: miniscule, ameboid creatures that lack most fundamental animal features. Despite high genetic diversity, only recently have the second and third species been named. While prior genomic studies suffer from incomplete placozoan taxon sampling, we more than double the count with protein sequences from seven key genomes and produce the first nuclear phylogenomic reconstruction of all major placozoan lineages. This leads us to the first complete Linnaean taxonomic classification of Placozoa, over a century after its discovery: This may be the only time in the 21st century when an entire higher taxonomy for a whole animal phylum is formalized. Our classification establishes 2 new classes, 4 new orders, 3 new families, 1 new genus, and 1 new species, namely classes Polyplacotomia and Uniplacotomia; orders Polyplacotomea, Trichoplacea, Cladhexea, and Hoilungea; families Polyplacotomidae, Cladtertiidae, and Hoilungidae; and genus Cladtertia with species Cladtertia collaboinventa, nov. Our likelihood and gene content tree topologies refine the relationships determined in previous studies. Adding morphological data into our phylogenomic matrices suggests sponges (Porifera) as the sister to other animals, indicating that modest data addition shifts this node away from comb jellies (Ctenophora). Furthermore, by adding the first genomic protein data of the exceptionally distinct and branching Polyplacotoma mediterranea, we solidify its position as sister to all other placozoans; a divergence we estimate to be over 400 million years old. Yet even this deep split sits on a long branch to other animals, suggesting a bottleneck event followed by diversification. Ancestral state reconstructions indicate large shifts in gene content within Placozoa, with Hoilungia hongkongensis and its closest relatives having the most unique genetics.
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5
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Wright BA, Kvansakul M, Schierwater B, Humbert PO. Cell polarity signalling at the birth of multicellularity: What can we learn from the first animals. Front Cell Dev Biol 2022; 10:1024489. [PMID: 36506100 PMCID: PMC9729800 DOI: 10.3389/fcell.2022.1024489] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
The innovation of multicellularity has driven the unparalleled evolution of animals (Metazoa). But how is a multicellular organism formed and how is its architecture maintained faithfully? The defining properties and rules required for the establishment of the architecture of multicellular organisms include the development of adhesive cell interactions, orientation of division axis, and the ability to reposition daughter cells over long distances. Central to all these properties is the ability to generate asymmetry (polarity), coordinated by a highly conserved set of proteins known as cell polarity regulators. The cell polarity complexes, Scribble, Par and Crumbs, are considered to be a metazoan innovation with apicobasal polarity and adherens junctions both believed to be present in all animals. A better understanding of the fundamental mechanisms regulating cell polarity and tissue architecture should provide key insights into the development and regeneration of all animals including humans. Here we review what is currently known about cell polarity and its control in the most basal metazoans, and how these first examples of multicellular life can inform us about the core mechanisms of tissue organisation and repair, and ultimately diseases of tissue organisation, such as cancer.
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Affiliation(s)
- Bree A. Wright
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marc Kvansakul
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia
| | - Bernd Schierwater
- Institute of Animal Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg, Hannover, Germany
| | - Patrick O. Humbert
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, VIC, Australia,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia,*Correspondence: Patrick O. Humbert,
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6
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Flom H, Adamska M, Lami R, Gazave E, D'Aniello S, Schierwater B, Boutet A. Digital Marine: An online platform for blended learning in a marine experimental biology module, the Schmid Training Course. Bioessays 2022; 44:e2100264. [DOI: 10.1002/bies.202100264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Haley Flom
- Sorbonne Université (SU) Centre National de la Recherche Scientifique (CNRS) Fédération de Recherche FR3724 Observatoire Océanologique de Banyuls‐sur‐Mer (OOB) France
| | - Maja Adamska
- Research School of Biology Australian National University (ANU) Canberra Australia
| | - Raphaël Lami
- Sorbonne Université CNRS Laboratoire de Biodiversité et Biotechnologies Microbiennes USR3579 Observatoire Océanologique de Banyuls‐sur‐Mer (OOB) France
| | - Eve Gazave
- Université de Paris CNRS Institut Jacques Monod Paris France
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM) Stazione Zoologica Anton Dohrn Napoli Italy
| | | | - Agnès Boutet
- SU, CNRS Integrative Biology of Marine Models (LBI2M) France
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7
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Osigus HJ, Eitel M, Horn K, Kamm K, Kosubek-Langer J, Schmidt MJ, Hadrys H, Schierwater B. Studying Placozoa WBR in the Simplest Metazoan Animal, Trichoplax adhaerens. Methods Mol Biol 2022; 2450:121-133. [PMID: 35359305 PMCID: PMC9761494 DOI: 10.1007/978-1-0716-2172-1_6] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Placozoans are a promising model system to study fundamental regeneration processes in a morphologically and genetically very simple animal. We here provide a brief introduction to the enigmatic Placozoa and summarize the state of the art of animal handling and experimental manipulation possibilities.
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Affiliation(s)
- Hans-Jürgen Osigus
- Institut für Tierökologie, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, GeoBio-Center, Ludwig-Maximilians Universität München, Munich, Germany
| | - Karolin Horn
- Institut für Tierökologie, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Kai Kamm
- Institut für Tierökologie, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Jennifer Kosubek-Langer
- Institut für Tierökologie, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
- Department of Animal Behavior, Freie Universität Berlin, Berlin, Germany
| | | | - Heike Hadrys
- Institut für Tierökologie, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Bernd Schierwater
- Institut für Tierökologie, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany.
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8
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Nanda S, Chon TY, Mahapatra S, Lindeen SA, Fischer KM, Krüger M, Schierwater B, Schmidt CO, Wahner-Roedler DL, Bauer BA. Preventiometer, a Novel Wellness Assessment Device, Used With Healthy Volunteers: A Phase 2 Study. Glob Adv Health Med 2021; 10:21649561211045016. [PMID: 34840917 PMCID: PMC8619782 DOI: 10.1177/21649561211045016] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background We previously reported on a pilot study to assess the incorporation of a novel wellness assessment device, the Preventiometer (iPEx5 GmbH, Greifswald, Germany), into an academic medical practice. The present follow-up study expands on those data and evaluates the acceptability of the assessment process in a larger sample population. Objective The aim of this study was to evaluate participant satisfaction with the Preventiometer wellness assessment. Methods A total of 60 healthy volunteers participated. Each participant underwent a comprehensive wellness assessment with the Preventiometer and received data from more than 30 diagnostic tests. A 32-question survey (with a numeric rating scale from 0 to 10) was used to rate the wellness assessment tests and participants' impressions of the wellness assessment. Results Each assessment had a significantly higher rating than 7 (P < .001), and the majority of participants agreed or strongly agreed that they were satisfied (98.3%), and they strongly agreed that they were engaged the entire time (93.2%), and liked the instant test results feature of the Preventiometer device (93.2%). Conclusion This study confirms findings from our previous pilot study regarding the feasibility of the Preventiometer as a wellness assessment tool. The study further demonstrated that 98% of participants were satisfied with the assessment and that all of them would recommend it to others.
