151
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De Robertis EM, Moriyama Y, Colozza G. Generation of animal form by the Chordin/Tolloid/BMP gradient: 100 years after D'Arcy Thompson. Dev Growth Differ 2017; 59:580-592. [PMID: 28815565 DOI: 10.1111/dgd.12388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/03/2017] [Accepted: 07/03/2017] [Indexed: 12/30/2022]
Abstract
The classic book "On Growth and Form" by naturalist D'Arcy Thompson was published 100 years ago. To celebrate this landmark, we present experiments in the Xenopus embryo that provide a framework for understanding how simple, quantitative transformations of a morphogen gradient might have affected evolution and morphological diversity of organisms. D'Arcy Thompson proposed that different morphologies might be generated by modifying physical parameters in an underlying system of Cartesian coordinates that pre-existed in Nature and arose during evolutionary history. Chordin is a BMP antagonist secreted by the Spemann organizer located on the dorsal side of the gastrula. Chordin generates a morphogen gradient as first proposed by mathematician Alan Turing. The rate-limiting step of this dorsal-ventral (D-V) morphogen is the degradation of Chordin by the Tolloid metalloproteinase in the ventral side. Chordin is expressed at gastrula on the dorsal side where BMP signaling is low, while at the opposite side peak levels of BMP signaling are reached. In fishes, amphibians, reptiles and birds, high BMP signaling in the ventral region induces transcription of a secreted inhibitor of Tolloid called Sizzled. By depleting Sizzled exclusively in the ventral half of the embryo we were able to expand the ventro-posterior region in an otherwise normal embryo. Conversely, ventral depletion of Tolloid, which stabilizes Chordin, decreased ventral and tail structures, phenocopying the tolloid zebrafish mutation. We explain how historical constraints recorded in the language of DNA become subject to the universal laws of physics when an ancestral reaction-diffusion morphogen gradient dictates form.
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Affiliation(s)
- Edward M De Robertis
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1662, USA
| | - Yuki Moriyama
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1662, USA
| | - Gabriele Colozza
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1662, USA
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152
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Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nat Commun 2017; 8:216. [PMID: 28790313 PMCID: PMC5548793 DOI: 10.1038/s41467-017-00238-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.
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Affiliation(s)
- Tamar Friedlander
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.,The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Roshan Prizak
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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153
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Poulin JF, Tasic B, Hjerling-Leffler J, Trimarchi JM, Awatramani R. Disentangling neural cell diversity using single-cell transcriptomics. Nat Neurosci 2017; 19:1131-41. [PMID: 27571192 DOI: 10.1038/nn.4366] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/22/2016] [Indexed: 12/12/2022]
Abstract
Cellular specialization is particularly prominent in mammalian nervous systems, which are composed of millions to billions of neurons that appear in thousands of different 'flavors' and contribute to a variety of functions. Even in a single brain region, individual neurons differ greatly in their morphology, connectivity and electrophysiological properties. Systematic classification of all mammalian neurons is a key goal towards deconstructing the nervous system into its basic components. With the recent advances in single-cell gene expression profiling technologies, it is now possible to undertake the enormous task of disentangling neuronal heterogeneity. High-throughput single-cell RNA sequencing and multiplexed quantitative RT-PCR have become more accessible, and these technologies enable systematic categorization of individual neurons into groups with similar molecular properties. Here we provide a conceptual and practical guide to classification of neural cell types using single-cell gene expression profiling technologies.
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Affiliation(s)
| | - Bosiljka Tasic
- Department of Molecular Genetics, Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jeffrey M Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
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154
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Abstract
A complex genetic repertoire underlies the apparently simple body plan of sponges. Among the genes present in poriferans are those fundamental to the sensory and nervous systems of other animals. Sponges are dynamic and sensitive animals and it is intuitive to link these genes to behaviour. The proposal that ctenophores are the earliest diverging metazoan has led to the question of whether sponges possess a 'pre-nervous' system or have undergone nervous system loss. Both lines of thought generally assume that the last common ancestor of sponges and eumetazoans possessed the genetic modules that underlie sensory abilities. By corollary extant sponges may possess a sensory cell homologous to one present in the last common ancestor, a hypothesis that has been studied by gene expression. We have performed a meta-analysis of all gene expression studies published to date to explore whether gene expression is indicative of a feature's sensory function. In sponges we find that eumetazoan sensory-neural markers are not particularly expressed in structures with known sensory functions. Instead it is common for these genes to be expressed in cells with no known or uncharacterized sensory function. Indeed, many sensory-neural markers so far studied are expressed during development, perhaps because many are transcription factors. This suggests that the genetic signal of a sponge sensory cell is dissimilar enough to be unrecognizable when compared to a bilaterian sensory or neural cell. It is possible that sensory-neural markers have as yet unknown functions in sponge cells, such as assembling an immunological synapse in the larval globular cell. Furthermore, the expression of sensory-neural markers in non-sensory cells, such as adult and larval epithelial cells, suggest that these cells may have uncharacterized sensory functions. While this does not rule out the co-option of ancestral sensory modules in later evolving groups, a distinct genetic foundation may underlie the sponge sensory system.
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Affiliation(s)
- Jasmine L Mah
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
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155
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Abstract
Regardless of how a nervous system is genetically built, natural selection is acting on the functional outcome of its activity. To understand how nervous systems evolve, it is essential to analyze how their functional units - the neural circuits - change and adapt over time. A neural circuit can evolve in many different ways, and the underlying developmental and genetic mechanisms involve different sets of genes. Therefore, the comparison of gene expression can help reconstructing circuit evolution, as demonstrated by several examples in sensory systems. Functional constraints on neural circuit evolution suggest that in nervous systems developmental and genetic variants do not appear randomly, and that the evolution of neuroanatomy might be biased. Sensory systems, in particular, seem to evolve along trajectories that enhance their evolvability, ensuring adaptation to different environments.
