1
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Gilbert E, Craggs J, Modepalli V. Gene Regulatory Network that Shaped the Evolution of Larval Apical Organ in Cnidaria. Mol Biol Evol 2024; 41:msad285. [PMID: 38152864 PMCID: PMC10781443 DOI: 10.1093/molbev/msad285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/24/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023] Open
Abstract
Among non-bilaterian animals, a larval apical sensory organ with integrated neurons is only found in cnidarians. Within cnidarians, an apical organ with a ciliary tuft is mainly found in Actiniaria. Whether this apical tuft has evolved independently in Actiniaria or alternatively originated in the common ancestor of Cnidaria and Bilateria and was lost in specific groups is uncertain. To test this hypothesis, we generated transcriptomes of the apical domain during the planula stage of four species representing three key groups of cnidarians: Aurelia aurita (Scyphozoa), Nematostella vectensis (Actiniaria), and Acropora millepora and Acropora tenuis (Scleractinia). We showed that the canonical genes implicated in patterning the apical domain of N. vectensis are largely absent in A. aurita. In contrast, the apical domain of the scleractinian planula shares gene expression pattern with N. vectensis. By comparing the larval single-cell transcriptomes, we revealed the apical organ cell type of Scleractinia and confirmed its homology to Actiniaria. However, Fgfa2, a vital regulator of the regionalization of the N. vectensis apical organ, is absent in the scleractinian genome. Likewise, we found that FoxJ1 and 245 genes associated with cilia are exclusively expressed in the N. vectensis apical domain, which is in line with the presence of ciliary apical tuft in Actiniaria and its absence in Scleractinia and Scyphozoa. Our findings suggest that the common ancestor of cnidarians lacked a ciliary apical tuft, and it could have evolved independently in the Actiniaria.
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Affiliation(s)
- Eleanor Gilbert
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Jamie Craggs
- Horniman Museum and Gardens, London SE23 3PQ, UK
| | - Vengamanaidu Modepalli
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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2
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Gharbaran R. Insights into the molecular roles of FOXR2 in the pathology of primary pediatric brain tumors. Crit Rev Oncol Hematol 2023; 192:104188. [PMID: 37879492 DOI: 10.1016/j.critrevonc.2023.104188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/23/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
Forkhead box gene R2 (FOXR2) belongs to the family of FOX genes which codes for highly conserved transcription factors (TFs) with critical roles in biological processes ranging from development to organogenesis to metabolic and immune regulation to cellular homeostasis. A number of FOX genes are associated with cancer development and progression and poor prognosis. A growing body of evidence suggests that FOXR2 is an oncogene. Studies suggested important roles for FOXR2 in cancer cell growth, metastasis, and drug resistance. Recent studies showed that FOXR2 is overexpressed by a subset of newly identified entities of embryonal tumors. This review discusses the role(s) FOXR2 plays in the pathology of pediatric brain cancers and its potential as a therapeutic target.
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Affiliation(s)
- Rajendra Gharbaran
- Biological Sciences Department, Bronx Community College/City University of New York, 2155 University Avenue, Bronx, NY 10453, USA.
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3
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Xu F, Deng S, Gavriouchkina D, Zhang G. Transcriptional regulation analysis reveals the complexity of metamorphosis in the Pacific oyster ( Crassostrea gigas). MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:467-477. [PMID: 38045547 PMCID: PMC10689616 DOI: 10.1007/s42995-023-00204-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Many marine invertebrate phyla are characterized by indirect development. These animals transit from planktonic larvae to benthic spats via settlement and metamorphosis, which contributes to their adaption to the marine environment. Studying the biological process of metamorphosis is, thus, key to understanding the origin and evolution of indirect development. Although numerous studies have been conducted on the relationship between metamorphosis and the marine environment, microorganisms, and neurohormones, little is known about gene regulation network (GRN) dynamics during metamorphosis. Metamorphosis-competent pediveligers of the Pacific oyster Crassostrea gigas were assayed in this study. By assaying gene expression patterns and open chromatin region changes of different samples of larvae and spats, the dynamics of molecular regulation during metamorphosis were examined. The results indicated significantly different gene regulation networks before, during and post-metamorphosis. Genes encoding membrane-integrated receptors and those related to the remodeling of the nervous system were upregulated before the initiation of metamorphosis. Massive biogenesis, e.g., of various enzymes and structural proteins, occurred during metamorphosis as inferred from the comprehensive upregulation of the protein synthesis system post epinephrine stimulation. Hierarchical downstream gene networks were then stimulated. Some transcription factors, including homeobox, basic helix-loop-helix and nuclear receptors, showed different temporal response patterns, suggesting a complex GRN during the transition stage. Nuclear receptors, as well as their retinoid X receptor partner, may participate in the GRN controlling oyster metamorphosis, indicating an ancient role of the nuclear receptor regulation system in animal metamorphosis. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00204-y.
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Affiliation(s)
- Fei Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laoshan Laboratory, Qingdao, 266237 China
- Shandong Technology Innovation Center of Oyster Seed Industry, Qingdao, 266105 China
| | - Shaoxi Deng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, 999077 China
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495 Japan
- UK Dementia Research Institute, University College London, London, WC1E 6BT UK
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laoshan Laboratory, Qingdao, 266237 China
- Shandong Technology Innovation Center of Oyster Seed Industry, Qingdao, 266105 China
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4
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Posnien N, Hunnekuhl VS, Bucher G. Gene expression mapping of the neuroectoderm across phyla - conservation and divergence of early brain anlagen between insects and vertebrates. eLife 2023; 12:e92242. [PMID: 37750868 PMCID: PMC10522337 DOI: 10.7554/elife.92242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
Gene expression has been employed for homologizing body regions across bilateria. The molecular comparison of vertebrate and fly brains has led to a number of disputed homology hypotheses. Data from the fly Drosophila melanogaster have recently been complemented by extensive data from the red flour beetle Tribolium castaneum with its more insect-typical development. In this review, we revisit the molecular mapping of the neuroectoderm of insects and vertebrates to reconsider homology hypotheses. We claim that the protocerebrum is non-segmental and homologous to the vertebrate fore- and midbrain. The boundary between antennal and ocular regions correspond to the vertebrate mid-hindbrain boundary while the deutocerebrum represents the anterior-most ganglion with serial homology to the trunk. The insect head placode is shares common embryonic origin with the vertebrate adenohypophyseal placode. Intriguingly, vertebrate eyes develop from a different region compared to the insect compound eyes calling organ homology into question. Finally, we suggest a molecular re-definition of the classic concepts of archi- and prosocerebrum.
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Affiliation(s)
- Nico Posnien
- Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute, University GoettingenGöttingenGermany
| | - Vera S Hunnekuhl
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, University of GöttingenGöttingenGermany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, University of GöttingenGöttingenGermany
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5
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Hulett RE, Kimura JO, Bolaños DM, Luo YJ, Rivera-López C, Ricci L, Srivastava M. Acoel single-cell atlas reveals expression dynamics and heterogeneity of adult pluripotent stem cells. Nat Commun 2023; 14:2612. [PMID: 37147314 PMCID: PMC10163032 DOI: 10.1038/s41467-023-38016-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
Adult pluripotent stem cell (aPSC) populations underlie whole-body regeneration in many distantly-related animal lineages, but how the underlying cellular and molecular mechanisms compare across species is unknown. Here, we apply single-cell RNA sequencing to profile transcriptional cell states of the acoel worm Hofstenia miamia during postembryonic development and regeneration. We identify cell types shared across stages and their associated gene expression dynamics during regeneration. Functional studies confirm that the aPSCs, also known as neoblasts, are the source of differentiated cells and reveal transcription factors needed for differentiation. Subclustering of neoblasts recovers transcriptionally distinct subpopulations, the majority of which are likely specialized to differentiated lineages. One neoblast subset, showing enriched expression of the histone variant H3.3, appears to lack specialization. Altogether, the cell states identified in this study facilitate comparisons to other species and enable future studies of stem cell fate potentials.
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Affiliation(s)
- Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - D Marcela Bolaños
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
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6
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Rehman S, Hadj-Moussa H, Hawkins L, Storey KB. Role of FOXO transcription factors in the tolerance of whole-body freezing in the wood frog, Rana sylvatica. Cryobiology 2023; 110:44-48. [PMID: 36539050 DOI: 10.1016/j.cryobiol.2022.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The wood frog (Rana Sylvatica) can endure the sub-zero temperatures of winter by freezing up to 65% of total body water as extracellular ice and retreating into a prolonged hypometabolic state. Freeze survival requires the coordination of various adaptations, including a global suppression of metabolic functions and select activation of pro-survival genes. Transcription factors playing roles in metabolism, stress tolerance, and cell proliferation may assist in making survival in a frozen state possible. In this study, the role of Forkhead box 'other' (FOXO) transcription factors in freeze tolerance, and related changes to the insulin pathway, are investigated. Immunoblotting was used to assess total and phosphorylated amounts of FOXO proteins in wood frogs subjected to freezing for 24 h and thawed recovery for 8 h. Levels of active FOXO3 increased in brain, kidney, and liver during freezing and thawing, suggesting a need to maintain or enhance antioxidant defenses under these stresses. Results implicate FOXO involvement in the metabolic regulation of natural freeze tolerance.
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Affiliation(s)
- Saif Rehman
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Hanane Hadj-Moussa
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Liam Hawkins
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada.