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Affiliation(s)
| | - Tony Y Chon
- Division of General Internal Medicine, MN, USA
| | | | | | | | - Markus Krüger
- Institute for Community Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Oral Health, Universitätsmedizin Greifswald, Germany
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9
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Schierwater B, Osigus HJ, Bergmann T, Blackstone NW, Hadrys H, Hauslage J, Humbert PO, Kamm K, Kvansakul M, Wysocki K, DeSalle R. The enigmatic Placozoa part 2: Exploring evolutionary controversies and promising questions on earth and in space. Bioessays 2021; 43:e2100083. [PMID: 34490659 DOI: 10.1002/bies.202100083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/21/2021] [Accepted: 08/16/2021] [Indexed: 12/28/2022]
Abstract
The placozoan Trichoplax adhaerens has been bridging gaps between research disciplines like no other animal. As outlined in part 1, placozoans have been subject of hot evolutionary debates and placozoans have challenged some fundamental evolutionary concepts. Here in part 2 we discuss the exceptional genetics of the phylum Placozoa and point out some challenging model system applications for the best known species, Trichoplax adhaerens.
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Affiliation(s)
- Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Hans-Jürgen Osigus
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Tjard Bergmann
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Heike Hadrys
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jens Hauslage
- Gravitational Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Patrick O Humbert
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, Australia
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, Australia
| | - Kathrin Wysocki
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Rob DeSalle
- American Museum of Natural History, New York, New York, USA
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10
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Schierwater B, Osigus HJ, Bergmann T, Blackstone NW, Hadrys H, Hauslage J, Humbert PO, Kamm K, Kvansakul M, Wysocki K, DeSalle R. The enigmatic Placozoa part 1: Exploring evolutionary controversies and poor ecological knowledge. Bioessays 2021; 43:e2100080. [PMID: 34472126 DOI: 10.1002/bies.202100080] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/21/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
The placozoan Trichoplax adhaerens is a tiny hairy plate and more simply organized than any other living metazoan. After its original description by F.E. Schulze in 1883, it attracted attention as a potential model for the ancestral state of metazoan organization, the "Urmetazoon". Trichoplax lacks any kind of symmetry, organs, nerve cells, muscle cells, basal lamina, and extracellular matrix. Furthermore, the placozoan genome is the smallest (not secondarily reduced) genome of all metazoan genomes. It harbors a remarkably rich diversity of genes and has been considered the best living surrogate for a metazoan ancestor genome. The phylum Placozoa presently harbors three formally described species, while several dozen "cryptic" species are yet awaiting their description. The phylogenetic position of placozoans has recently become a contested arena for modern phylogenetic analyses and view-driven claims. Trichoplax offers unique prospects for understanding the minimal requirements of metazoan animal organization and their corresponding malfunctions.
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Affiliation(s)
- Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Hans-Jürgen Osigus
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Tjard Bergmann
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Heike Hadrys
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jens Hauslage
- Gravitational Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Patrick O Humbert
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Kathrin Wysocki
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Rob DeSalle
- American Museum of Natural History, New York, New York, USA
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11
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Neumann JS, Desalle R, Narechania A, Schierwater B, Tessler M. Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets. Syst Biol 2021; 70:360-375. [PMID: 32462193 PMCID: PMC7875439 DOI: 10.1093/sysbio/syaa038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 12/19/2022] Open
Abstract
There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10$\times $ in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.].
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Affiliation(s)
- Johannes S Neumann
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Rob Desalle
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Bernd Schierwater
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
- ITZ, Division of Ecology and Evolution, Tierärztliche Hochschule Hannover, Bünteweg 9, 30559 Hannover, Germany
| | - Michael Tessler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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12
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Miyazawa H, Osigus HJ, Rolfes S, Kamm K, Schierwater B, Nakano H. Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions. Genome Biol Evol 2020; 13:5919586. [PMID: 33031489 PMCID: PMC7813641 DOI: 10.1093/gbe/evaa213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Accepted: 09/30/2020] [Indexed: 12/16/2022] Open
Abstract
Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32–43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon–intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.
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Affiliation(s)
- Hideyuki Miyazawa
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan.,Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Hans-Jürgen Osigus
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Sarah Rolfes
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Kai Kamm
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Bernd Schierwater
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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13
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Popgeorgiev N, Sa JD, Jabbour L, Banjara S, Nguyen TTM, Akhavan-E-Sabet A, Gadet R, Ralchev N, Manon S, Hinds MG, Osigus HJ, Schierwater B, Humbert PO, Rimokh R, Gillet G, Kvansakul M. Ancient and conserved functional interplay between Bcl-2 family proteins in the mitochondrial pathway of apoptosis. Sci Adv 2020; 6:6/40/eabc4149. [PMID: 32998881 PMCID: PMC7527217 DOI: 10.1126/sciadv.abc4149] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/10/2020] [Indexed: 06/10/2023]
Abstract
In metazoans, Bcl-2 family proteins are major regulators of mitochondrially mediated apoptosis; however, their evolution remains poorly understood. Here, we describe the molecular characterization of the four members of the Bcl-2 family in the most primitive metazoan, Trichoplax adhaerens All four trBcl-2 homologs are multimotif Bcl-2 group, with trBcl-2L1 and trBcl-2L2 being highly divergent antiapoptotic Bcl-2 members, whereas trBcl-2L3 and trBcl-2L4 are homologs of proapoptotic Bax and Bak, respectively. trBax expression permeabilizes the mitochondrial outer membrane, while trBak operates as a BH3-only sensitizer repressing antiapoptotic activities of trBcl-2L1 and trBcl-2L2. The crystal structure of a trBcl-2L2:trBak BH3 complex reveals that trBcl-2L2 uses the canonical Bcl-2 ligand binding groove to sequester trBak BH3, indicating that the structural basis for apoptosis control is conserved from T. adhaerens to mammals. Finally, we demonstrate that both trBax and trBak BH3 peptides bind selectively to human Bcl-2 homologs to sensitize cancer cells to chemotherapy treatment.