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Affiliation(s)
- Maria Antonietta Tosches
- Max Planck Institute for Brain Research, Max-von-Laue Strasse 4, 60438 Frankfurt am Main, Germany.
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156
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Cuevas-Diaz Duran R, Wei H, Wu JQ. Single-cell RNA-sequencing of the brain. Clin Transl Med 2017; 6:20. [PMID: 28597408 PMCID: PMC5465230 DOI: 10.1186/s40169-017-0150-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is revolutionizing our understanding of the genomic, transcriptomic and epigenomic landscapes of cells within organs. The mammalian brain is composed of a complex network of millions to billions of diverse cells with either highly specialized functions or support functions. With scRNA-seq it is possible to comprehensively dissect the cellular heterogeneity of brain cells, and elucidate their specific functions and state. In this review, we describe the current experimental methods used for scRNA-seq. We also review bioinformatic tools and algorithms for data analyses and discuss critical challenges. Additionally, we summarized recent mouse brain scRNA-seq studies and systematically compared their main experimental approaches, computational tools implemented, and important findings. scRNA-seq has allowed researchers to identify diverse cell subpopulations within many brain regions, pinpointing gene signatures and novel cell markers, as well as addressing functional differences. Due to the complexity of the brain, a great deal of work remains to be accomplished. Defining specific brain cell types and functions is critical for understanding brain function as a whole in development, health, and diseases.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA.
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157
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Abstract
The first animals evolved from an unknown single-celled ancestor in the Precambrian period. Recently, the identification and characterization of the genomic and cellular traits of the protists most closely related to animals have shed light on the origin of animals. Comparisons of animals with these unicellular relatives allow us to reconstruct the first evolutionary steps towards animal multicellularity. Here, we review the results of these investigations and discuss their implications for understanding the earliest stages of animal evolution, including the origin of metazoan genes and genome function.
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158
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Suzuki TK. On the Origin of Complex Adaptive Traits: Progress Since the Darwin Versus Mivart Debate. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:304-320. [PMID: 28397400 DOI: 10.1002/jez.b.22740] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 01/12/2023]
Abstract
The evolutionary origin of complex adaptive traits has been a controversial topic in the history of evolutionary biology. Although Darwin argued for the gradual origins of complex adaptive traits within the theory of natural selection, Mivart insisted that natural selection could not account for the incipient stages of complex traits. The debate starting from Darwin and Mivart eventually engendered two opposite views: gradualism and saltationism. Although this has been a long-standing debate, the issue remains unresolved. However, recent studies have interrogated classic examples of complex traits, such as the asymmetrical eyes of flatfishes and leaf mimicry of butterfly wings, whose origins were debated by Darwin and Mivart. Here, I review recent findings as a starting point to provide a modern picture of the evolution of complex adaptive traits. First, I summarize the empirical evidence that unveils the evolutionary steps toward complex traits. I then argue that the evolution of complex traits could be understood within the concept of "reducible complexity." Through these discussions, I propose a conceptual framework for the formation of complex traits, named as reducible-composable multicomponent systems, that satisfy two major characteristics: reducibility into a sum of subcomponents and composability to construct traits from various additional and combinatorial arrangements of the subcomponents. This conceptual framework provides an analytical foundation for exploring evolutionary pathways to build up complex traits. This review provides certain essential avenues for deciphering the origin of complex adaptive traits.
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Affiliation(s)
- Takao K Suzuki
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, NARO, Ibaraki, 305-8634, Japan
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159
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Griffith OW, Wagner GP. The placenta as a model for understanding the origin and evolution of vertebrate organs. Nat Ecol Evol 2017; 1:72. [DOI: 10.1038/s41559-017-0072] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/06/2017] [Indexed: 12/19/2022]
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160
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Tschopp P, Tabin CJ. Deep homology in the age of next-generation sequencing. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150475. [PMID: 27994118 PMCID: PMC5182409 DOI: 10.1098/rstb.2015.0475] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2016] [Indexed: 12/14/2022] Open
Abstract
The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term 'deep homology' was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput next-generation sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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161
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Leclère L, Röttinger E. Diversity of Cnidarian Muscles: Function, Anatomy, Development and Regeneration. Front Cell Dev Biol 2017; 4:157. [PMID: 28168188 PMCID: PMC5253434 DOI: 10.3389/fcell.2016.00157] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/30/2016] [Indexed: 12/12/2022] Open
Abstract
The ability to perform muscle contractions is one of the most important and distinctive features of eumetazoans. As the sister group to bilaterians, cnidarians (sea anemones, corals, jellyfish, and hydroids) hold an informative phylogenetic position for understanding muscle evolution. Here, we review current knowledge on muscle function, diversity, development, regeneration and evolution in cnidarians. Cnidarian muscles are involved in various activities, such as feeding, escape, locomotion and defense, in close association with the nervous system. This variety is reflected in the large diversity of muscle organizations found in Cnidaria. Smooth epithelial muscle is thought to be the most common type, and is inferred to be the ancestral muscle type for Cnidaria, while striated muscle fibers and non-epithelial myocytes would have been convergently acquired within Cnidaria. Current knowledge of cnidarian muscle development and its regeneration is limited. While orthologs of myogenic regulatory factors such as MyoD have yet to be found in cnidarian genomes, striated muscle formation potentially involves well-conserved myogenic genes, such as twist and mef2. Although satellite cells have yet to be identified in cnidarians, muscle plasticity (e.g., de- and re-differentiation, fiber repolarization) in a regenerative context and its potential role during regeneration has started to be addressed in a few cnidarian systems. The development of novel tools to study those organisms has created new opportunities to investigate in depth the development and regeneration of cnidarian muscle cells and how they contribute to the regenerative process.