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7
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De novo genome assembly and annotation of Holothuria scabra (Jaeger, 1833) from nanopore sequencing reads. Genes Genomics 2022; 44:1487-1498. [DOI: 10.1007/s13258-022-01322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022]
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8
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Seudre O, Martín-Zamora FM, Rapisarda V, Luqman I, Carrillo-Baltodano AM, Martín-Durán JM. The Fox Gene Repertoire in the Annelid Owenia fusiformis Reveals Multiple Expansions of the foxQ2 Class in Spiralia. Genome Biol Evol 2022; 14:evac139. [PMID: 36099507 PMCID: PMC9539403 DOI: 10.1093/gbe/evac139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Fox genes are a large and conserved family of transcription factors involved in many key biological processes, including embryogenesis and body patterning. Although the role of Fox genes has been studied in an array of model systems, comprehensive comparative studies in Spiralia-a large clade of invertebrate animals including molluscs and annelids-are scarce but much needed to better understand the evolutionary history of this gene family. Here, we reconstruct and functionally characterize the Fox gene complement in the annelid Owenia fusiformis, a slow evolving species and member of the sister group to all remaining annelids. The genome of O. fusiformis contains at least a single ortholog for 20 of the 22 Fox gene classes that are ancestral to Bilateria, including an ortholog of the recently discovered foxT class. Temporal and spatial expression dynamics reveal a conserved role of Fox genes in gut formation, mesoderm patterning, and apical organ and cilia formation in Annelida and Spiralia. Moreover, we uncover an ancestral expansion of foxQ2 genes in Spiralia, represented by 11 paralogs in O. fusiformis. Notably, although all foxQ2 copies have apical expression in O. fusiformis, they show variable spatial domains and staggered temporal activation, which suggest cooperation and sub-functionalization among foxQ2 genes for the development of apical fates in this annelid. Altogether, our study informs the evolution and developmental roles of Fox genes in Annelida and Spiralia generally, providing the basis to explore how regulatory changes in Fox gene expression might have contributed to developmental and morphological diversification in Spiralia.
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Affiliation(s)
- Océane Seudre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Valentina Rapisarda
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Imran Luqman
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
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9
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Yuan H, Hatleberg WL, Degnan BM, Degnan SM. Gene activation of metazoan Fox transcription factors at the onset of metamorphosis in the marine demosponge Amphimedon queenslandica. Dev Growth Differ 2022; 64:455-468. [PMID: 36155915 PMCID: PMC9828451 DOI: 10.1111/dgd.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 01/12/2023]
Abstract
Transcription factors encoded by the Forkhead (Fox) gene family have diverse, sometimes conserved, regulatory roles in eumetazoan development, immunity, and physiology. Although this gene family includes members that predate the origin of the animal kingdom, the majority of metazoan Fox genes evolved after the divergence of animals and choanoflagellates. Here, we characterize the composition, structure, and expression of Fox genes in the marine demosponge Amphimedon queenslandica to better understand the origin and evolution of this family. The Fox gene repertoire in A. queenslandica appears to be similar to the ancestral metazoan Fox gene family. All 17 A. queenslandica Fox genes are differentially expressed during development and in adult cell types. Remarkably, eight of these, all of which appear to be metazoan-specific, are induced within just 1 h of larval settlement and commencement of metamorphosis. Gene co-expression analyses suggest that these eight Fox genes regulate developmental and physiological processes similar to their roles in other animals. These findings are consistent with Fox genes playing deeply ancestral roles in animal development and physiology, including in response to changes in the external environment.
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Affiliation(s)
- Huifang Yuan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
| | - William L. Hatleberg
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia,Present address:
Department of Biological SciencesCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Bernard M. Degnan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Sandie M. Degnan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
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10
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Janssen R, Schomburg C, Prpic NM, Budd GE. A comprehensive study of arthropod and onychophoran Fox gene expression patterns. PLoS One 2022; 17:e0270790. [PMID: 35802758 PMCID: PMC9269926 DOI: 10.1371/journal.pone.0270790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
Fox genes represent an evolutionary old class of transcription factor encoding genes that evolved in the last common ancestor of fungi and animals. They represent key-components of multiple gene regulatory networks (GRNs) that are essential for embryonic development. Most of our knowledge about the function of Fox genes comes from vertebrate research, and for arthropods the only comprehensive gene expression analysis is that of the fly Drosophila melanogaster. For other arthropods, only selected Fox genes have been investigated. In this study, we provide the first comprehensive gene expression analysis of arthropod Fox genes including representative species of all main groups of arthropods, Pancrustacea, Myriapoda and Chelicerata. We also provide the first comprehensive analysis of Fox gene expression in an onychophoran species. Our data show that many of the Fox genes likely retained their function during panarthropod evolution highlighting their importance in development. Comparison with published data from other groups of animals shows that this high degree of evolutionary conservation often dates back beyond the last common ancestor of Panarthropoda.
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Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Christoph Schomburg
- AG Zoologie mit dem Schwerpunkt Molekulare Entwicklungsbiologie, Institut für Allgemeine Zoologie und Entwicklungsbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
- Fachgebiet Botanik, Institut für Biologie, Universität Kassel, Kassel, Germany
| | - Nikola-Michael Prpic
- AG Zoologie mit dem Schwerpunkt Molekulare Entwicklungsbiologie, Institut für Allgemeine Zoologie und Entwicklungsbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Graham E. Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden
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11
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Álvarez-Armada N, Cameron CB, Bauer JE, Rahman IA. Heterochrony and parallel evolution of echinoderm, hemichordate and cephalochordate internal bars. Proc Biol Sci 2022; 289:20220258. [PMID: 35538784 PMCID: PMC9091856 DOI: 10.1098/rspb.2022.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Deuterostomes comprise three phyla with radically different body plans. Phylogenetic bracketing of the living deuterostome clades suggests the latest common ancestor of echinoderms, hemichordates and chordates was a bilaterally symmetrical worm with pharyngeal openings, with these characters lost in echinoderms. Early fossil echinoderms with pharyngeal openings have been described, but their interpretation is highly controversial. Here, we critically evaluate the evidence for pharyngeal structures (gill bars) in the extinct stylophoran echinoderms Lagynocystis pyramidalis and Jaekelocarpus oklahomensis using virtual models based on high-resolution X-ray tomography scans of three-dimensionally preserved fossil specimens. Multivariate analyses of the size, spacing and arrangement of the internal bars in these fossils indicate they are substantially more similar to gill bars in modern enteropneust hemichordates and cephalochordates than to other internal bar-like structures in fossil blastozoan echinoderms. The close similarity between the internal bars of the stylophorans L. pyramidalis and J. oklahomensis and the gill bars of extant chordates and hemichordates is strong evidence for their homology. Differences between these internal bars and bar-like elements of the respiratory systems in blastozoans suggest these structures might have arisen through parallel evolution across deuterostomes, perhaps underpinned by a common developmental genetic mechanism.
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Affiliation(s)
| | - Christopher B Cameron
- Département de sciences biologiques, Université de Montréal C.P. 6128, Succursale Centre-ville, Montréal, QC, Canada H3C 3J7
| | - Jennifer E Bauer
- University of Michigan Museum of Paleontology, Ann Arbor, MI 48109-1085, USA
| | - Imran A Rahman
- The Natural History Museum, London SW7 5BD, UK.,Oxford University Museum of Natural History, Oxford OX1 3PW, UK
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12
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Schomburg C, Janssen R, Prpic NM. Phylogenetic analysis of forkhead transcription factors in the Panarthropoda. Dev Genes Evol 2022; 232:39-48. [PMID: 35230523 PMCID: PMC8918179 DOI: 10.1007/s00427-022-00686-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/07/2022] [Indexed: 02/05/2023]
Abstract
Fox genes encode transcription factors that contain a DNA binding domain, the forkhead domain, and are known from diverse animal species. The exact homology of the Fox genes of different species is debated and this makes inferences about the evolution of the Fox genes, and their duplications and losses difficult. We have performed phylogenetic analyses of the Fox gene complements of 32 panarthropod species. Our results confirm an ancestral complement of FoxA, FoxB, FoxC, FoxD, FoxF, FoxG, FoxJ1, FoxJ2/3, FoxK, FoxL1, FoxL2, FoxN1/4, FoxN2/3, FoxO, FoxP, and FoxQ2 in the Arthropoda, and additionally FoxH and FoxQ1 in the Panarthropoda (including tardigrades and onychophorans). We identify a novel Fox gene sub-family, that we designate as FoxT that includes two genes in Drosophila melanogaster, Circadianly Regulated Gene (Crg-1) and forkhead domain 3F (fd3F). In a very recent paper, the same new Fox gene sub-family was identified in insects (Lin et al. 2021). Our analysis confirms the presence of FoxT and shows that its members are present throughout Panarthropoda. We show that the hitherto unclassified gene CG32006 from the fly Drosophila melanogaster belongs to FoxJ1. We also detect gene losses: FoxE and FoxM were lost already in the panarthropod ancestor, whereas the loss of FoxH occurred in the arthropod ancestor. Finally, we find an ortholog of FoxQ1 in the bark scorpion Centruroides sculpturatus, confirmed not only by phylogenetic analysis, but also by forming an evolutionarily conserved gene cluster with FoxF, FoxC, and FoxL1. This suggests that FoxQ1 belongs to the ancestral Fox gene complement in panarthropods and also in chelicerates, but has been lost at the base of the mandibulate arthropods.