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Affiliation(s)
- Nikolay Popgeorgiev
- Université de Lyon, Centre de recherche en cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France.
| | - Jaison D Sa
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Lea Jabbour
- Université de Lyon, Centre de recherche en cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France
| | - Suresh Banjara
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Trang Thi Minh Nguyen
- Université de Lyon, Centre de recherche en cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France
| | - Aida Akhavan-E-Sabet
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Rudy Gadet
- Université de Lyon, Centre de recherche en cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France
| | - Nikola Ralchev
- Université de Lyon, Centre de recherche en cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France
| | - Stéphen Manon
- Institut de Biochimie et de Génétique Cellulaires, UMR5095, CNRS et Université de Bordeaux, CS61390, 1 Rue Camille Saint-Saëns, 33000 Bordeaux, France
| | - Mark G Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne 3050, Australia
| | - Hans-Jürgen Osigus
- Institute of Animal Ecology, Division of Molecular Evolution, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Bernd Schierwater
- Institute of Animal Ecology, Division of Molecular Evolution, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Patrick O Humbert
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Ruth Rimokh
- Université de Lyon, Centre de recherche en cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France
| | - Germain Gillet
- Université de Lyon, Centre de recherche en cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France.
| | - Marc Kvansakul
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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14
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Abstract
The enigmatic phylum Placozoa is harboring an unknown number of cryptic species and has become a challenge for modern systematics. Only recently, a second species has been described [1], while the presence of more than a hundred additional species has been suggested [2]. The original placozoan species Trichoplax adhaerens[3], the second species Hoilungia hongkongensis[1] and all yet undescribed species are morphologically indistinguishable (i.e. no species diagnostic characters are available [4]). Here, we report on a new placozoan species, Polyplacotoma mediterranea gen. nov., spec. nov., which differs from other placozoans in its completely different morphological habitus, including long polytomous body branches and a maximum body length of more than 10 mm. Polyplacotoma mediterranea also necessitates a different view of placozoan mitochondrial genetics. P. mediterranea harbors a highly compact mitochondrial genome with overlapping mitochondrial tRNA and protein coding genes. Furthermore, the new species lacks typical placozoan features, including the cox1 micro exon and cox1 barcode intron. As phylogenetic analyses suggest a sister group relationship of P. mediterranea to all other placozoans, this new species may also be relevant for studies addressing the relationships at the base of the metazoan tree of life.
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Affiliation(s)
- Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany.
| | - Sarah Rolfes
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany
| | - Rebecca Herzog
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany
| | - Kai Kamm
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany
| | - Bernd Schierwater
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany; American Museum of Natural History, Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, New York, NY, USA; Yale University, Department of Ecology & Evolutionary Biology, New Haven, CT, USA.
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15
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Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B. Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits. Sci Rep 2019; 9:17561. [PMID: 31772223 PMCID: PMC6879607 DOI: 10.1038/s41598-019-54037-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 01/25/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
Symbiotic relationships between eukaryotic hosts and bacteria range from parasitism to mutualism and may deeply influence both partners' fitness. The presence of intracellular bacteria in the metazoan phylum Placozoa has been reported several times, but without any knowledge about the nature of this relationship and possible implications for the placozoan holobiont. This information may be of crucial significance since little is known about placozoan ecology and how different species adapt to different environmental conditions, despite being almost invariable at the morphological level. We here report on the novel genome of the rickettsial endosymbiont of Trichoplax sp. H2 (strain "Panama"). The combination of eliminated and retained metabolic pathways of the bacterium indicates a potential for a mutualistic as well as for a parasitic relationship, whose outcome could depend on the environmental context. In particular we show that the endosymbiont is dependent on the host for growth and reproduction and that the latter could benefit from a supply with essential amino acids and important cofactors. These findings call for further studies to clarify the actual benefit for the placozoan host and to investigate a possible role of the endosymbiont for ecological separation between placozoan species.
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Affiliation(s)
- Kai Kamm
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany.
| | - Hans-Jürgen Osigus
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Bernd Schierwater
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany. .,Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA.
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16
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Nanda S, Mahapatra S, Lindeen SA, Bernau JL, Cutshall SM, Schierwater B, Chon TY, Wahner-Roedler DL, Bauer BA. Evaluation of a Novel Wellness Assessment Device (Preventiometer): A Feasibility Pilot Study. Glob Adv Health Med 2019; 8:2164956119881096. [PMID: 31637111 PMCID: PMC6785912 DOI: 10.1177/2164956119881096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/08/2019] [Revised: 08/14/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022] Open
Abstract
Background Periodic wellness assessments can provide an estimate of a person’s relative risks for major diseases, but wellness visits are underused. Our suggestion is to use a comprehensive device during a single visit. Objective The goal of this pilot study was to evaluate the feasibility of a novel one-stop wellness device (Preventiometer; iPEx5 GmbH, Greifswald, Germany) for performing multiple tests and providing a comprehensive wellness assessment in a short period. Methods A Preventiometer was used to provide wellness assessments for 10 healthy volunteers who then answered a 25-question survey to rate their satisfaction with the testing and their overall impression. Results All volunteers agreed or strongly agreed with the following: The assessment reports were easy to understand, the Preventiometer met their satisfaction, the participants were comfortable during the assessment, and all measurements and testing were well coordinated. Participants liked the instant test result feature. Most (90%) agreed that the machine was useful for a quick health assessment for busy people, and 70% felt that it was time efficient. Conclusion In this feasibility pilot study, the Preventiometer performed multiple tasks and provided a comprehensive wellness assessment in a short period. Participants reported remarkably high satisfaction with the tests. A larger study is needed to prove that this is a pragmatic approach to help individuals improve their health.
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Affiliation(s)
- Sanjeev Nanda
- Division of General Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Saswati Mahapatra
- Division of General Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | | | | | - Susanne M Cutshall
- Division of General Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Tony Y Chon
- Division of General Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Brent A Bauer
- Division of General Internal Medicine, Mayo Clinic, Rochester, Minnesota.,Center For Innovation, Mayo Clinic, Rochester, Minnesota
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17
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Blackstone N, Bridge D, Cartwright P, Hadrys H, Schierwater B. Germline evo-devo - a history in two steps. Nature 2019; 573:34. [PMID: 31481783 DOI: 10.1038/d41586-019-02609-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Abstract
Schierwater & DeSalle introduce the enigmatic phylum Placozoa.