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Affiliation(s)
- Lucas Leclère
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV) Villefranche-sur-mer, France
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN) Nice, France
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162
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Veiga-Fernandes H, Pachnis V. Neuroimmune regulation during intestinal development and homeostasis. Nat Immunol 2017; 18:116-122. [DOI: 10.1038/ni.3634] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/07/2016] [Indexed: 12/22/2022]
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163
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Veiga-Fernandes H, Mucida D. Neuro-Immune Interactions at Barrier Surfaces. Cell 2017; 165:801-11. [PMID: 27153494 DOI: 10.1016/j.cell.2016.04.041] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/23/2022]
Abstract
Multidirectional interactions between the nervous and immune systems have been documented in homeostasis and pathologies ranging from multiple sclerosis to autism, and from leukemia to acute and chronic inflammation. Recent studies have addressed this crosstalk using cell-specific targeting, novel sequencing, imaging, and analytical tools, shedding light on unappreciated mechanisms of neuro-immune regulation. This Review focuses on neuro-immune interactions at barrier surfaces-mostly the gut, but also including the skin and the airways, areas densely populated by neurons and immune cells that constantly sense and adapt to tissue-specific environmental challenges.
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Affiliation(s)
- Henrique Veiga-Fernandes
- Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028 Lisboa, Portugal.
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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164
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Aquatic Model Organisms in Neurosciences: The Genome-Editing Revolution. RESEARCH AND PERSPECTIVES IN NEUROSCIENCES 2017. [DOI: 10.1007/978-3-319-60192-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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165
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Brunet T, Fischer AH, Steinmetz PR, Lauri A, Bertucci P, Arendt D. The evolutionary origin of bilaterian smooth and striated myocytes. eLife 2016; 5. [PMID: 27906129 PMCID: PMC5167519 DOI: 10.7554/elife.19607] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/01/2016] [Indexed: 12/25/2022] Open
Abstract
The dichotomy between smooth and striated myocytes is fundamental for bilaterian musculature, but its evolutionary origin is unsolved. In particular, interrelationships of visceral smooth muscles remain unclear. Absent in fly and nematode, they have not yet been characterized molecularly outside vertebrates. Here, we characterize expression profile, ultrastructure, contractility and innervation of the musculature in the marine annelid Platynereis dumerilii and identify smooth muscles around the midgut, hindgut and heart that resemble their vertebrate counterparts in molecular fingerprint, contraction speed and nervous control. Our data suggest that both visceral smooth and somatic striated myocytes were present in the protostome-deuterostome ancestor and that smooth myocytes later co-opted the striated contractile module repeatedly – for example, in vertebrate heart evolution. During these smooth-to-striated myocyte conversions, the core regulatory complex of transcription factors conveying myocyte identity remained unchanged, reflecting a general principle in cell type evolution. DOI:http://dx.doi.org/10.7554/eLife.19607.001
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Affiliation(s)
- Thibaut Brunet
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antje Hl Fischer
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patrick Rh Steinmetz
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonella Lauri
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paola Bertucci
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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166
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Valero-Gracia A, Petrone L, Oliveri P, Nilsson DE, Arnone MI. Non-directional Photoreceptors in the Pluteus of Strongylocentrotus purpuratus. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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167
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Abstract
Cell types are the basic building blocks of multicellular organisms and are extensively diversified in animals. Despite recent advances in characterizing cell types, classification schemes remain ambiguous. We propose an evolutionary definition of a cell type that allows cell types to be delineated and compared within and between species. Key to cell type identity are evolutionary changes in the 'core regulatory complex' (CoRC) of transcription factors, that make emergent sister cell types distinct, enable their independent evolution and regulate cell type-specific traits termed apomeres. We discuss the distinction between developmental and evolutionary lineages, and present a roadmap for future research.
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168
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Wollny D, Zhao S, Everlien I, Lun X, Brunken J, Brüne D, Ziebell F, Tabansky I, Weichert W, Marciniak-Czochra A, Martin-Villalba A. Single-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult Pancreas. Dev Cell 2016; 39:289-301. [DOI: 10.1016/j.devcel.2016.10.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/09/2023]
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169
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Drexel T, Mahofsky K, Latham R, Zimmer M, Cochella L. Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegans. Genes Dev 2016; 30:2042-2047. [PMID: 27688400 PMCID: PMC5066611 DOI: 10.1101/gad.287904.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/29/2016] [Indexed: 11/24/2022]
Abstract
In this study, Drexel et al. research miRNA-mediated repression of broadly transcribed genes as a strategy for cellular specialization. They show that mir-791, expressed exclusively in the CO2-sensing neurons in C. elegans, represses two otherwise broadly expressed genes, which are needed for normal neuronal function and behavior of the animals toward CO2. Two broad gene classes are distinguished within multicellular organisms: cell type-specific genes, which confer particular cellular properties, and ubiquitous genes that support general cellular functions. However, certain so-called ubiquitous genes show functionally relevant cell type-specific repression. How such repression is achieved is poorly understood. MicroRNAs (miRNAs) are repressors, many of which are expressed with high cell type specificity. Here we show that mir-791, expressed exclusively in the CO2-sensing neurons in Caenorhabditis elegans, represses two otherwise broadly expressed genes. This repression is necessary for normal neuronal function and behavior of the animals toward CO2. miRNA-mediated repression of broadly transcribed genes is a previously unappreciated strategy for cellular specialization.