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Affiliation(s)
- Christoph Schomburg
- Fachgebiet Botanik, Institut Für Biologie, Universität Kassel, Heinrich-Plett-Straße 40, 34132, Kassel, Germany
- Institut Für Allgemeine Zoologie Und Entwicklungsbiologie, AG Zoologie Mit Dem Schwerpunkt Molekulare Entwicklungsbiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 38, 35392, Gießen, Germany
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden.
| | - Nikola-Michael Prpic
- Institut Für Allgemeine Zoologie Und Entwicklungsbiologie, AG Zoologie Mit Dem Schwerpunkt Molekulare Entwicklungsbiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 38, 35392, Gießen, Germany
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13
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Ogawa Y, Shiraki T, Fukada Y, Kojima D. Foxq2 determines blue cone identity in zebrafish. SCIENCE ADVANCES 2021; 7:eabi9784. [PMID: 34613771 PMCID: PMC8494292 DOI: 10.1126/sciadv.abi9784] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/13/2021] [Indexed: 05/26/2023]
Abstract
Most vertebrate lineages retain a tetrachromatic visual system, which is supported by a functional combination of spectrally distinct multiple cone photoreceptors, ultraviolet (UV), blue, green, and red cones. The blue cone identity is ensured by selective expression of blue (sws2) opsin, and the mechanism is poorly understood because sws2 gene has been lost in mammalian species such as mouse, whose visual system has been extensively studied. Here, we pursued loss-of-function studies on transcription factors expressed predominantly in zebrafish cone photoreceptors and identified Foxq2 as a blue cone–specific factor driving sws2 gene expression. Foxq2 has dual functions acting as an activator of sws2 transcription and as a suppressor of UV (sws1) opsin transcription in blue cones. A wide range of vertebrate species retain both foxq2 and sws2 genes. We propose that Foxq2-dependent sws2 expression is a prevalent regulatory mechanism that was acquired at the early stage of vertebrate evolution.
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14
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Lin HY, Zhu CQ, Zhang HH, Shen ZC, Zhang CX, Ye YX. The Genetic Network of Forkhead Gene Family in Development of Brown Planthoppers. BIOLOGY 2021; 10:867. [PMID: 34571744 PMCID: PMC8469257 DOI: 10.3390/biology10090867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022]
Abstract
We identified 18 distinct Fox genes in the genome of the brown planthopper, Nilaparvata lugens, and further found a novel insect-specific subfamily that we temporarily named FoxT. A total of 16 genes were highly expressed in the eggs, while NlFoxL2 and NlFoxT are female- and male-specific genes, respectively. Large scale RNAi and RNA-seq analyses were used to reveal the functions and potential targets of NlFoxs. In the eggs, NlFoxA, NlFoxN1 and NlFoxN2 are indispensable to early embryogenesis by regulating different target genes; NlFoxG and NlFoxQ co-regulate NlSix3 for brain development; and NlFoxC, NlFoxJ1 and NlFoxP have complementary effects on late embryogenesis. Moreover, NlFoxA, NlFoxNl and NlFoxQ have pleiotropism. NlFoxA and NlFoxQ regulate the expression of NlCHS1 and cuticular proteins, respectively, thereby participating in the formation of cuticles. NlFoxN1, which regulates the expression of NlKrt9 is involved in the formation of intermediate filament frameworks. Our previous studies have revealed that NlFoxL2 and NlFoxO play important roles in chorion formation and wing polyphenism. Altogether, N. lugens Fox genes exhibit functional diversity in embryonic development and organogenesis. This comprehensive study combines genomics, transcriptomics and phenomics, thereby constructing a complex genetic network that spans the entire life cycle of the brown planthopper.
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Affiliation(s)
- Hai-Yan Lin
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (C.-Q.Z.)
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (H.-H.Z.); (Z.-C.S.); (C.-X.Z.)
| | - Cheng-Qi Zhu
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (C.-Q.Z.)
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (H.-H.Z.); (Z.-C.S.); (C.-X.Z.)
| | - Hou-Hong Zhang
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (H.-H.Z.); (Z.-C.S.); (C.-X.Z.)
| | - Zhi-Cheng Shen
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (H.-H.Z.); (Z.-C.S.); (C.-X.Z.)
| | - Chuan-Xi Zhang
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (H.-H.Z.); (Z.-C.S.); (C.-X.Z.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yu-Xuan Ye
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (C.-Q.Z.)
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (H.-H.Z.); (Z.-C.S.); (C.-X.Z.)
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15
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Beckers A, Fuhl F, Ott T, Boldt K, Brislinger MM, Walentek P, Schuster-Gossler K, Hegermann J, Alten L, Kremmer E, Przykopanski A, Serth K, Ueffing M, Blum M, Gossler A. The highly conserved FOXJ1 target CFAP161 is dispensable for motile ciliary function in mouse and Xenopus. Sci Rep 2021; 11:13333. [PMID: 34172766 PMCID: PMC8233316 DOI: 10.1038/s41598-021-92495-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Cilia are protrusions of the cell surface and composed of hundreds of proteins many of which are evolutionary and functionally well conserved. In cells assembling motile cilia the expression of numerous ciliary components is under the control of the transcription factor FOXJ1. Here, we analyse the evolutionary conserved FOXJ1 target CFAP161 in Xenopus and mouse. In both species Cfap161 expression correlates with the presence of motile cilia and depends on FOXJ1. Tagged CFAP161 localises to the basal bodies of multiciliated cells of the Xenopus larval epidermis, and in mice CFAP161 protein localises to the axoneme. Surprisingly, disruption of the Cfap161 gene in both species did not lead to motile cilia-related phenotypes, which contrasts with the conserved expression in cells carrying motile cilia and high sequence conservation. In mice mutation of Cfap161 stabilised the mutant mRNA making genetic compensation triggered by mRNA decay unlikely. However, genes related to microtubules and cilia, microtubule motor activity and inner dyneins were dysregulated, which might buffer the Cfap161 mutation.
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Affiliation(s)
- Anja Beckers
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Franziska Fuhl
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany
| | - Tim Ott
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany
| | - Karsten Boldt
- Institute of Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076, Tübingen, Germany
| | - Magdalena Maria Brislinger
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany.,Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine & CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Habsburger Str. 49, 79104, Freiburg, Germany
| | - Peter Walentek
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine & CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg, Habsburger Str. 49, 79104, Freiburg, Germany
| | - Karin Schuster-Gossler
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, OE8840, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Leonie Alten
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Twist Bioscience, 681 Gateway Blvd South, South San Francisco, CA, 94080, USA
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Core Facility Monoclonal Antibodies, Marchioninistr. 25, 81377, München, Germany.,Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Adina Przykopanski
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Institute for Toxicology, OE 5340, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Katrin Serth
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Marius Ueffing
- Institute of Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076, Tübingen, Germany
| | - Martin Blum
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany.
| | - Achim Gossler
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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16
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Andrikou C, Hejnol A. FGF signaling acts on different levels of mesoderm development within Spiralia. Development 2021; 148:264929. [PMID: 33999997 PMCID: PMC8180254 DOI: 10.1242/dev.196089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 04/08/2021] [Indexed: 01/23/2023]
Abstract
FGF signaling is involved in mesoderm induction in members of deuterostomes (e.g. tunicates, hemichordates), but not in flies and nematodes, in which it has a role in mesoderm patterning and migration. However, we need comparable studies in other protostome taxa in order to decipher whether this mesoderm-inducing function of FGF extends beyond the lineage of deuterostomes. Here, we investigated the role of FGF signaling in mesoderm development in three species of lophophorates, a clade within the protostome group Spiralia. Our gene expression analyses show that the mesodermal molecular patterning is conserved between brachiopods and phoronids, but the spatial and temporal recruitment of transcription factors differs significantly. Moreover, the use of the inhibitor SU5402 demonstrates that FGF signaling is involved in different steps of mesoderm development, as well as in morphogenetic movements of gastrulation and axial elongation. Our findings suggest that the mesoderm-inducing role of FGF extends beyond the group of deuterostomes.
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Affiliation(s)
- Carmen Andrikou
- University of Bergen, Department of Biological Sciences, Thormøhlensgate 55, 5006 Bergen, Norway.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Andreas Hejnol
- University of Bergen, Department of Biological Sciences, Thormøhlensgate 55, 5006 Bergen, Norway.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
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17
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Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death. Sci Rep 2021; 11:2947. [PMID: 33536473 PMCID: PMC7859237 DOI: 10.1038/s41598-020-80627-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/18/2020] [Indexed: 01/30/2023] Open
Abstract
The forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa clade, and specifically from planarians, which are a unique model for understanding development, due to the striking plasticity of the adult. The aim of this study was to identify and perform evolutionary and functional studies of the Fox genes of lophotrochozoan species and, specifically, of the planarian Schmidtea mediterranea. Generating a pipeline for identifying Forkhead domains and using phylogenetics allowed us the phylogenetic reconstruction of Fox genes. We corrected the annotation for misannotated genes and uncovered a new family, the QD, present in all metazoans. According to the new phylogeny, the 27 Fox genes found in Schmidtea mediterranea were classified into 12 families. In Platyhelminthes, family losses were accompanied by extensive gene diversification and the appearance of specific families, the A(P) and N(P). Among the newly identified planarian Fox genes, we found a single copy of foxO, which shows an evolutionary conserved role in controlling cell death.
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18
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Abstract
Hemichordates, along with echinoderms and chordates, belong to the lineage of bilaterians called the deuterostomes. Their phylogenetic position as an outgroup to chordates provides an opportunity to investigate the evolutionary origins of the chordate body plan and reconstruct ancestral deuterostome characters. The body plans of the hemichordates and chordates are organizationally divergent making anatomical comparisons very challenging. The developmental underpinnings of animal body plans are often more conservative than the body plans they regulate, and offer a novel data set for making comparisons between morphologically divergent body architectures. Here I review the hemichordate developmental data generated over the past 20 years that further test hypotheses of proposed morphological affinities between the two taxa, but also compare the conserved anteroposterior, dorsoventral axial patterning programs and germ layer specification programs. These data provide an opportunity to determine which developmental programs are ancestral deuterostome or bilaterian innovations, and which ones occurred in stem chordates or vertebrates representing developmental novelties of the chordate body plan.