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Affiliation(s)
- Bernd Schierwater
- TiHo Hannover, ITZ Ecology & Evolution, Buenteweg 17d, 30559 Hannover.
| | - Rob DeSalle
- Comparative Genomics Institute at the American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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19
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Abstract
BACKGROUND Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our knowledge about innate immunity stems from a few animal model systems, but substantial variation between metazoan phyla has been revealed by comparative genomic studies. The exploration of more taxa is still needed to better understand the evolution of immunity related mechanisms. Placozoans are morphologically the simplest organized metazoans and the association between these enigmatic animals and their rickettsial endosymbionts has recently been elucidated. Our analyses of the novel placozoan nuclear genome of Trichoplax sp. H2 and its associated rickettsial endosymbiont genome clearly pointed to a mutualistic and co-evolutionary relationship. This discovery raises the question of how the placozoan holobiont manages symbiosis and, conversely, how it defends against harmful microorganisms. In this study, we examined the annotated genome of Trichoplax sp. H2 for the presence of genes involved in innate immune recognition and downstream signaling. RESULTS A rich repertoire of genes belonging to the Toll-like and NOD-like receptor pathways, to scavenger receptors and to secreted fibrinogen-related domain genes was identified in the genome of Trichoplax sp. H2. Nevertheless, the innate immunity related pathways in placozoans deviate in several instances from well investigated vertebrates and invertebrates. While true Toll- and NOD-like receptors are absent, the presence of many genes of the downstream signaling cascade suggests at least primordial Toll-like receptor signaling in Placozoa. An abundance of scavenger receptors, fibrinogen-related domain genes and Apaf-1 genes clearly constitutes an expansion of the immunity related gene repertoire specific to Placozoa. CONCLUSIONS The found wealth of immunity related genes present in Placozoa is surprising and quite striking in light of the extremely simple placozoan body plan and their sparse cell type makeup. Research is warranted to reveal how Placozoa utilize this immune repertoire to manage and maintain their associated microbiota as well as to fend-off pathogens.
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Affiliation(s)
- Kai Kamm
- ITZ Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17d, D-30559 Hannover, Germany
| | - Bernd Schierwater
- ITZ Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17d, D-30559 Hannover, Germany
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
- Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
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20
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Gul IS, Staal J, Hulpiau P, De Keuckelaere E, Kamm K, Deroo T, Sanders E, Staes K, Driege Y, Saeys Y, Beyaert R, Technau U, Schierwater B, van Roy F. GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines. Genome Biol Evol 2018; 10:909-917. [PMID: 29608715 PMCID: PMC5952964 DOI: 10.1093/gbe/evy040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Accepted: 02/20/2018] [Indexed: 01/20/2023] Open
Abstract
With the genomes available for many animal clades, including the early-branching metazoans, one can readily study the functional conservation of genes across a diversity of animal lineages. Ectopic expression of an animal protein in, for instance, a mammalian cell line is a generally used strategy in structure–function analysis. However, this might turn out to be problematic in case of distantly related species. Here we analyzed the GC content of the coding sequences of basal animals and show its impact on gene expression levels in human cell lines, and, importantly, how this expression efficiency can be improved. Optimization of the GC3 content in the coding sequences of cadherin, alpha-catenin, and paracaspase of Trichoplax adhaerens dramatically increased the expression of these basal animal genes in human cell lines.
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Affiliation(s)
- Ismail Sahin Gul
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Jens Staal
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Paco Hulpiau
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Evi De Keuckelaere
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Kai Kamm
- Institut für Tierökologie und Zellbiologie (ITZ), Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
| | - Tom Deroo
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Ellen Sanders
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Katrien Staes
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Yasmine Driege
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Yvan Saeys
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Ulrich Technau
- Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Austria
| | - Bernd Schierwater
- Institut für Tierökologie und Zellbiologie (ITZ), Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
| | - Frans van Roy
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
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21
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Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G. Correction: Comparative genomics and the nature of placozoan species. PLoS Biol 2018; 16:e3000032. [PMID: 30231017 PMCID: PMC6145499 DOI: 10.1371/journal.pbio.3000032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pbio.2005359.].
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22
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Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B. Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction. Sci Rep 2018; 8:11168. [PMID: 30042472 PMCID: PMC6057997 DOI: 10.1038/s41598-018-29400-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
The phylum Placozoa officially consists of only a single described species, Trichoplax adhaerens, although several lineages can be separated by molecular markers, geographical distributions and environmental demands. The placozoan 16S haplotype H2 (Trichoplax sp. H2) is the most robust and cosmopolitan lineage of placozoans found to date. In this study, its genome was found to be distinct but highly related to the Trichoplax adhaerens reference genome, for remarkably unique reasons. The pattern of variation and allele distribution between the two lineages suggests that both originate from a single interbreeding event in the wild, dating back at least several decades ago, and both seem not to have engaged in sexual reproduction since. We conclude that populations of certain placozoan haplotypes remain stable for long periods without bisexual reproduction. Furthermore, allelic variation within and between the two Trichoplax lineages indicates that successful bisexual reproduction between related placozoan lineages might serve to either counter accumulated negative somatic mutations or to cope with changing environmental conditions. On the other hand, enrichment of neutral or beneficial somatic mutations by vegetative reproduction, combined with rare sexual reproduction, could instantaneously boost genetic variation, generating novel ecotypes and eventually species.
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Affiliation(s)
- Kai Kamm
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany.
| | - Hans-Jürgen Osigus
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Bernd Schierwater
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany. .,Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA. .,Yale University, Molecular, Cellular and Developmental Biology, New Haven, CT, 06520, USA.
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23
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Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G. Comparative genomics and the nature of placozoan species. PLoS Biol 2018; 16:e2005359. [PMID: 30063702 PMCID: PMC6067683 DOI: 10.1371/journal.pbio.2005359] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 01/05/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites.
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Affiliation(s)
- Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Frédérique Varoqueaux
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gray A. Williams
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Bernd Schierwater
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Ecology & Evolution, Yale University, New Haven, Connecticut, United States of America
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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Novotný JP, Chughtai AA, Kostrouchová M, Kostrouchová V, Kostrouch D, Kaššák F, Kaňa R, Schierwater B, Kostrouchová M, Kostrouch Z. Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9- cis-retinoic acid at the base of metazoan evolution. PeerJ 2017; 5:e3789. [PMID: 28975052 PMCID: PMC5624297 DOI: 10.7717/peerj.3789] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 04/21/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022] Open
Abstract
Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely orthologue of RXR (NR2B), HNF4 (NR2A), COUP-TF (NR2F) and ERR (NR3B) that show a high degree of similarity with human orthologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70% in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens orthologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has a profound effect on T. adhaerens growth and appearance. We show that nanomolar concentrations of 9-cis-RA interfere with T. adhaerens growth response to specific algal food and causes growth arrest. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution.