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Affiliation(s)
- Tanja Drexel
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Katharina Mahofsky
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Richard Latham
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Manuel Zimmer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
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170
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Affiliation(s)
- Casey W. Dunn
- Department of Ecology and Evolutionary Biology Brown University 80 Waterman St Providence RIUSA
| | - Catriona Munro
- Department of Ecology and Evolutionary Biology Brown University 80 Waterman St Providence RIUSA
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171
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Wenger Y, Buzgariu W, Galliot B. Loss of neurogenesis in Hydra leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150040. [PMID: 26598723 PMCID: PMC4685579 DOI: 10.1098/rstb.2015.0040] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hydra continuously differentiates a sophisticated nervous system made of mechanosensory cells (nematocytes) and sensory-motor and ganglionic neurons from interstitial stem cells. However, this dynamic adult neurogenesis is dispensable for morphogenesis. Indeed animals depleted of their interstitial stem cells and interstitial progenitors lose their active behaviours but maintain their developmental fitness, and regenerate and bud when force-fed. To characterize the impact of the loss of neurogenesis in Hydra, we first performed transcriptomic profiling at five positions along the body axis. We found neurogenic genes predominantly expressed along the central body column, which contains stem cells and progenitors, and neurotransmission genes predominantly expressed at the extremities, where the nervous system is dense. Next, we performed transcriptomics on animals depleted of their interstitial cells by hydroxyurea, colchicine or heat-shock treatment. By crossing these results with cell-type-specific transcriptomics, we identified epithelial genes up-regulated upon loss of neurogenesis: transcription factors (Dlx, Dlx1, DMBX1/Manacle, Ets1, Gli3, KLF11, LMX1A, ZNF436, Shox1), epitheliopeptides (Arminins, PW peptide), neurosignalling components (CAMK1D, DDCl2, Inx1), ligand-ion channel receptors (CHRNA1, NaC7), G-Protein Coupled Receptors and FMRFRL. Hence epitheliomuscular cells seemingly enhance their sensing ability when neurogenesis is compromised. This unsuspected plasticity might reflect the extended multifunctionality of epithelial-like cells in early eumetazoan evolution.
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Affiliation(s)
- Y Wenger
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (IGe3), Faculty of Sciences, University of Geneva, 30 quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - W Buzgariu
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (IGe3), Faculty of Sciences, University of Geneva, 30 quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - B Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (IGe3), Faculty of Sciences, University of Geneva, 30 quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
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172
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Arendt D, Benito-Gutierrez E, Brunet T, Marlow H. Gastric pouches and the mucociliary sole: setting the stage for nervous system evolution. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0286. [PMID: 26554050 PMCID: PMC4650134 DOI: 10.1098/rstb.2015.0286] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Prerequisite for tracing nervous system evolution is understanding of the body plan, feeding behaviour and locomotion of the first animals in which neurons evolved. Here, a comprehensive scenario is presented for the diversification of cell types in early metazoans, which enhanced feeding efficiency and led to the emergence of larger animals that were able to move. Starting from cup-shaped, gastraea-like animals with outer and inner choanoflagellate-like cells, two major innovations are discussed that set the stage for nervous system evolution. First, the invention of a mucociliary sole entailed a switch from intra- to extracellular digestion and increased the concentration of nutrients flowing into the gastric cavity. In these animals, an initial nerve net may have evolved via division of labour from mechanosensory-contractile cells in the lateral body wall, enabling coordinated movement of the growing body that involved both mucociliary creeping and changes of body shape. Second, the inner surface of the animals folded into metameric series of gastric pouches, which optimized nutrient resorption and allowed larger body sizes. The concomitant acquisition of bilateral symmetry may have allowed more directed locomotion and, with more demanding coordinative tasks, triggered the evolution of specialized nervous subsystems. Animals of this organizational state would have resembled Ediacarian fossils such as Dickinsonia and may have been close to the cnidarian–bilaterian ancestor. In the bilaterian lineage, the mucociliary sole was used mostly for creeping, or frequently lost. One possible remnant is the enigmatic Reissner's fibre in the ventral neural tube of cephalochordates and vertebrates.
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Affiliation(s)
- Detlev Arendt
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | | | - Thibaut Brunet
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Heather Marlow
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
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173
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Kin K, Maziarz J, Chavan AR, Kamat M, Vasudevan S, Birt A, Emera D, Lynch VJ, Ott TL, Pavlicev M, Wagner GP. The Transcriptomic Evolution of Mammalian Pregnancy: Gene Expression Innovations in Endometrial Stromal Fibroblasts. Genome Biol Evol 2016; 8:2459-73. [PMID: 27401177 PMCID: PMC5010902 DOI: 10.1093/gbe/evw168] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The endometrial stromal fibroblast (ESF) is a cell type present in the uterine lining of therian mammals. In the stem lineage of eutherian mammals, ESF acquired the ability to differentiate into decidual cells in order to allow embryo implantation. We call the latter cell type "neo-ESF" in contrast to "paleo-ESF" which is homologous to eutherian ESF but is not able to decidualize. In this study, we compare the transcriptomes of ESF from six therian species: Opossum (Monodelphis domestica; paleo-ESF), mink, rat, rabbit, human (all neo-ESF), and cow (secondarily nondecidualizing neo-ESF). We find evidence for strong stabilizing selection on transcriptome composition suggesting that the expression of approximately 5,600 genes is maintained by natural selection. The evolution of neo-ESF from paleo-ESF involved the following gene expression changes: Loss of expression of genes related to inflammation and immune response, lower expression of genes opposing tissue invasion, increased markers for proliferation as well as the recruitment of FOXM1, a key gene transiently expressed during decidualization. Signaling pathways also evolve rapidly and continue to evolve within eutherian lineages. In the bovine lineage, where invasiveness and decidualization were secondarily lost, we see a re-expression of genes found in opossum, most prominently WISP2, and a loss of gene expression related to angiogenesis. The data from this and previous studies support a scenario, where the proinflammatory paleo-ESF was reprogrammed to express anti-inflammatory genes in response to the inflammatory stimulus coming from the implanting conceptus and thus paving the way for extended, trans-cyclic gestation.