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19
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Larouche‐Bilodeau C, Guilbeault‐Mayers X, Cameron CB. Filter feeding, deviations from bilateral symmetry, developmental noise, and heterochrony of hemichordate and cephalochordate gills. Ecol Evol 2020; 10:13544-13554. [PMID: 33304558 PMCID: PMC7713955 DOI: 10.1002/ece3.6962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/02/2022] Open
Abstract
We measured gill slit fluctuating asymmetry (FA), a measure of developmental noise, in adults of three invertebrate deuterostomes with different feeding modes: the cephalochordate Branchiostoma floridae (an obligate filter feeder), the enteropneusts Protoglossus graveolens (a facultative filter feeder/deposit feeder) and Saccoglossus bromophenolosus (a deposit feeder). FA was substantially and significantly low in B. floridae and P. graveolens and high in S. bromophenolosus. Our results suggest that the gills of species that have experienced a relaxation of the filter feeding trait exhibit elevated FA. We found that the timing of development of the secondary collagenous gill bars, compared to the primary gill bars, was highly variable in P. graveolens but not the other two species, demonstrating an independence of gill FA from gill bar heterochrony. We also discovered the occasional ectopic expression of a second set of paired gills posterior to the first set of gills in the enteropneusts and that these were more common in S. bromophenolosus. Moreover, our finding that gill slits in enteropneusts exhibit bilateral symmetry suggests that the left-sidedness of larval cephalochordate gills, and the directional asymmetry of Cambrian stylophoran echinoderm fossil gills, evolved independently from a bilaterally symmetrical ancestor.
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20
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Johnson CJ, Razy-Krajka F, Stolfi A. Expression of smooth muscle-like effectors and core cardiomyocyte regulators in the contractile papillae of Ciona. EvoDevo 2020; 11:15. [PMID: 32774829 PMCID: PMC7397655 DOI: 10.1186/s13227-020-00162-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/22/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The evolution of vertebrate smooth muscles is obscured by lack of identifiable smooth muscle-like cells in tunicates, the invertebrates most closely related to vertebrates. A recent evolutionary model was proposed in which smooth muscles arose before the last bilaterian common ancestor, and were later diversified, secondarily lost or modified in the branches leading to extant animal taxa. However, there is currently no data from tunicates to support this scenario. METHODS AND RESULTS Here, we show that the axial columnar cells, a unique cell type in the adhesive larval papillae of the tunicate Ciona, are enriched for orthologs of vertebrate smooth/non-muscle-specific effectors of contractility, in addition to developing from progenitors that express conserved cardiomyocyte regulatory factors. We show that these cells contract during the retraction of the Ciona papillae during larval settlement and metamorphosis. CONCLUSIONS We propose that the axial columnar cells of Ciona are a myoepithelial cell type required for transducing external stimuli into mechanical forces that aid in the attachment of the motile larva to its final substrate. Furthermore, they share developmental and functional features with vertebrate myoepithelial cells, vascular smooth muscle cells, and cardiomyocytes. We discuss these findings in the context of the proposed models of vertebrate smooth muscle and cardiomyocyte evolution.
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21
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Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
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Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
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22
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Schacht MI, Schomburg C, Bucher G. six3 acts upstream of foxQ2 in labrum and neural development in the spider Parasteatoda tepidariorum. Dev Genes Evol 2020; 230:95-104. [PMID: 32040712 PMCID: PMC7128001 DOI: 10.1007/s00427-020-00654-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/29/2020] [Indexed: 12/12/2022]
Abstract
Anterior patterning in animals is based on a gene regulatory network, which comprises highly conserved transcription factors like six3, pax6 and otx. More recently, foxQ2 was found to be an ancestral component of this network but its regulatory interactions showed evolutionary differences. In most animals, foxQ2 is a downstream target of six3 and knockdown leads to mild or no epidermal phenotypes. In contrast, in the red flour beetle Tribolium castaneum, foxQ2 gained a more prominent role in patterning leading to strong epidermal and brain phenotypes and being required for six3 expression. However, it has remained unclear which of these novel aspects were insect or arthropod specific. Here, we study expression and RNAi phenotype of the single foxQ2 ortholog of the spider Parasteatoda tepidariorum. We find early anterior expression similar to the one of insects. Further, we show an epidermal phenotype in the labrum similar to the insect phenotype. However, our data indicate that foxQ2 is positioned downstream of six3 like in other animals but unlike insects. Hence, the epidermal and neural pattering function of foxQ2 is ancestral for arthropods while the upstream role of foxQ2 may have evolved in the lineage leading to the insects.
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Affiliation(s)
- Magdalena Ines Schacht
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Christoph Schomburg
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
- Institut für Allgemeine Zoologie und Entwicklungsbiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 38, 35392, Giessen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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23
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Gąsiorowski L, Hejnol A. Hox gene expression during development of the phoronid Phoronopsis harmeri. EvoDevo 2020; 11:2. [PMID: 32064072 PMCID: PMC7011278 DOI: 10.1186/s13227-020-0148-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background Phoronida is a small group of marine worm-like suspension feeders, which together with brachiopods and bryozoans form the clade Lophophorata. Although their development is well studied on the morphological level, data regarding gene expression during this process are scarce and restricted to the analysis of relatively few transcription factors. Here, we present a description of the expression patterns of Hox genes during the embryonic and larval development of the phoronid Phoronopsis harmeri. Results We identified sequences of eight Hox genes in the transcriptome of Ph. harmeri and determined their expression pattern during embryonic and larval development using whole mount in situ hybridization. We found that none of the Hox genes is expressed during embryonic development. Instead their expression is initiated in the later developmental stages, when the larval body is already formed. In the investigated initial larval stages the Hox genes are expressed in the non-collinear manner in the posterior body of the larvae: in the telotroch and the structures that represent rudiments of the adult worm. Additionally, we found that certain head-specific transcription factors are expressed in the oral hood, apical organ, preoral coelom, digestive system and developing larval tentacles, anterior to the Hox-expressing territories. Conclusions The lack of Hox gene expression during early development of Ph. harmeri indicates that the larval body develops without positional information from the Hox patterning system. Such phenomenon might be a consequence of the evolutionary intercalation of the larval form into an ancestral life cycle of phoronids. The observed Hox gene expression can also be a consequence of the actinotrocha representing a “head larva”, which is composed of the most anterior body region that is devoid of Hox gene expression. Such interpretation is further supported by the expression of head-specific transcription factors. This implies that the Hox patterning system is used for the positional information of the trunk rudiments and is, therefore, delayed to the later larval stages. We propose that a new body form was intercalated to the phoronid life cycle by precocious development of the anterior structures or by delayed development of the trunk rudiment in the ancestral phoronid larva.
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Affiliation(s)
- Ludwik Gąsiorowski
- 1Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway.,2Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Andreas Hejnol
- 1Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway.,2Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
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24
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Wu S, Zhang Y, Li Y, Wei H, Guo Z, Wang S, Zhang L, Bao Z. Identification and expression profiles of Fox transcription factors in the Yesso scallop (Patinopecten yessoensis). Gene 2020; 733:144387. [PMID: 31972308 DOI: 10.1016/j.gene.2020.144387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 02/07/2023]
Abstract
The forkhead box (Fox) gene family is a family of transcription factors that play important roles in a variety of biological processes in vertebrates, including early development and cell proliferation and differentiation. However, at present, studies on the mollusk Fox family are relatively lacking. In the present study, the Fox gene family of the Yesso scallop (Patinopecten yessoensis) was systematically identified. In addition, the expression profiles of the Fox gene family in early development and adult tissues were analyzed. The results showed that there were 26 Fox genes in P. yessoensis. Of the 26 genes, 24 belonged to 20 subfamilies. The Fox genes belonging to the I, Q1, R and S subfamilies were absent in P. yessoensis. The other 2 genes formed 2 independent clades with the Fox genes of other mollusks and protostomes. They might be new members of the Fox family and were named FoxY and FoxZ. P. yessoensis contained a FoxC-FoxL1 gene cluster similar in structure to that of Branchiostoma floridae, suggesting that the cluster might already exist in the ancestors of bilaterally symmetrical animals. The gene expression analysis of Fox showed that most of the genes were continuously expressed in multiple stages of early development, suggesting that Fox genes might be widely involved in the regulation of embryo and larval development of P. yessoensis. Nine Fox genes were specifically expressed in certain tissues, such as the nerve ganglia, foot, ovary, testis, and gills. For the 9 genes that were differentially expressed between the testis and ovary, their expression levels were analyzed during the 4 developmental stages of gonads. The results showed that FoxL2, FoxE and FoxY were highly expressed in the ovary during all developmental stages, while FoxZ was highly expressed in the testis during all developmental stages. The results suggested that these genes might play an important role in sex maintenance or gametogenesis. The present study could provide a reference for evolutionary and functional studies of the Fox family in metazoans.