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Affiliation(s)
- Jan Philipp Novotný
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Medicine V., University of Heidelberg, Heidelberg, Germany
| | - Ahmed Ali Chughtai
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Markéta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - David Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Filip Kaššák
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Radek Kaňa
- Institute of Microbiology, Laboratory of Photosynthesis, Czech Academy of Sciences, Třeboň, Czech Republic
| | - Bernd Schierwater
- Institute for Animal Ecology and Cell Biology, University of Veterinary Medicine, Hannover, Germany.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Marta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Zdenek Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
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25
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Osigus HJ, Eitel M, Schierwater B. Deep RNA sequencing reveals the smallest known mitochondrial micro exon in animals: The placozoan cox1 single base pair exon. PLoS One 2017; 12:e0177959. [PMID: 28542197 PMCID: PMC5436844 DOI: 10.1371/journal.pone.0177959] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 05/05/2017] [Indexed: 11/18/2022] Open
Abstract
The phylum Placozoa holds a key position for our understanding of the evolution of mitochondrial genomes in Metazoa. Placozoans possess large mitochondrial genomes which harbor several remarkable characteristics such as a fragmented cox1 gene and trans-splicing cox1 introns. A previous study also suggested the existence of cox1 mRNA editing in Trichoplax adhaerens, yet the only formally described species in the phylum Placozoa. We have analyzed RNA-seq data of the undescribed sister species, Placozoa sp. H2 ("Panama" clone), with special focus on the mitochondrial mRNA. While we did not find support for a previously postulated cox1 mRNA editing mechanism, we surprisingly found two independent transcripts representing intermediate cox1 mRNA splicing stages. Both transcripts consist of partial cox1 exon as well as overlapping intron fragments. The data suggest that the cox1 gene harbors a single base pair (cytosine) micro exon. Furthermore, conserved group I intron structures flank this unique micro exon also in other placozoans. We discuss the evolutionary origin of this micro exon in the context of a self-splicing intron gain in the cox1 gene of the last common ancestor of extant placozoans.
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Affiliation(s)
- Hans-Jürgen Osigus
- ITZ, Ecology & Evolution, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Michael Eitel
- ITZ, Ecology & Evolution, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Bernd Schierwater
- ITZ, Ecology & Evolution, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
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26
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Rach J, Bergmann T, Paknia O, DeSalle R, Schierwater B, Hadrys H. The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches. PLoS One 2017; 12:e0174842. [PMID: 28406914 PMCID: PMC5390999 DOI: 10.1371/journal.pone.0174842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 10/28/2016] [Accepted: 03/16/2017] [Indexed: 01/13/2023] Open
Abstract
The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent “Folmer region”, a 648 basepair fragment at the 5’ end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the “Folmer region”, the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the “Folmer region” using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic “environment”, this new marker will further enhance the discrimination power at the species level.
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Affiliation(s)
- Jessica Rach
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Tjard Bergmann
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Omid Paknia
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Bernd Schierwater
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Heike Hadrys
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
- * E-mail:
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27
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Schleicherová D, Dulias K, Osigus HJ, Paknia O, Hadrys H, Schierwater B. The most primitive metazoan animals, the placozoans, show high sensitivity to increasing ocean temperatures and acidities. Ecol Evol 2017; 7:895-904. [PMID: 28168026 PMCID: PMC5288258 DOI: 10.1002/ece3.2678] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 03/15/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 01/14/2023] Open
Abstract
The increase in atmospheric carbon dioxide (CO2) leads to rising temperatures and acidification in the oceans, which directly or indirectly affects all marine organisms, from bacteria to animals. We here ask whether the simplest-and possibly also the oldest-metazoan animals, the placozoans, are particularly sensitive to ocean warming and acidification. Placozoans are found in all warm and temperate oceans and are soft-bodied, microscopic invertebrates lacking any calcified structures, organs, or symmetry. We here show that placozoans respond highly sensitive to temperature and acidity stress. The data reveal differential responses in different placozoan lineages and encourage efforts to develop placozoans as a potential biomarker system.
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Affiliation(s)
| | - Katharina Dulias
- ITZ, Ecology and EvolutionTiHo Hannover Hannover Germany; Present address: Department of Biological Sciences School of Applied Sciences University of Huddersfield Huddersfield UK
| | | | - Omid Paknia
- ITZ, Ecology and Evolution TiHo Hannover Hannover Germany
| | - Heike Hadrys
- ITZ, Ecology and Evolution TiHo Hannover Hannover Germany
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28
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Herzog R, Osigus H, Feindt W, Schierwater B, Hadrys H. The complete mitochondrial genome of the emperor dragonfly Anax imperator LEACH, 1815 (Odonata : Aeshnidae) via NGS sequencing. Mitochondrial DNA B Resour 2016; 1:783-786. [PMID: 33473626 PMCID: PMC7799497 DOI: 10.1080/23802359.2016.1186523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 11/05/2022] Open
Abstract
Here we report the complete mitochondrial genome of the emperor dragonfly, Anax imperator (Odonata: Aeshnidae) as the first of its genus. Data were generated via next generation sequencing (NGS) and assembled using an iterative approach. The typical metazoan set of 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) was detected in the same gene order as in other odonate mitogenomes. However, only three intergenic spacer regions are present in A. imperator lacking the distinct s5 spacer, which was regarded as informative feature of the odonate suborder Anisoptera (dragonflies) but absent in Zygoptera (damselflies). With 16,087 bp, it is the longest anisopteran mitogenome to date, mainly due to the long A + T-rich control region of 1291 bp.
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Affiliation(s)
- Rebecca Herzog
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Hans − Jürgen Osigus
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wiebke Feindt
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Bernd Schierwater
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
- EEB, Yale University, New Haven, CT, USA
| | - Heike Hadrys
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
- EEB, Yale University, New Haven, CT, USA
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29
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Feindt W, Herzog R, Osigus HJ, Schierwater B, Hadrys H. Short read sequencing assembly revealed the complete mitochondrial genome of Ischnura elegans Vander Linden, 1820 (Odonata: Zygoptera). Mitochondrial DNA B Resour 2016; 1:574-576. [PMID: 33473559 PMCID: PMC7800176 DOI: 10.1080/23802359.2016.1192510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/11/2016] [Accepted: 05/18/2016] [Indexed: 11/23/2022] Open
Abstract
Damselflies of the genus Ischnura emerge as organisms with high potential in ecological, evolutionary and developmental research at the base of flying insects. Ischnura elegans and Ischnura hastata are for example one of the few odonate species where a complete life cycle over generations can be reared under laboratory conditions. We here report the complete mitochondrial genome of Ischnura elegans as a valuable genomic resource for future eco-evo-devo studies at the base of flying insects. The genome has a total length of 15,962 bp and displays all typical features of Odonata (dragonflies and damselflies) mitochondrial genomes in gene content and order as well as A + T content. Start and stop codons of all protein-coding genes are consistent. Most interestingly, we found four intergenic spacer regions and a long A + T rich (control) region of 1196 bp, which is almost double the size of the close relative Ischnura pumilio. We assume that the adequate insert size and iterative mapping may be more efficient in assembling this duplicated and repetitive region.