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Affiliation(s)
- Koryu Kin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut Yale Systems Biology Institute, Yale University, West Haven, Connecticut
| | - Jamie Maziarz
- Yale Systems Biology Institute, Yale University, West Haven, Connecticut
| | - Arun R Chavan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut Yale Systems Biology Institute, Yale University, West Haven, Connecticut
| | - Manasi Kamat
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, Stage College, Pennsylvania
| | - Sreelakshmi Vasudevan
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, Stage College, Pennsylvania
| | - Alyssa Birt
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, Stage College, Pennsylvania
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Vincent J Lynch
- Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Troy L Ott
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, Stage College, Pennsylvania
| | - Mihaela Pavlicev
- Department of Pediatrics, Cincinnati Children's Hospital and Medical Center, Cincinnati, Ohio
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut Yale Systems Biology Institute, Yale University, West Haven, Connecticut Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School, New Haven, Connecticut Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan
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174
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Coskun AF, Eser U, Islam S. Cellular identity at the single-cell level. MOLECULAR BIOSYSTEMS 2016; 12:2965-79. [PMID: 27460751 DOI: 10.1039/c6mb00388e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine.
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Affiliation(s)
- Ahmet F Coskun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, California, USA.
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175
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Abstract
Our skeletons evolved from cartilaginous tissue, but it remains a mystery how cartilage itself first arose in evolution. Characterization of cartilage in cuttlefish and horseshoe crabs reveals surprising commonalities with chordate chondrocytes, suggesting a common evolutionary origin.
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Affiliation(s)
- Thibaut Brunet
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69017 Heidelberg, Germany.
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69017 Heidelberg, Germany.
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176
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Adamska M. Sponges as models to study emergence of complex animals. Curr Opin Genet Dev 2016; 39:21-28. [PMID: 27318691 DOI: 10.1016/j.gde.2016.05.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/20/2016] [Accepted: 05/30/2016] [Indexed: 02/05/2023]
Abstract
The emergence of complex animal life forms remains poorly understood despite substantial interest and research in this area. To be informative, the ideal models to study transitions from single-cell organisms to the first animals and then to mammalian-level complexity should be phylogenetically strategically placed and retain ancestral characters. Sponges (Porifera) are likely to be the earliest branching animal phylum. When analysed from morphological, genomic and developmental perspectives, sponges appear to combine features of single-cell eukaryotic organisms and the complex multicellular animals (Eumetazoa). Intriguingly, homologues of components of the eumetazoan regulatory networks specifying the endoderm, the germ-cells and stem cells and (neuro) sensory cells are expressed in sponge choanocytes, archaeocytes and larval sensory cells. Studies using sponges as model systems are already bringing insights into animal evolution, and have opened avenues to further research benefitting from the recent spectacular expansion of genomic technologies.
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Affiliation(s)
- Maja Adamska
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
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177
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Tissue biology perspective on macrophages. Nat Immunol 2016; 17:9-17. [PMID: 26681457 DOI: 10.1038/ni.3320] [Citation(s) in RCA: 440] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
Macrophages are essential components of mammalian tissues. Although historically known mainly for their function in host defense and the clearance of apoptotic cells, macrophages are now increasingly recognized as serving many roles in tissue development, homeostasis and repair. In addition, tissue-resident macrophages have many tissue-specific functional characteristics, which are a reflection of distinct gene-expression programs. Here we discuss the emerging views of macrophage biology from evolutionary, developmental and homeostatic perspectives.
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178
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The genetic program for cartilage development has deep homology within Bilateria. Nature 2016; 533:86-9. [PMID: 27111511 DOI: 10.1038/nature17398] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 02/04/2016] [Indexed: 12/28/2022]
Abstract
The evolution of novel cell types led to the emergence of new tissues and organs during the diversification of animals. The origin of the chondrocyte, the cell type that synthesizes cartilage matrix, was central to the evolution of the vertebrate endoskeleton. Cartilage-like tissues also exist outside the vertebrates, although their relationship to vertebrate cartilage is enigmatic. Here we show that protostome and deuterostome cartilage share structural and chemical properties, and that the mechanisms of cartilage development are extensively conserved--from induction of chondroprogenitor cells by Hedgehog and β-catenin signalling, to chondrocyte differentiation and matrix synthesis by SoxE and SoxD regulation of clade A fibrillar collagen (ColA) genes--suggesting that the chondrogenic gene regulatory network evolved in the common ancestor of Bilateria. These results reveal deep homology of the genetic program for cartilage development in Bilateria and suggest that activation of this ancient core chondrogenic network underlies the parallel evolution of cartilage tissues in Ecdysozoa, Lophotrochozoa and Deuterostomia.