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Affiliation(s)
- Shaoxuan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yang Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Huilan Wei
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zhenyi Guo
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, Shandong, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, Shandong, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, Shandong, China
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25
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He B, Buescher M, Farnworth MS, Strobl F, Stelzer EHK, Koniszewski NDB, Muehlen D, Bucher G. An ancestral apical brain region contributes to the central complex under the control of foxQ2 in the beetle Tribolium. eLife 2019; 8:e49065. [PMID: 31625505 PMCID: PMC6837843 DOI: 10.7554/elife.49065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/17/2019] [Indexed: 12/11/2022] Open
Abstract
The genetic control of anterior brain development is highly conserved throughout animals. For instance, a conserved anterior gene regulatory network specifies the ancestral neuroendocrine center of animals and the apical organ of marine organisms. However, its contribution to the brain in non-marine animals has remained elusive. Here, we study the function of the Tc-foxQ2 forkhead transcription factor, a key regulator of the anterior gene regulatory network of insects. We characterized four distinct types of Tc-foxQ2 positive neural progenitor cells based on differential co-expression with Tc-six3/optix, Tc-six4, Tc-chx/vsx, Tc-nkx2.1/scro, Tc-ey, Tc-rx and Tc-fez1. An enhancer trap line built by genome editing marked Tc-foxQ2 positive neurons, which projected through the primary brain commissure and later through a subset of commissural fascicles. Eventually, they contributed to the central complex. Strikingly, in Tc-foxQ2 RNAi knock-down embryos the primary brain commissure did not split and subsequent development of midline brain structures stalled. Our work establishes foxQ2 as a key regulator of brain midline structures, which distinguish the protocerebrum from segmental ganglia. Unexpectedly, our data suggest that the central complex evolved by integrating neural cells from an ancestral anterior neuroendocrine center.
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Affiliation(s)
- Bicheng He
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Marita Buescher
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Max Stephen Farnworth
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
- Göttingen Graduate Center for Molecular BiosciencesNeurosciences and BiophysicsGöttingenGermany
| | - Frederic Strobl
- Buchmann Institute for Molecular Life Sciences (BMLS)Goethe UniversityFrankfurtGermany
| | - Ernst HK Stelzer
- Buchmann Institute for Molecular Life Sciences (BMLS)Goethe UniversityFrankfurtGermany
| | - Nikolaus DB Koniszewski
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Dominik Muehlen
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
| | - Gregor Bucher
- Johann Friedrich Blumenbach Institute of Zoology, GZMBUniversity of GöttingenGöttingenGermany
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Yamazaki A, Yamamoto A, Yaguchi J, Yaguchi S. cis-Regulatory analysis for later phase of anterior neuroectoderm-specific foxQ2 expression in sea urchin embryos. Genesis 2019; 57:e23302. [PMID: 31025827 DOI: 10.1002/dvg.23302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/31/2023]
Abstract
The specification of anterior neuroectoderm is controlled by a highly conserved molecular mechanism in bilaterians. A forkhead family gene, foxQ2, is known to be one of the pivotal regulators, which is zygotically expressed in this region during embryogenesis of a broad range of bilaterians. However, what controls the expression of this essential factor has remained unclear to date. To reveal the regulatory mechanism of foxQ2, we performed cis-regulatory analysis of two foxQ2 genes, foxQ2a and foxQ2b, in a sea urchin Hemicentrotus pulcherrimus. In sea urchin embryos, foxQ2 is initially expressed in the entire animal hemisphere and subsequently shows narrower expression restricted to the anterior pole region. In this study, as a first step to understand the foxQ2 regulation, we focused on the later restricted expression and analyzed the upstream cis-regulatory sequences of foxQ2a and foxQ2b by using the constructs fused to short half-life green fluorescent protein. Based on deletion and mutation analyses of both foxQ2, we identified each of the five regulatory sequences, which were 4-9 bp long. Neither of the regulatory sequences contains any motifs for ectopic activation or spatial repression, suggesting that later mRNA localization is regulated in situ. We also suggest that the three amino acid loop extension-class homeobox gene Meis is involved in the maintenance of foxQ2b, the expression of which is dominant during embryogenesis.
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Affiliation(s)
- Atsuko Yamazaki
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Akane Yamamoto
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Junko Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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Minor PJ, Clarke DN, Andrade López JM, Fritzenwanker JH, Gray J, Lowe CJ. I-SceI Meganuclease-mediated transgenesis in the acorn worm, Saccoglossus kowalevskii. Dev Biol 2019; 445:8-15. [PMID: 30412702 PMCID: PMC6327965 DOI: 10.1016/j.ydbio.2018.10.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022]
Abstract
Hemichordates are a phylum of marine invertebrate deuterostomes that are closely related to chordates, and represent one of the most promising models to provide insights into early deuterostome evolution. The genome of the hemichordate, Saccoglossus kowalevskii, reveals an extensive set of non-coding elements conserved across all three deuterostome phyla. Functional characterization and cross-phyla comparisons of these putative regulatory elements will enable a better understanding of enhancer evolution, and subsequently how changes in gene regulation give rise to morphological innovation. Here, we describe an efficient method of transgenesis for the characterization of non-coding elements in S. kowalevskii. We first test the capacity of an I-SceI transgenesis system to drive ubiquitous or regionalized gene expression, and to label specific cell types. Finally, we identified a minimal promoter that can be used to test the capacity of putative enhancers in S. kowalevskii. This work demonstrates that this I-SceI transgenesis technique, when coupled with an understanding of chromatin accessibility, can be a powerful tool for studying how evolutionary changes in gene regulatory mechanisms contributed to the diversification of body plans in deuterostomes.
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Affiliation(s)
- Paul J Minor
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, United States.
| | - D Nathaniel Clarke
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, United States
| | - José M Andrade López
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, United States
| | - Jens H Fritzenwanker
- Department of Biology, Georgetown University, 411 Regents Hall, 37th and O Streets, NW, Washington DC 20057, United States
| | - Jessica Gray
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, United States
| | - Christopher J Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, United States.
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Olson PD, Zarowiecki M, James K, Baillie A, Bartl G, Burchell P, Chellappoo A, Jarero F, Tan LY, Holroyd N, Berriman M. Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms. EvoDevo 2018; 9:21. [PMID: 30455861 PMCID: PMC6225667 DOI: 10.1186/s13227-018-0110-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tapeworms are agents of neglected tropical diseases responsible for significant health problems and economic loss. They also exhibit adaptations to a parasitic lifestyle that confound comparisons of their development with other animals. Identifying the genetic factors regulating their complex ontogeny is essential to understanding unique aspects of their biology and for advancing novel therapeutics. Here we use RNA sequencing to identify up-regulated signalling components, transcription factors and post-transcriptional/translational regulators (genes of interest, GOI) in the transcriptomes of Larvae and different regions of segmented worms in the tapeworm Hymenolepis microstoma and combine this with spatial gene expression analyses of a selection of genes. RESULTS RNA-seq reads collectively mapped to 90% of the > 12,000 gene models in the H. microstoma v.2 genome assembly, demonstrating that the transcriptome profiles captured a high percentage of predicted genes. Contrasts made between the transcriptomes of Larvae and whole, adult worms, and between the Scolex-Neck, mature strobila and gravid strobila, resulted in 4.5-30% of the genes determined to be differentially expressed. Among these, we identified 190 unique GOI up-regulated in one or more contrasts, including a large range of zinc finger, homeobox and other transcription factors, components of Wnt, Notch, Hedgehog and TGF-β/BMP signalling, and post-transcriptional regulators (e.g. Boule, Pumilio). Heatmap clusterings based on overall expression and on select groups of genes representing 'signals' and 'switches' showed that expression in the Scolex-Neck region is more similar to that of Larvae than to the mature or gravid regions of the adult worm, which was further reflected in large overlap of up-regulated GOI. CONCLUSIONS Spatial expression analyses in Larvae and adult worms corroborated inferences made from quantitative RNA-seq data and in most cases indicated consistency with canonical roles of the genes in other animals, including free-living flatworms. Recapitulation of developmental factors up-regulated during larval metamorphosis suggests that strobilar growth involves many of the same underlying gene regulatory networks despite the significant disparity in developmental outcomes. The majority of genes identified were investigated in tapeworms for the first time, setting the stage for advancing our understanding of developmental genetics in an important group of flatworm parasites.
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Affiliation(s)
- Peter D. Olson
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Magdalena Zarowiecki
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Katherine James
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Andrew Baillie
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Georgie Bartl
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Phil Burchell
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Azita Chellappoo
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Francesca Jarero
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Li Ying Tan
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Nancy Holroyd
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matt Berriman
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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Evolution of the bilaterian mouth and anus. Nat Ecol Evol 2018; 2:1358-1376. [PMID: 30135501 DOI: 10.1038/s41559-018-0641-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 06/26/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
It is widely held that the bilaterian tubular gut with mouth and anus evolved from a simple gut with one major gastric opening. However, there is no consensus on how this happened. Did the single gastric opening evolve into a mouth, with the anus forming elsewhere in the body (protostomy), or did it evolve into an anus, with the mouth forming elsewhere (deuterostomy), or did it evolve into both mouth and anus (amphistomy)? These questions are addressed by the comparison of developmental fates of the blastopore, the opening of the embryonic gut, in diverse animals that live today. Here we review comparative data on the identity and fate of blastoporal tissue, investigate how the formation of the through-gut relates to the major body axes, and discuss to what extent evolutionary scenarios are consistent with these data. Available evidence indicates that stem bilaterians had a slit-like gastric opening that was partially closed in subsequent evolution, leaving open the anus and most likely also the mouth, which would favour amphistomy. We discuss remaining difficulties, and outline directions for future research.