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Affiliation(s)
- Wiebke Feindt
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Rebecca Herzog
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Hans-Jürgen Osigus
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Bernd Schierwater
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Heike Hadrys
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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30
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Schierwater B, Holland PWH, Miller DJ, Stadler PF, Wiegmann BM, Wörheide G, Wray GA, DeSalle R. Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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31
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Abstract
The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km2 resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing “no biogeography.”
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Affiliation(s)
- Omid Paknia
- ITZ, Ecology and Evolution, TiHo Hannover, Hannover, Germany
- * E-mail:
| | - Bernd Schierwater
- ITZ, Ecology and Evolution, TiHo Hannover, Hannover, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
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32
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Affiliation(s)
- Bernd Schierwater
- ITZ, TiHo Hannover, Buenteweg 17d, 30559 Hannover, Germany; Yale University, MCDB, 165 Prospect St, New Haven, CT 06511, USA; AMNH New York, Central Park West at 79th Street, New York, NY 10024, USA
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33
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von der Chevallerie K, Rolfes S, Schierwater B. Inhibitors of the p53-Mdm2 interaction increase programmed cell death and produce abnormal phenotypes in the placozoon Trichoplax adhaerens (F.E. Schulze). Dev Genes Evol 2014; 224:79-85. [DOI: 10.1007/s00427-014-0465-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/17/2014] [Indexed: 01/21/2023]
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34
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Osigus HJ, Eitel M, Bernt M, Donath A, Schierwater B. Mitogenomics at the base of Metazoa. Mol Phylogenet Evol 2013; 69:339-51. [PMID: 23891951 DOI: 10.1016/j.ympev.2013.07.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [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: 01/03/2013] [Revised: 05/29/2013] [Accepted: 07/09/2013] [Indexed: 11/25/2022]
Abstract
Unraveling the base of metazoan evolution is of crucial importance for rooting the metazoan Tree of Life. This subject has attracted substantial attention for more than a century and recently fueled a burst of modern phylogenetic studies. Conflicting scenarios from different studies and incongruent results from nuclear versus mitochondrial markers challenge current molecular phylogenetic approaches. Here we analyze the presently most comprehensive data sets of mitochondrial genomes from non-bilaterian animals to illuminate the phylogenetic relationships among early branching metazoan phyla. The results of our analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data.
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Affiliation(s)
- Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Buenteweg 17d, D-30559 Hannover, Germany.
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35
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Bergmann T, Rach J, Damm S, DeSalle R, Schierwater B, Hadrys H. The potential of distance-based thresholds and character-based DNA barcoding for defining problematic taxonomic entities by CO1 and ND1. Mol Ecol Resour 2013; 13:1069-81. [DOI: 10.1111/1755-0998.12125] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 04/09/2013] [Indexed: 11/28/2022]
Affiliation(s)
- T. Bergmann
- ITZ Ecology & Evolution; TiHo Hannover; Bünteweg 17d; D-30559; Hannover; Germany
| | - J. Rach
- ITZ Ecology & Evolution; TiHo Hannover; Bünteweg 17d; D-30559; Hannover; Germany
| | - S. Damm
- ITZ Ecology & Evolution; TiHo Hannover; Bünteweg 17d; D-30559; Hannover; Germany
| | - R. DeSalle
- American Museum of Natural History; The Sackler Institute for Comparative Genomics; New York; NY; 10024; USA
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36
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Bernt M, Bleidorn C, Braband A, Dambach J, Donath A, Fritzsch G, Golombek A, Hadrys H, Jühling F, Meusemann K, Middendorf M, Misof B, Perseke M, Podsiadlowski L, von Reumont B, Schierwater B, Schlegel M, Schrödl M, Simon S, Stadler PF, Stöger I, Struck TH. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogenet Evol 2013; 69:352-64. [PMID: 23684911 DOI: 10.1016/j.ympev.2013.05.002] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [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: 12/28/2012] [Revised: 04/27/2013] [Accepted: 05/03/2013] [Indexed: 12/16/2022]
Abstract
About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.
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Affiliation(s)
- Matthias Bernt
- Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.
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Abstract
The enigmatic animal phylum Placozoa holds a key position in the metazoan Tree of Life. A simple bauplan makes it appear to be the most basal metazoan known and genetic evidence also points to a position close to the last common metazoan ancestor. Trichoplax adhaerens is the only formally described species in the phylum to date, making the Placozoa the only monotypic phylum in the animal kingdom. However, recent molecular genetic as well as morphological studies have identified a high level of diversity, and hence a potential high level of taxonomic diversity, within this phylum. Different taxa, possibly at different taxonomic levels, are awaiting description. In this review we firstly summarize knowledge on the morphology, phylogenetic position and ecology of the Placozoa. Secondly, we give an overview of placozoan morphological and genetic diversity and finally present an updated distribution of placozoan populations. We conclude that there is great potential and need to erect new taxa and to establish a firm system for this taxonomic tabula rasa.
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Affiliation(s)
- Michael Eitel
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany.