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179
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Sigola LB, Fuentes AL, Millis LM, Vapenik J, Murira A. Effects of Toll-like receptor ligands on RAW 264.7 macrophage morphology and zymosan phagocytosis. Tissue Cell 2016; 48:389-96. [PMID: 27157550 DOI: 10.1016/j.tice.2016.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 02/01/2016] [Accepted: 04/21/2016] [Indexed: 01/21/2023]
Abstract
In this study we compared the effects of the Toll-like receptor (TLR) ligands lipopolysaccharide (LPS), flagellin, the synthetic bacterial triacylated lipopeptide Pam3-Cys-Ser-Lys4 (Pam3CSK4), Polyinosinic:polycytidylic acid (Poly I:C), and macrophage-activating lipopeptide (MALP-2), which are TLR4, TLR5, TLR1/2, TLR3, and TLR2/6 agonists, respectively, on cell morphology and phagocytosis of zymosan particles, derived from Saccharomyces cerevisiae, and rich in fungal PAMPs including beta-glucan, mannose, and chitin. LPS, Pam3CSK4, and MALP-2 induced an activated macrophage phenotype and enhanced zymosan phagocytosis. In contrast, flagellin and Poly I:C, respectively, had little effect on cell morphology and phagocytosis. We examined the role of scavenger receptor A (SR-A) on zymosan phagocytosis. Cells cultured in medium alone expressed SR-A, and LPS induced further expression of the receptor. We also observed inhibitory effects of scavenger receptor antagonists fucoidan, dextran sulphate, and Polyinosinic (Poly I), respectively, on zymosan phagocytosis of cells in medium alone and those pre-treated with LPS. We conclude that exposure to specific TLR ligands impacts both cellular morphology and phagocytic capacity, and that scavenger receptors contribute to zymosan ingestion as well as LPS-induced augmentation of phagocytosis.
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Affiliation(s)
- Lynette B Sigola
- Biology Department, Douglas College, P.O. Box 2503, New Westminster B.C. V3L 5B2, Canada.
| | - Ana-Lucía Fuentes
- Biology Department, Douglas College, P.O. Box 2503, New Westminster B.C. V3L 5B2, Canada
| | - Leonard M Millis
- Biology Department, Douglas College, P.O. Box 2503, New Westminster B.C. V3L 5B2, Canada
| | - Jacqueline Vapenik
- Faculty of Health Sciences, Douglas College, P.O. Box 2503, New Westminster B.C. V3L 5B2, Canada
| | - Armstrong Murira
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6 Canada
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180
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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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181
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What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy. Placenta 2016; 40:40-51. [DOI: 10.1016/j.placenta.2016.02.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023]
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182
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Nair NU, Hunter L, Shao M, Grnarova P, Lin Y, Bucher P, E Moret BM. A maximum-likelihood approach for building cell-type trees by lifting. BMC Genomics 2016; 17 Suppl 1:14. [PMID: 26819094 PMCID: PMC4895258 DOI: 10.1186/s12864-015-2297-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modifications are known to play a significant role in cell differentiation. We previously introduce cell-type trees to represent the differentiation of cells into more specialized types, a representation that partakes of both ontogeny and phylogeny. RESULTS We propose a maximum-likelihood (ML) approach to build cell-type trees and show that this ML approach outperforms our earlier distance-based and parsimony-based approaches. We then study the reconstruction of ancestral cell types; since both ancestral and derived cell types can coexist in adult organisms, we propose a lifting algorithm to infer internal nodes. We present results on our lifting algorithm obtained both through simulations and on real datasets. CONCLUSIONS We show that our ML-based approach outperforms previously proposed techniques such as distance-based and parsimony-based methods. We show our lifting-based approach works well on both simulated and real data.
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Affiliation(s)
- Nishanth Ulhas Nair
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
| | - Laura Hunter
- Computer Science Department, Stanford University, Stanford, USA.
| | - Mingfu Shao
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
| | - Paulina Grnarova
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
| | - Yu Lin
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, USA.
| | - Philipp Bucher
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Bernard M E Moret
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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183
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Moroz LL, Kohn AB. Independent origins of neurons and synapses: insights from ctenophores. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150041. [PMID: 26598724 PMCID: PMC4685580 DOI: 10.1098/rstb.2015.0041] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2015] [Indexed: 12/29/2022] Open
Abstract
There is more than one way to develop neuronal complexity, and animals frequently use different molecular toolkits to achieve similar functional outcomes. Genomics and metabolomics data from basal metazoans suggest that neural signalling evolved independently in ctenophores and cnidarians/bilaterians. This polygenesis hypothesis explains the lack of pan-neuronal and pan-synaptic genes across metazoans, including remarkable examples of lineage-specific evolution of neurogenic and signalling molecules as well as synaptic components. Sponges and placozoans are two lineages without neural and muscular systems. The possibility of secondary loss of neurons and synapses in the Porifera/Placozoa clades is a highly unlikely and less parsimonious scenario. We conclude that acetylcholine, serotonin, histamine, dopamine, octopamine and gamma-aminobutyric acid (GABA) were recruited as transmitters in the neural systems in cnidarian and bilaterian lineages. By contrast, ctenophores independently evolved numerous secretory peptides, indicating extensive adaptations within the clade and suggesting that early neural systems might be peptidergic. Comparative analysis of glutamate signalling also shows numerous lineage-specific innovations, implying the extensive use of this ubiquitous metabolite and intercellular messenger over the course of convergent and parallel evolution of mechanisms of intercellular communication. Therefore: (i) we view a neuron as a functional character but not a genetic character, and (ii) any given neural system cannot be considered as a single character because it is composed of different cell lineages with distinct genealogies, origins and evolutionary histories. Thus, when reconstructing the evolution of nervous systems, we ought to start with the identification of particular cell lineages by establishing distant neural homologies or examples of convergent evolution. In a corollary of the hypothesis of the independent origins of neurons, our analyses suggest that both electrical and chemical synapses evolved more than once.