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Jiang SY, Xu HY, Shen ZN, Zhao CJ, Wu C. Genome-wide association analysis reveals novel loci for hypoxia adaptability in Tibetan chicken. Anim Genet 2018; 49:337-339. [DOI: 10.1111/age.12678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2018] [Indexed: 01/14/2023]
Affiliation(s)
- S. Y. Jiang
- College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - H. Y. Xu
- Division of Molecular Pharmaceutics and Drug Delivery; College of Pharmacy; University of Texas at Austin; Austin TX 78712 USA
| | - Z. N. Shen
- College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - C. J. Zhao
- College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
- National Engineering Laboratory for Animal Breeding; Beijing 100193 China
- Key Laboratory of Animal Genetics, Breeding and Reproduction; Ministry of Agriculture; Beijing 100193 China
- Beijing Key Laboratory of Animal Genetic Improvement; Beijing 100193 China
| | - C. Wu
- College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
- National Engineering Laboratory for Animal Breeding; Beijing 100193 China
- Key Laboratory of Animal Genetics, Breeding and Reproduction; Ministry of Agriculture; Beijing 100193 China
- Beijing Key Laboratory of Animal Genetic Improvement; Beijing 100193 China
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Soukup V, Mrstakova S, Kozmik Z. Asymmetric pitx2 expression in medaka epithalamus is regulated by nodal signaling through an intronic enhancer. Dev Genes Evol 2018; 228:131-139. [PMID: 29663064 DOI: 10.1007/s00427-018-0611-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/03/2018] [Indexed: 12/23/2022]
Abstract
The epithalamic region of fishes shows prominent left-right asymmetries that are executed by nodal signaling upstream of the asymmetry-determining transcription factor pitx2. Previous reports have identified that nodal controls the left-sided pitx2 expression in the lateral plate mesoderm through an enhancer present in the last intron of this gene. However, whether similar regulation occurs also in the case of epithalamic asymmetry is currently unresolved. Here, we address some of the cis-regulatory information that control asymmetric pitx2 expression in epithalamus by presenting a Tg(pitx2:EGFP) 116-17 transgenic medaka model, which expresses enhanced green fluorescent protein (EGFP) under control of an intronic enhancer. We show that this transgene recapitulates epithalamic expression of the endogenous pitx2 and that it responds to nodal signaling inhibition. Further, we identify that three foxh1-binding sites present in this enhancer modulate expression of the transgene and that the second site is absolutely necessary for the left-sided epithalamic expression while the other two sites may have subtler regulative roles. We provide evidence that left-sided epithalamic pitx2 expression is controlled through an enhancer present in the last intron of this gene and that the regulatory logic underlying asymmetric pitx2 expression is shared between epithalamic and lateral plate mesoderm regions.
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Affiliation(s)
- Vladimir Soukup
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44, Prague, Czech Republic.
| | - Simona Mrstakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
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Onai T. The evolutionary origin of chordate segmentation: revisiting the enterocoel theory. Theory Biosci 2018; 137:1-16. [PMID: 29488055 DOI: 10.1007/s12064-018-0260-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/10/2018] [Indexed: 11/28/2022]
Abstract
One of the definitive characteristics of chordates (cephalochordates, vertebrates) is the somites, which are a series of paraxial mesodermal blocks exhibiting segmentation. The presence of somites in the basal chordate amphioxus and in vertebrates, but not in tunicates (the sister group of vertebrates), suggests that the tunicates lost the somites secondarily. Somites are patterned from anterior to posterior during embryogenesis. How such a segmental pattern evolved from deuterostome ancestors is mysterious. The classic enterocoel theory claims that chordate mesoderm evolved from the ancestral deuterostome mesoderm that organizes the trimeric body parts seen in extant hemichordates. Recent progress in molecular embryology has been tremendous, which has enabled us to test this classic theory. In this review, the history of the study on the evolution of the chordate mesoderm is summarized. This is followed by a review of the current understanding of genetic mapping on anterior/posterior (A/P) mesodermal patterning between chordates (cephalochordates, vertebrates) and a direct developing hemichordate (Saccoglossus kowalevskii). Finally, a possible scenario about the evolution of the chordate mesoderm from deuterostome ancestors is discussed.
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Affiliation(s)
- Takayuki Onai
- Department of Anatomy, School of Medical Sciences, University of Fukui, 23-3, Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan. .,Life Science Innovation Center, University of Fukui, 23-3, Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan.
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Kuo DH, Hsiao YH. Duplicated FoxA genes in the leech Helobdella: Insights into the evolution of direct development in clitellate annelids. Dev Dyn 2018; 247:763-778. [PMID: 29396890 DOI: 10.1002/dvdy.24621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND As an adaptation to the land, the clitellate annelid had reorganized its embryogenesis to develop "directly" without the ancestral planktonic larval stage. To study the evolution of gut development in the directly developing clitellates, we characterized the expression pattern of the conserved gut gene, FoxA, in the embryonic development of the leech. RESULTS The leech has three FoxA paralogs. Hau-FoxA1 is first expressed in a subset of endoderm cells and then in the foregut and the midgut. Hau-FoxA2 is expressed in the stomodeum, which is secondarily derived from the anterior ectoderm in the clitellates rather than the tissue around the blastopore, the ancestral site of mouth formation in Phylum Annelida. Hau-FoxA3 is expressed during the morphogenesis of segmental ganglia from the ectodermal teloblast lineages, a clitellate-specific trait. Hau-FoxA1 and Hau-FoxA2 are also expressed during the morphogenesis of the leech-specific front sucker. CONCLUSIONS The expression patterns suggested that Hau-FoxA1 carries out most of the conserved function in the endoderm and gut development, while the other two duplicates appear to have evolved unique novel functions in the directly developing clitellate embryos. Therefore, neofunctionalization and co-option of FoxA might have made a significant contribution to the evolution of direct development in Clitellata. Developmental Dynamics 247:763-778, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsiang Hsiao
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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The sea cucumber genome provides insights into morphological evolution and visceral regeneration. PLoS Biol 2017; 15:e2003790. [PMID: 29023486 PMCID: PMC5638244 DOI: 10.1371/journal.pbio.2003790] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/11/2017] [Indexed: 11/25/2022] Open
Abstract
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs. Echinoderms, ubiquitous in the marine environment, are important from evolutionary, ecological, and socioeconomic perspectives. Together with chordates and hemichordates, they form the deuterostome clade, making them a crucial node in the study of chordate ancestry. Within echinoderms, class Holothuroidea is unique; its members (the sea cucumbers) display remarkable regenerative abilities and play key roles as sediment bioturbators and symbiotic hosts, and many are prized in the seafood and pharmaceutical industries. The sea cucumber genome therefore has the potential to significantly contribute to our understanding of important evolutionary and biological processes and help enhance aquaculture programs. Here we present a high-quality genome sequence for the economically important species Apostichopus japonicus. Through comparative analyses, we identified 763 echinoderm-specific gene families enriched in genes encoding membrane proteins, ion channels, and signal transduction proteins. Marker genes associated with the notochord and gill slits were also found, providing valuable insight into the origin of chordates. The reduced number and low expression levels of biomineralization genes reflect the skeletal degeneration seen in sea cucumbers. Importantly, 2 gene families appeared to be expanded in A. japonicus and may play crucial roles in its heightened regenerative potential. Together, findings from the sea cucumber genome provide important and novel insights into echinoderm and deuterostome biology.
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Busengdal H, Rentzsch F. Unipotent progenitors contribute to the generation of sensory cell types in the nervous system of the cnidarian Nematostella vectensis. Dev Biol 2017; 431:59-68. [PMID: 28827097 DOI: 10.1016/j.ydbio.2017.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 08/08/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022]
Abstract
Nervous systems often consist of a large number of different types of neurons which are generated from neural stem and progenitor cells by a series of symmetric and asymmetric divisions. The origin and early evolution of these neural progenitor systems is not well understood. Here we use a cnidarian model organism, Nematostella vectensis, to gain insight into the generation of neural cell type diversity in a non-bilaterian animal. We identify NvFoxQ2d as a transcription factor that is expressed in a population of spatially restricted, proliferating ectodermal cells that are derived from NvSoxB(2)-expressing neural progenitor cells. Using a transgenic reporter line we show that the NvFoxQ2d cells undergo a terminal, symmetric division to generate a morphologically homogeneous population of putative sensory cells. The abundance of these cells, but not their proliferation status is affected by treatment with the γ-secretase inhibitor DAPT, suggesting regulation by Notch signalling. Our data suggest that intermediate progenitor cells and symmetric divisions contribute to the formation of the seemingly simple nervous system of a sea anemone.
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Affiliation(s)
- Henriette Busengdal
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway
| | - Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway.
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Kitzmann P, Weißkopf M, Schacht MI, Bucher G. A key role for foxQ2 in anterior head and central brain patterning in insects. Development 2017; 144:2969-2981. [PMID: 28811313 PMCID: PMC5592812 DOI: 10.1242/dev.147637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 07/05/2017] [Indexed: 01/14/2023]
Abstract
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the red flour beetle Tribolium castaneum ortholog of foxQ2 (Tc-foxQ2) as a novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression. Surprisingly, Tc-foxQ2 and Tc-six3 mutually activate each other, forming a novel regulatory module at the top of the aGRN. Comparisons of our results with those of sea urchins and cnidarians suggest that foxQ2 has acquired more upstream functions in the aGRN during protostome evolution. Our findings expand the knowledge on foxQ2 gene function to include essential roles in epidermal development and central brain patterning.