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38
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Vij S, Rink JC, Ho HK, Babu D, Eitel M, Narasimhan V, Tiku V, Westbrook J, Schierwater B, Roy S. Evolutionarily ancient association of the FoxJ1 transcription factor with the motile ciliogenic program. PLoS Genet 2012; 8:e1003019. [PMID: 23144623 PMCID: PMC3493443 DOI: 10.1371/journal.pgen.1003019] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [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: 11/01/2011] [Accepted: 08/22/2012] [Indexed: 01/03/2023] Open
Abstract
It is generally believed that the last eukaryotic common ancestor (LECA) was a unicellular organism with motile cilia. In the vertebrates, the winged-helix transcription factor FoxJ1 functions as the master regulator of motile cilia biogenesis. Despite the antiquity of cilia, their highly conserved structure, and their mechanism of motility, the evolution of the transcriptional program controlling ciliogenesis has remained incompletely understood. In particular, it is presently not known how the generation of motile cilia is programmed outside of the vertebrates, and whether and to what extent the FoxJ1-dependent regulation is conserved. We have performed a survey of numerous eukaryotic genomes and discovered that genes homologous to foxJ1 are restricted only to organisms belonging to the unikont lineage. Using a mis-expression assay, we then obtained evidence of a conserved ability of FoxJ1 proteins from a number of diverse phyletic groups to activate the expression of a host of motile ciliary genes in zebrafish embryos. Conversely, we found that inactivation of a foxJ1 gene in Schmidtea mediterranea, a platyhelminth (flatworm) that utilizes motile cilia for locomotion, led to a profound disruption in the differentiation of motile cilia. Together, all of these findings provide the first evolutionary perspective into the transcriptional control of motile ciliogenesis and allow us to propose a conserved FoxJ1-regulated mechanism for motile cilia biogenesis back to the origin of the metazoans. Cilia are microtubule-based, hair-like organelles that project from the surfaces of eukaryotic cells. Protists use motile cilia for locomotion as well as for sensory perception. In metazoans, motile cilia also function in fluid transport over epithelia, such as in the mammalian lungs. Most vertebrate and some invertebrate cell-types differentiate non-motile primary cilia, which function exclusively in sensory transduction. It is believed that primary cilia arose from motile cilia through the loss of the motility apparatus. Cilia are complex organelles: a large number of proteins are involved in their assembly and maintenance. FoxJ1, a forkhead-domain transcription factor, is the master regulator of motile ciliogenesis in vertebrates. It is not known to what extent this transcriptional control is conserved and how it may have evolved. Here, we document the existence of FoxJ1 orthologs in several eukaryotic groups besides the vertebrates. FoxJ1 proteins from three representative phyla—Placozoa, Platyhelminthes, and Echinodermata—were able to activate the expression of ciliary genes when mis-expressed in zebrafish embryos. Moreover, inactivation of FoxJ1 in planaria (Platyhelminthes) abolished motile cilia differentiation. These results provide new insights into the transcriptional regulation of motile cilia biogenesis outside the vertebrates and demonstrate a remarkable conservation of the activity of FoxJ1.
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Affiliation(s)
- Shubha Vij
- Institute of Molecular and Cell Biology, Proteos, Singapore, Singapore
| | - Jochen C. Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Hao Kee Ho
- Institute of Molecular and Cell Biology, Proteos, Singapore, Singapore
| | - Deepak Babu
- Institute of Molecular and Cell Biology, Proteos, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Michael Eitel
- ITZ Division of Ecology and Evolution, Stiftung Tierärztliche Hochschule, Hannover, Germany
| | | | - Varnesh Tiku
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jody Westbrook
- Department of Molecular and Cell Biology and Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America
| | - Bernd Schierwater
- ITZ Division of Ecology and Evolution, Stiftung Tierärztliche Hochschule, Hannover, Germany
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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39
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Bernt M, Braband A, Schierwater B, Stadler PF. Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol 2012; 69:328-38. [PMID: 23142697 DOI: 10.1016/j.ympev.2012.10.020] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [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: 05/05/2012] [Revised: 10/20/2012] [Accepted: 10/22/2012] [Indexed: 11/30/2022]
Abstract
Many years of extensive studies of metazoan mitochondrial genomes have established differences in gene arrangements and genetic codes as valuable phylogenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different gene orders is important to assess the phylogenetic signal of such events. This review summarises and discusses, for the Metazoa, the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial gene transfer to the nucleus are reported. Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.
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Affiliation(s)
- Matthias Bernt
- Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.
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40
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Abstract
In comparative studies using model organisms, extant taxa are often referred to as basal. The term suggests that such taxa are descendants of lineages that diverged early in the history of some larger taxon. By this usage, the basal metazoans comprise just four phyla (Placozoa, Porifera, Cnidaria, and Ctenophora) and the large clade Bilateria. We advise against this practice because basal refers to a region at the base or root of a phylogenetic tree. Thus, referring to an extant taxon or species as basal, or as more basal than another, can be misleading. While much progress has been made toward understanding some of the phylogenetic relationships within these groups, the relationships among them are still largely not known with certainty. Thus, sound inferences from comparative studies of model organisms demand continued illumination of phylogeny. Hypotheses about the mechanisms underlying metazoan evolution can be drawn from the study of model organisms in Cnidaria, Ctenophora, Placozoa, and Porifera, but it is clear that these model organisms are likely to be derived in many respects. Therefore, testing these hypotheses requires the study of yet additional model organisms. The most effective tests are those that investigate model organisms with phylogenetic positions among two sister groups comprising a larger clade of interest.
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Affiliation(s)
- Allen G Collins
- ITZ, Ecology & Evolution, TiHo Hannover, Bünteweg 17d, D-30559 Hannover, Germany
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41
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Hadrys H, Simon S, Kaune B, Schmitt O, Schöner A, Jakob W, Schierwater B. Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate. PLoS One 2012; 7:e34682. [PMID: 22685537 PMCID: PMC3369913 DOI: 10.1371/journal.pone.0034682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 01/18/2012] [Accepted: 03/08/2012] [Indexed: 01/10/2023] Open
Abstract
Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.
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Affiliation(s)
- Heike Hadrys
- ITZ, Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany.
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42
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Osigus HJ, Eitel M, Schierwater B. Chasing the urmetazoon: striking a blow for quality data? Mol Phylogenet Evol 2012; 66:551-7. [PMID: 22683435 DOI: 10.1016/j.ympev.2012.05.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/24/2012] [Indexed: 10/28/2022]
Abstract
The ever-lingering question: "What did the urmetazoan look like?" has not lost its charm, appeal or elusiveness for one and a half centuries. A solid amount of organismal data give what some feel is a clear answer (e.g. Placozoa are at the base of the metazoan tree of life (ToL)), but a diversity of modern molecular data gives almost as many answers as there are exemplars, and even the largest molecular data sets could not solve the question and sometimes even suggest obvious zoological nonsense. Since the problems involved in this phylogenetic conundrum encompass a wide array of analytical freedom and uncertainty it seems questionable whether a further increase in molecular data (quantity) can solve this classical deep phylogeny problem. This review thus strikes a blow for evaluating quality data (including morphological, molecule morphologies, gene arrangement, and gene loss versus gene gain data) in an appropriate manner.