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Affiliation(s)
- Peter Kitzmann
- Department of Evolutionary Developmental Genetics, GZMB, Universität Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Matthias Weißkopf
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Staudtstraße 5, 91058 Erlangen, Germany
| | - Magdalena Ines Schacht
- Department of Evolutionary Developmental Genetics, GZMB, Universität Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, Universität Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
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Janssen R, Budd GE. Investigation of endoderm marker-genes during gastrulation and gut-development in the velvet worm Euperipatoides kanangrensis. Dev Biol 2017; 427:155-164. [DOI: 10.1016/j.ydbio.2017.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 04/14/2017] [Accepted: 04/23/2017] [Indexed: 11/30/2022]
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Simakov O, Kawashima T. Independent evolution of genomic characters during major metazoan transitions. Dev Biol 2016; 427:179-192. [PMID: 27890449 DOI: 10.1016/j.ydbio.2016.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages. In this review we describe recent advances in our understanding of ancestral metazoan coding and non-coding features, as deduced from genomic comparisons. Some genomic changes such as innovations in gene and linkage content occur at different rates across metazoan clades, suggesting some level of independence among genomic characters. While their contribution to biological innovation remains largely unclear, we review recent literature about certain genomic changes that do correlate with changes to specific developmental pathways and metazoan innovations. In particular, we discuss the origins of the recently described pharyngeal cluster which is conserved across deuterostome genomes, and highlight different genomic features that have contributed to the evolution of this group. We also assess our current capacity to infer ancestral metazoan states from gene models and comparative genomics tools and elaborate on the future directions of metazoan comparative genomics relevant to evo-devo studies.
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Affiliation(s)
- Oleg Simakov
- Okinawa Institute of Science and Technology, Okinawa, Japan.
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Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins. Proc Natl Acad Sci U S A 2016; 113:E7202-E7211. [PMID: 27810959 DOI: 10.1073/pnas.1612820113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Developmental gene regulatory networks (GRNs) are assemblages of gene regulatory interactions that direct ontogeny of animal body plans. Studies of GRNs operating in the early development of euechinoid sea urchins have revealed that little appreciable change has occurred since their divergence ∼90 million years ago (mya). These observations suggest that strong conservation of GRN architecture was maintained in early development of the sea urchin lineage. Testing whether this holds for all sea urchins necessitates comparative analyses of echinoid taxa that diverged deeper in geological time. Recent studies highlighted extensive divergence of skeletogenic mesoderm specification in the sister clade of euechinoids, the cidaroids, suggesting that comparative analyses of cidaroid GRN architecture may confer a greater understanding of the evolutionary dynamics of developmental GRNs. Here I report spatiotemporal patterning of 55 regulatory genes and perturbation analyses of key regulatory genes involved in euechinoid oral-aboral patterning of nonskeletogenic mesodermal and ectodermal domains in early development of the cidaroid Eucidaris tribuloides These results indicate that developmental GRNs directing mesodermal and ectodermal specification have undergone marked alterations since the divergence of cidaroids and euechinoids. Notably, statistical and clustering analyses of echinoid temporal gene expression datasets indicate that regulation of mesodermal genes has diverged more markedly than regulation of ectodermal genes. Although research on indirect-developing euechinoid sea urchins suggests strong conservation of GRN circuitry during early embryogenesis, this study indicates that since the divergence of cidaroids and euechinoids, developmental GRNs have undergone significant, cell type-biased alterations.
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Bertho S, Pasquier J, Pan Q, Le Trionnaire G, Bobe J, Postlethwait JH, Pailhoux E, Schartl M, Herpin A, Guiguen Y. Foxl2 and Its Relatives Are Evolutionary Conserved Players in Gonadal Sex Differentiation. Sex Dev 2016; 10:111-29. [PMID: 27441599 DOI: 10.1159/000447611] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 11/19/2022] Open
Abstract
Foxl2 is a member of the large family of Forkhead Box (Fox) domain transcription factors. It emerged during the last 15 years as a key player in ovarian differentiation and oogenesis in vertebrates and especially mammals. This review focuses on Foxl2 genes in light of recent findings on their evolution, expression, and implication in sex differentiation in animals in general. Homologs of Foxl2 and its paralog Foxl3 are found in all metazoans, but their gene evolution is complex, with multiple gains and losses following successive whole genome duplication events in vertebrates. This review aims to decipher the evolutionary forces that drove Foxl2/3 gene specialization through sub- and neo-functionalization during evolution. Expression data in metazoans suggests that Foxl2/3 progressively acquired a role in both somatic and germ cell gonad differentiation and that a certain degree of sub-functionalization occurred after its duplication in vertebrates. This generated a scenario where Foxl2 is predominantly expressed in ovarian somatic cells and Foxl3 in male germ cells. To support this hypothesis, we provide original results showing that in the pea aphid (insects) foxl2/3 is predominantly expressed in sexual females and showing that in bovine ovaries FOXL2 is specifically expressed in granulosa cells. Overall, current results suggest that Foxl2 and Foxl3 are evolutionarily conserved players involved in somatic and germinal differentiation of gonadal sex.
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Affiliation(s)
- Sylvain Bertho
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
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Range RC, Wei Z. An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo. Development 2016; 143:1523-33. [PMID: 26952978 PMCID: PMC4909856 DOI: 10.1242/dev.128165] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 02/23/2016] [Indexed: 01/17/2023]
Abstract
Anterior signaling centers help specify and pattern the early anterior neuroectoderm (ANE) in many deuterostomes. In sea urchin the ANE is restricted to the anterior of the late blastula stage embryo, where it forms a simple neural territory comprising several types of neurons as well as the apical tuft. Here, we show that during early development, the sea urchin ANE territory separates into inner and outer regulatory domains that express the cardinal ANE transcriptional regulators FoxQ2 and Six3, respectively. FoxQ2 drives this patterning process, which is required to eliminate six3 expression from the inner domain and activate the expression of Dkk3 and sFRP1/5, two secreted Wnt modulators. Dkk3 and low expression levels of sFRP1/5 act additively to potentiate the Wnt/JNK signaling pathway governing the positioning of the ANE territory around the anterior pole, whereas high expression levels of sFRP1/5 antagonize Wnt/JNK signaling. sFRP1/5 and Dkk3 levels are rigidly maintained via autorepressive and cross-repressive interactions with Wnt signaling components and additional ANE transcription factors. Together, these data support a model in which FoxQ2 initiates an anterior patterning center that implements correct size and positions of ANE structures. Comparisons of functional and expression studies in sea urchin, hemichordate and chordate embryos reveal striking similarities among deuterostome ANE regulatory networks and the molecular mechanism that positions and defines ANE borders. These data strongly support the idea that the sea urchin embryo uses an ancient anterior patterning system that was present in the common ambulacrarian/chordate ancestor.
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Affiliation(s)
- Ryan C Range
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zheng Wei
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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Arendt D, Tosches MA, Marlow H. From nerve net to nerve ring, nerve cord and brain--evolution of the nervous system. Nat Rev Neurosci 2016; 17:61-72. [PMID: 26675821 DOI: 10.1038/nrn.2015.15] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The puzzle of how complex nervous systems emerged remains unsolved. Comparative studies of neurodevelopment in cnidarians and bilaterians suggest that this process began with distinct integration centres that evolved on opposite ends of an initial nerve net. The 'apical nervous system' controlled general body physiology, and the 'blastoporal nervous system' coordinated feeding movements and locomotion. We propose that expansion, integration and fusion of these centres gave rise to the bilaterian nerve cord and brain.
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Affiliation(s)
- Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 699117 Heidelberg, Germany
| | - Maria Antonietta Tosches
- Max Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt am Main, Germany
| | - Heather Marlow
- Pasteur Institute, 25-28 Rue du Dr Roux, 75015 Paris, France
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Vöcking O, Kourtesis I, Hausen H. Posterior eyespots in larval chitons have a molecular identity similar to anterior cerebral eyes in other bilaterians. EvoDevo 2015; 6:40. [PMID: 26702352 PMCID: PMC4689004 DOI: 10.1186/s13227-015-0036-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/19/2015] [Indexed: 11/17/2022] Open
Abstract
Background Development of cerebral eyes is generally based on fine-tuned networks and closely intertwined with the formation of brain and head. Consistently and best studied in insects and vertebrates, many signaling pathways relaying the activity of eye developmental factors to positional information in the head region are characterized. Though known from several organisms, photoreceptors developing outside the head region are much less studied and the course of their development, relation to cerebral eyes and evolutionary origin is in most cases unknown. To explore how position influences development of otherwise similar photoreceptors, we analyzed the molecular characteristics of photoreceptors we discovered at the very anterior, the posttrochal mid-body and posterior body region of larval Leptochiton asellus, a representative of the chiton subgroup of mollusks. Results Irrespective of their position, all found photoreceptors exhibit a molecular signature highly similar to cerebral eye photoreceptors of related animals. All photoreceptors employ the same subtype of visual pigments (r-opsin), and the same key elements for phototransduction such as GNAq, trpC and arrestin and intracellular r-opsin transport such as rip11 and myosinV as described from other protostome cerebral eyes. Several transcription factors commonly involved in cerebral eye and brain development such as six1/2, eya, dachshund, lhx2/9 and prox are also expressed by all found photoreceptor cells, only pax6 being restricted to the anterior most cells. Coexpression of pax6 and MITF in photoreceptor-associated shielding pigment cells present at the mid-body position matches the common situation in cerebral eye retinal pigment epithelium specification and differentiation. Notably, all photoreceptors, even the posterior ones, further express clear anterior markers such as foxq2, irx, otx, and six3/6 (only the latter absent in the most posterior photoreceptors), which play important roles in the early patterning of the anterior neurogenic area throughout the animal kingdom. Conclusions Our data suggest that anterior eyes with brain-associated development can indeed be subject to heterotopic replication to developmentally distinct and even posterior body regions. Retention of the transcriptional activity of a broad set of eye developmental factors and common anterior markers suggests a mode of eye development induction, which is largely independent of body regionalization. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0036-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oliver Vöcking
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway ; Department of Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Ioannis Kourtesis
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Harald Hausen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
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Andrikou C, Pai CY, Su YH, Arnone MI. Logics and properties of a genetic regulatory program that drives embryonic muscle development in an echinoderm. eLife 2015. [PMID: 26218224 PMCID: PMC4549668 DOI: 10.7554/elife.07343] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Evolutionary origin of muscle is a central question when discussing mesoderm evolution. Developmental mechanisms underlying somatic muscle development have mostly been studied in vertebrates and fly where multiple signals and hierarchic genetic regulatory cascades selectively specify myoblasts from a pool of naive mesodermal progenitors. However, due to the increased organismic complexity and distant phylogenetic position of the two systems, a general mechanistic understanding of myogenesis is still lacking. In this study, we propose a gene regulatory network (GRN) model that promotes myogenesis in the sea urchin embryo, an early branching deuterostome. A fibroblast growth factor signaling and four Forkhead transcription factors consist the central part of our model and appear to orchestrate the myogenic process. The topological properties of the network reveal dense gene interwiring and a multilevel transcriptional regulation of conserved and novel myogenic genes. Finally, the comparison of the myogenic network architecture among different animal groups highlights the evolutionary plasticity of developmental GRNs. DOI:http://dx.doi.org/10.7554/eLife.07343.001 Muscles, bones, and blood vessels all develop from a tissue called the mesoderm, which forms early on in the development of an embryo. Networks of genes control which parts of the mesoderm transform into different cell types. The gene networks that control the development of muscle cells from the mesoderm have so far been investigated in flies and several species of animals with backbones. However, these species are complex, which makes it difficult to work out the general principles that control muscle cell development. Sea urchins are often studied in developmental biology as they have many of the same genes as more complex animals, but are much simpler and easier to study in the laboratory. Andrikou et al. therefore investigated the ‘gene regulatory network’ that controls muscle development in sea urchins. This revealed that proteins called Forkhead transcription factors and a process called FGF signaling are crucial for controlling muscle development in sea urchins. These are also important factors for developing muscles in other animals. Andrikou et al. then produced models that show the interactions between the genes that control muscle formation at three different stages of embryonic development. These models reveal several important features of the muscle development gene regulatory network. For example, the network is robust: if one gene fails, the network is connected in a way that allows it to still make muscle. This also allows the network to adapt and evolve without losing the ability to perform any of its existing roles. Comparing the gene regulatory network that controls muscle development in sea urchins with the networks found in other animals showed that many of the same genes are used across different species, but are connected into different network structures. Investigating the similarities and differences of the regulatory networks in different species could help us to understand how muscles have evolved and could ultimately lead to a better understanding of the causes of developmental diseases. DOI:http://dx.doi.org/10.7554/eLife.07343.002
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Affiliation(s)
- Carmen Andrikou
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Chih-Yu Pai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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Aldea D, Leon A, Bertrand S, Escriva H. Expression of Fox genes in the cephalochordate Branchiostoma lanceolatum. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Brunet T, Lauri A, Arendt D. Did the notochord evolve from an ancient axial muscle? The axochord hypothesis. Bioessays 2015; 37:836-50. [PMID: 26172338 PMCID: PMC5054868 DOI: 10.1002/bies.201500027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/20/2022]
Abstract
The origin of the notochord is one of the key remaining mysteries of our evolutionary ancestry. Here, we present a multi‐level comparison of the chordate notochord to the axochord, a paired axial muscle spanning the ventral midline of annelid worms and other invertebrates. At the cellular level, comparative molecular profiling in the marine annelids P. dumerilii and C. teleta reveals expression of similar, specific gene sets in presumptive axochordal and notochordal cells. These cells also occupy corresponding positions in a conserved anatomical topology and undergo similar morphogenetic movements. At the organ level, a detailed comparison of bilaterian musculatures reveals that most phyla form axochord‐like muscles, suggesting that such a muscle was already present in urbilaterian ancestors. Integrating comparative evidence at the cell and organ level, we propose that the notochord evolved by modification of a ventromedian muscle followed by the assembly of an axial complex supporting swimming in vertebrate ancestors.
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Affiliation(s)
- Thibaut Brunet
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonella Lauri
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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47
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The deuterostome context of chordate origins. Nature 2015; 520:456-65. [PMID: 25903627 DOI: 10.1038/nature14434] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/03/2015] [Indexed: 01/08/2023]
Abstract
Our understanding of vertebrate origins is powerfully informed by comparative morphology, embryology and genomics of chordates, hemichordates and echinoderms, which together make up the deuterostome clade. Striking body-plan differences among these phyla have historically hindered the identification of ancestral morphological features, but recent progress in molecular genetics and embryology has revealed deep similarities in body-axis formation and organization across deuterostomes, at stages before morphological differences develop. These developmental genetic features, along with robust support of pharyngeal gill slits as a shared deuterostome character, provide the foundation for the emergence of chordates.
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Martín-Durán JM, Hejnol A. The study of Priapulus caudatus reveals conserved molecular patterning underlying different gut morphogenesis in the Ecdysozoa. BMC Biol 2015; 13:29. [PMID: 25895830 PMCID: PMC4434581 DOI: 10.1186/s12915-015-0139-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 04/13/2015] [Indexed: 12/14/2022] Open
Abstract
Background The digestive systems of animals can become highly specialized in response to their exploration and occupation of new ecological niches. Although studies on different animals have revealed commonalities in gut formation, the model systems Caenorhabditis elegans and Drosophila melanogaster, which belong to the invertebrate group Ecdysozoa, exhibit remarkable deviations in how their intestines develop. Their morphological and developmental idiosyncrasies have hindered reconstructions of ancestral gut characters for the Ecdysozoa, and limit comparisons with vertebrate models. In this respect, the phylogenetic position, and slow evolving morphological and molecular characters of marine priapulid worms advance them as a key group to decipher evolutionary events that occurred in the lineages leading to C. elegans and D. melanogaster. Results In the priapulid Priapulus caudatus, the gut consists of an ectodermal foregut and anus, and a mid region of at least partial endodermal origin. The inner gut develops into a 16-cell primordium devoid of visceral musculature, arranged in three mid tetrads and two posterior duplets. The mouth invaginates ventrally and shifts to a terminal anterior position as the ventral anterior ectoderm differentially proliferates. Contraction of the musculature occurs as the head region retracts into the trunk and resolves the definitive larval body plan. Despite obvious developmental differences with C. elegans and D. melanogaster, the expression in P. caudatus of the gut-related candidate genes NK2.1, foxQ2, FGF8/17/18, GATA456, HNF4, wnt1, and evx demonstrate three distinct evolutionarily conserved molecular profiles that correlate with morphologically identified sub-regions of the gut. Conclusions The comparative analysis of priapulid development suggests that a midgut formed by a single endodermal population of vegetal cells, a ventral mouth, and the blastoporal origin of the anus are ancestral features in the Ecdysozoa. Our molecular data on P. caudatus reveal a conserved ecdysozoan gut-patterning program and demonstrates that extreme morphological divergence has not been accompanied by major molecular innovations in transcriptional regulators during digestive system evolution in the Ecdysozoa. Our data help us understand the origins of the ecdysozoan body plan, including those of C. elegans and D. melanogaster, and this is critical for comparisons between these two prominent model systems and their vertebrate counterparts. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0139-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José M Martín-Durán
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway.
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway.
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50
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Passamaneck YJ, Hejnol A, Martindale MQ. Mesodermal gene expression during the embryonic and larval development of the articulate brachiopod Terebratalia transversa. EvoDevo 2015; 6:10. [PMID: 25897375 PMCID: PMC4404124 DOI: 10.1186/s13227-015-0004-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
Background Brachiopods undergo radial cleavage, which is distinct from the stereotyped development of closely related spiralian taxa. The mesoderm has been inferred to derive from the archenteron walls following gastrulation, and the primary mesoderm derivative in the larva is a complex musculature. To investigate the specification and differentiation of the mesoderm in the articulate brachiopod Terebratalia transversa, we have identified orthologs of genes involved in mesoderm development in other taxa and investigated their spatial and temporal expression during the embryonic and larval development of T. transversa. Results Orthologs of 17 developmental regulatory genes with roles in the development of the mesoderm in other bilaterian animals were found to be expressed in the developing mesoderm of T. transversa. Five genes, Tt.twist, Tt.GATA456, Tt.dachshund, Tt.mPrx, and Tt.NK1, were found to have expression throughout the archenteron wall at the radial gastrula stage, shortly after the initiation of gastrulation. Three additional genes, Tt.Pax1/9, Tt.MyoD, and Tt.Six1/2, showed expression at this stage in only a portion of the archenteron wall. Tt.eya, Tt.FoxC, Tt.FoxF, Tt.Mox, Tt.paraxis, Tt.Limpet, and Tt.Mef2 all showed initial mesodermal expression during later gastrula or early larval stages. At the late larval stage, Tt.dachshund, Tt.Limpet, and Tt.Mef2 showed expression in nearly all mesoderm cells, while all other genes were localized to specific regions of the mesoderm. Tt.FoxD and Tt.noggin both showed expression in the ventral mesoderm at the larval stages, with gastrula expression patterns in the archenteron roof and blastopore lip, respectively. Conclusions Expression analyses support conserved roles for developmental regulators in the specification and differentiation of the mesoderm during the development of T. transversa. Expression of multiple mesodermal factors in the archenteron wall during gastrulation supports previous morphological observations that this region gives rise to larval mesoderm. Localized expression domains during gastrulation and larval development evidence early regionalization of the mesoderm and provide a basis for hypotheses regarding the molecular regulation underlying the complex system of musculature observed in the larva. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0004-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yale J Passamaneck
- Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813 USA ; The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate, 55, 5008 Bergen, Norway
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
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