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Affiliation(s)
- Hans-Jürgen Osigus
- ITZ, Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Germany
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43
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Abstract
Unraveling animal life cycles and embryonic development is basic to understanding animal biology and often sheds light on phylogenetic relationships. A key group for understanding the evolution of the Metazoa is the early branching phylum Placozoa, which has attracted rapidly increasing attention. Despite over a hundred years of placozoan research the life cycle of this enigmatic phylum remains unknown. Placozoa are a unique model system for which the nuclear genome was published before the basic biology (i.e. life cycle and development) has been unraveled. Four organismal studies have reported the development of oocytes and one genetic study has nourished the hypothesis of sexual reproduction in natural populations at least in the past. Here we report new observations on sexual reproduction and embryonic development in the Placozoa and support the hypothesis of current sexual reproduction. The regular observation of oocytes and expressed sperm markers provide support that placozoans reproduce sexually in the field. Using whole genome and EST sequences and additional cDNA cloning we identified five conserved sperm markers, characteristic for different stages in spermatogenesis. We also report details on the embryonic development up to a 128-cell stage and new ultrastructural features occurring during early development. These results suggest that sperm and oocyte generation and maturation occur in different placozoans and that clonal lineages reproduce bisexually in addition to the standard mode of vegetative reproduction. The sum of observations is best congruent with the hypothesis of a simple life cycle with an alternation of reproductive modes between bisexual and vegetative reproduction.
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Affiliation(s)
- Michael Eitel
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Hannover, Germany.
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44
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Guidi L, Eitel M, Cesarini E, Schierwater B, Balsamo M. Ultrastructural analyses support different morphological lineages in the phylum Placozoa Grell, 1971. J Morphol 2011; 272:371-8. [PMID: 21246596 DOI: 10.1002/jmor.10922] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/01/2010] [Accepted: 10/03/2010] [Indexed: 11/12/2022]
Abstract
The morphology and ultrastructure of 10 clonal placozoan lineages were studied. We scored several morphological characters at a cellular and intracellular level and identified a number of morphological differences among clones. Some differences appear clone specific and allow recognizing five distinct lineages based on morphological criteria only. These data will be crucial for a yet to be established placozoan systematics. Furthermore, we here describe three new diagnostic morphological characters for Placozoa: a new structure in the upper epithelium, called "concave disc," two distinct subpopulations of fiber cells, and especially small cells in the body margin. Besides the fiber cells appear to be arranged in several layers forming a complex, three-dimensional net not previously described. We also describe the marginal cells as the formerly suggested potential stem-cell type. The basic morphology is revised.
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Affiliation(s)
- Loretta Guidi
- Dipartimento di Scienze dell'Uomo, dell'Ambiente e della Natura, Università degli Studi di Urbino Carlo Bo, Campus Scientifico, Località Crocicchia, 61029 Urbino, Italy.
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45
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Abstract
Modern taxonomy requires an analytical approach incorporating all lines of evidence into decision-making. Such an approach can enhance both species identification and species discovery. The character-based DNA barcode method provides a molecular data set that can be incorporated into classical taxonomic data such that the discovery of new species can be made in an analytical framework that includes multiple sources of data. We here illustrate such a corroborative framework in a dragonfly model system that permits the discovery of two new, but visually cryptic species. In the African dragonfly genus Trithemis three distinct genetic clusters can be detected which could not be identified by using classical taxonomic characters. In order to test the hypothesis of two new species, DNA-barcodes from different sequence markers (ND1 and COI) were combined with morphological, ecological and biogeographic data sets. Phylogenetic analyses and incorporation of all data sets into a scheme called taxonomic circle highly supports the hypothesis of two new species. Our case study suggests an analytical approach to modern taxonomy that integrates data sets from different disciplines, thereby increasing the ease and reliability of both species discovery and species assignment.
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Affiliation(s)
- Sandra Damm
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, Germany.
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46
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Loenarz C, Coleman ML, Boleininger A, Schierwater B, Holland PWH, Ratcliffe PJ, Schofield CJ. The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens. EMBO Rep 2010; 12:63-70. [PMID: 21109780 DOI: 10.1038/embor.2010.170] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 10/05/2010] [Accepted: 10/06/2010] [Indexed: 01/09/2023] Open
Abstract
The hypoxic response in humans is mediated by the hypoxia-inducible transcription factor (HIF), for which prolyl hydroxylases (PHDs) act as oxygen-sensing components. The evolutionary origins of the HIF system have been previously unclear. We demonstrate a functional HIF system in the simplest animal, Trichoplax adhaerens: HIF targets in T. adhaerens include glycolytic and metabolic enzymes, suggesting a role for HIF in the adaptation of basal multicellular animals to fluctuating oxygen levels. Characterization of the T. adhaerens PHDs and cross-species complementation assays reveal a conserved oxygen-sensing mechanism. Cross-genomic analyses rationalize the relative importance of HIF system components, and imply that the HIF system is likely to be present in all animals, but is unique to this kingdom.
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Affiliation(s)
- Christoph Loenarz
- Chemistry Research Laboratory and the Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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47
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Abstract
Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades.
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Affiliation(s)
- M Eitel
- Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Hannover, Germany.
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48
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Schierwater B, Kolokotronis SO, Eitel M, DeSalle R. The Diploblast-Bilateria Sister hypothesis: parallel revolution of a nervous systems may have been a simple step. Commun Integr Biol 2010; 2:403-5. [PMID: 19907700 DOI: 10.4161/cib.2.5.8763] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [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: 04/16/2009] [Accepted: 04/17/2009] [Indexed: 11/19/2022] Open
Abstract
For many familiar with metazoan relationships and body plans, the hypothesis of a sister group relationship between Diploblasta and Bilateria1 comes as a surprise. One of the consequences of this hypothesis-the independent evolution of a nervous system in Coelenterata and Bilateria-seems highly unlikely to many. However, to a small number of scientists working on Metazoa, the parallel evolution of the nervous system is not surprising at all and rather a confirmation of old morphological and new genetic knowledge.2-4 The controversial hypothesis that the Diploblasta and Bilateria are sister taxa is, therefore, tantamount to reconciling the parallel evolution of the nervous system in Coelenterata and Bilateria. In this addendum to Schierwater et al.1 we discuss two aspects critical to the controversy. First we discuss the strength of the inference of the proposed sister relationship of Diploblasta and Bilateria and second we discuss the implications for the evolution of nerve cells and nervous systems.
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Affiliation(s)
- Bernd Schierwater
- ITZ, Ecology and Evolution, Tierärztliche Hochschule Hannover, D-30559 Hannover, Germany.
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49
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Simon S, Schierwater B, Hadrys H. On the value of Elongation factor-1α for reconstructing pterygote insect phylogeny. Mol Phylogenet Evol 2010; 54:651-6. [DOI: 10.1016/j.ympev.2009.09.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 09/12/2009] [Accepted: 09/22/2009] [Indexed: 11/25/2022]
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50
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Schierwater B, Kamm K. The Early Evolution of Hox Genes: A Battle of Belief? Advances in Experimental Medicine and Biology 2010; 689:81-90. [DOI: 10.1007/978-1-4419-6673-5_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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