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Affiliation(s)
- Leonid L Moroz
- The Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Andrea B Kohn
- The Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA
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184
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Brunet T, Arendt D. From damage response to action potentials: early evolution of neural and contractile modules in stem eukaryotes. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150043. [PMID: 26598726 PMCID: PMC4685582 DOI: 10.1098/rstb.2015.0043] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells convert external stimuli into membrane depolarization, which in turn triggers effector responses such as secretion and contraction. Here, we put forward an evolutionary hypothesis for the origin of the depolarization-contraction-secretion (DCS) coupling, the functional core of animal neuromuscular circuits. We propose that DCS coupling evolved in unicellular stem eukaryotes as part of an 'emergency response' to calcium influx upon membrane rupture. We detail how this initial response was subsequently modified into an ancient mechanosensory-effector arc, present in the last eukaryotic common ancestor, which enabled contractile amoeboid movement that is widespread in extant eukaryotes. Elaborating on calcium-triggered membrane depolarization, we reason that the first action potentials evolved alongside the membrane of sensory-motile cilia, with the first voltage-sensitive sodium/calcium channels (Nav/Cav) enabling a fast and coordinated response of the entire cilium to mechanosensory stimuli. From the cilium, action potentials then spread across the entire cell, enabling global cellular responses such as concerted contraction in several independent eukaryote lineages. In animals, this process led to the invention of mechanosensory contractile cells. These gave rise to mechanosensory receptor cells, neurons and muscle cells by division of labour and can be regarded as the founder cell type of the nervous system.
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Affiliation(s)
- Thibaut Brunet
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg 69012, Germany
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg 69012, Germany
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185
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Borowiec ML, Lee EK, Chiu JC, Plachetzki DC. Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics 2015; 16:987. [PMID: 26596625 PMCID: PMC4657218 DOI: 10.1186/s12864-015-2146-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/26/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans. RESULTS To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction. CONCLUSIONS Our study further clarifies relationships among early branching metazoan lineages. Our phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans. This study also provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses. Future studies of metazoan phylogeny will benefit from ongoing efforts to sequence the genomes of additional invertebrate taxa that will continue to inform our view of the relationships among the major lineages of animals.
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Affiliation(s)
- Marek L Borowiec
- Department of Entomology and Nematology, University of California, Davis, USA.
| | - Ernest K Lee
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, USA.
| | - Joanna C Chiu
- Department of Entomology and Nematology, University of California, Davis, USA.
| | - David C Plachetzki
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, USA.
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186
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Wagner GP. What is “homology thinking” and what is it for? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 326:3-8. [DOI: 10.1002/jez.b.22656] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/29/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Günter P. Wagner
- Departments of Ecology and Evolutionary Biology, Obstetrics, Gynecology and Reproductive SciencesYale Systems Biology InstituteYale UniversityNew HavenConnecticut
- Department of Obstetrics and GynecologyWayne State UniversityDetroitMichigan
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187
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Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP. BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses. BMC Genomics 2015; 16:814. [PMID: 26481321 PMCID: PMC4617899 DOI: 10.1186/s12864-015-2012-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 10/07/2015] [Indexed: 12/21/2022] Open
Abstract
Background Recent advances in the analysis of high-throughput expression data have led to the development of tools that scaled-up their focus from single-gene to gene set level. For example, the popular Gene Set Enrichment Analysis (GSEA) algorithm can detect moderate but coordinated expression changes of groups of presumably related genes between pairs of experimental conditions. This considerably improves extraction of information from high-throughput gene expression data. However, although many gene sets covering a large panel of biological fields are available in public databases, the ability to generate home-made gene sets relevant to one’s biological question is crucial but remains a substantial challenge to most biologists lacking statistic or bioinformatic expertise. This is all the more the case when attempting to define a gene set specific of one condition compared to many other ones. Thus, there is a crucial need for an easy-to-use software for generation of relevant home-made gene sets from complex datasets, their use in GSEA, and the correction of the results when applied to multiple comparisons of many experimental conditions. Result We developed BubbleGUM (GSEA Unlimited Map), a tool that allows to automatically extract molecular signatures from transcriptomic data and perform exhaustive GSEA with multiple testing correction. One original feature of BubbleGUM notably resides in its capacity to integrate and compare numerous GSEA results into an easy-to-grasp graphical representation. We applied our method to generate transcriptomic fingerprints for murine cell types and to assess their enrichments in human cell types. This analysis allowed us to confirm homologies between mouse and human immunocytes. Conclusions BubbleGUM is an open-source software that allows to automatically generate molecular signatures out of complex expression datasets and to assess directly their enrichment by GSEA on independent datasets. Enrichments are displayed in a graphical output that helps interpreting the results. This innovative methodology has recently been used to answer important questions in functional genomics, such as the degree of similarities between microarray datasets from different laboratories or with different experimental models or clinical cohorts. BubbleGUM is executable through an intuitive interface so that both bioinformaticians and biologists can use it. It is available at http://www.ciml.univ-mrs.fr/applications/BubbleGUM/index.html. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2012-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lionel Spinelli
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
| | | | - Frédéric Montañana Sanchis
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
| | - Marc Dalod
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
| | - Thien-Phong Vu Manh
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
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188
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de Mendoza A, Suga H, Permanyer J, Irimia M, Ruiz-Trillo I. Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. eLife 2015; 4:e08904. [PMID: 26465111 PMCID: PMC4739763 DOI: 10.7554/elife.08904] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/13/2015] [Indexed: 12/14/2022] Open
Abstract
Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. To address this question, we investigated transcriptional dynamics in the ichthyosporean Creolimax fragrantissima, a relative of animals that undergoes coenocytic development. We find that Creolimax utilizes dynamic regulation of alternative splicing, long inter-genic non-coding RNAs and co-regulated gene modules associated with animal multicellularity in a cell-type specific manner. Moreover, our study suggests that the different cell types of the three closest animal relatives (ichthyosporeans, filastereans and choanoflagellates) are the product of lineage-specific innovations. Additionally, a proteomic survey of the secretome reveals adaptations to a fungal-like lifestyle. In summary, the diversity of cell types among protistan relatives of animals and their complex genome regulation demonstrates that the last unicellular ancestor of animals was already capable of elaborate specification of cell types. DOI:http://dx.doi.org/10.7554/eLife.08904.001 All living animals are descended from a single-celled ancestor, and understanding how these ancestors became the first multicellular animals remains a major challenge in the field of evolutionary biology. An early breakthrough towards this goal was the realization that, even though they’re mostly single-celled organisms, the closest living relatives of animals share most of the basic gene toolkit that animals use to support their multicellular lifestyles. This shared toolkit also includes the genes that allow each specialized cell type in an animal (for example, a skin cell or liver cell) to express the subset of genes that it needs to fulfil its specific role. Discovering how the single-celled relatives of animals regulate these and other “multicellularity-related” genes during their life cycles is the next crucial step towards understanding how animals became multicellular. Creolimax fragrantissima is a single-celled relative of animals. One stage in this organism’s life cycle involves its nucleus (which contains its genetic material) replicating multiple times without the cell itself dividing. After this stage of development, new cells are formed, each receiving with a single nucleus, and released to live freely in the environment. Characterizing how C. fragrantissima regulates which genes are expressed during these two very different stages of development could shed new light on how multicellular animals evolved to regulate their genes in specific cell types. However, little is known about these processes in C. fragrantissima. Now, de Mendoza et al. have both sequenced C. fragrantissima’s genome and analysed which genes are expressed during the stages of its life cycle. This analysis reveals that this organism regulates its gene expression in several ways that are more commonly associated with gene regulation in multicellular animals. Furthermore, when compared to two other living relatives of animals that have brief multicellular stages in their life cycles, de Mendoza et al. found that the three organisms expressed similar genes during these similar life cycle stages. Furthermore, like fungi, C. fragrantissima digests its food externally and then absorbs the nutrients. Using a range of techniques, de Mendoza et al. identified the proteins involved in these processes and discovered that many had evolved independently from their counterparts in fungi. Furthermore, in some cases, the genes for these proteins had actually been acquired from bacteria via a process called lateral gene transfer. Together these findings suggest that it was likely that the last single-celled ancestor of multicellular animals already had the biological ability to create different cell types. Understanding if the cell types found in single-celled species resemble cell types from simple animals, such as sponges and comb jellies, at a molecular level is the next step towards determining what the ancestor of living animals looked like. DOI:http://dx.doi.org/10.7554/eLife.08904.002
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Affiliation(s)
- Alex de Mendoza
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
| | - Hiroshi Suga
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain.,Prefectural University of Hiroshima, Shobara, Japan
| | - Jon Permanyer
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Irimia
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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189
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Kin K. Inferring cell type innovations by phylogenetic methods-concepts, methods, and limitations. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:653-61. [PMID: 26462996 DOI: 10.1002/jez.b.22657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 09/29/2015] [Indexed: 12/17/2022]
Abstract
Multicellular organisms are composed of distinct cell types that have specific roles in the body. Each cell type is a product of two kinds of historical processes-development and evolution. Although the concept of a cell type is difficult to define, the cell type concept based on the idea of the core regulatory network (CRN), a gene regulatory network that determines the identity of a cell type, illustrates the essential aspects of the cell type concept. The first step toward elucidating cell type evolution is to reconstruct the evolutionary relationships of cell types, or the cell type tree. The sister cell type model assumes that a new cell type evolves through divergence from a multifunctional ancestral cell type, creating tree-like evolutionary relationships between cell types. The process of generating a cell type tree can also be understood as the sequential addition of a new branching point on an ancestral cell differentiation hierarchy in evolution. A cell type tree thus represents an intertwined history of cell type evolution and development. Cell type trees can be reconstructed from high-throughput sequencing data, and the reconstruction of a cell type tree leads to the discovery of genes that are functionally important for a cell type. Although many issues including the lack of cross-species comparisons and the lack of a proper model for cell type evolution remain, the study of the origin of a new cell type using phylogenetic methods offers a promising new research avenue in developmental evolution. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 653-661, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Koryu Kin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut.,Yale Systems Biology Institute, Yale University, West Haven, Connecticut
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190
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Gómez-Picos P, Eames BF. On the evolutionary relationship between chondrocytes and osteoblasts. Front Genet 2015; 6:297. [PMID: 26442113 PMCID: PMC4585068 DOI: 10.3389/fgene.2015.00297] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/07/2015] [Indexed: 11/17/2022] Open
Abstract
Vertebrates are the only animals that produce bone, but the molecular genetic basis for this evolutionary novelty remains obscure. Here, we synthesize information from traditional evolutionary and modern molecular genetic studies in order to generate a working hypothesis on the evolution of the gene regulatory network (GRN) underlying bone formation. Since transcription factors are often core components of GRNs (i.e., kernels), we focus our analyses on Sox9 and Runx2. Our argument centers on three skeletal tissues that comprise the majority of the vertebrate skeleton: immature cartilage, mature cartilage, and bone. Immature cartilage is produced during early stages of cartilage differentiation and can persist into adulthood, whereas mature cartilage undergoes additional stages of differentiation, including hypertrophy and mineralization. Functionally, histologically, and embryologically, these three skeletal tissues are very similar, yet unique, suggesting that one might have evolved from another. Traditional studies of the fossil record, comparative anatomy and embryology demonstrate clearly that immature cartilage evolved before mature cartilage or bone. Modern molecular approaches show that the GRNs regulating differentiation of these three skeletal cell fates are similar, yet unique, just like the functional and histological features of the tissues themselves. Intriguingly, the Sox9 GRN driving cartilage formation appears to be dominant to the Runx2 GRN of bone. Emphasizing an embryological and evolutionary transcriptomic view, we hypothesize that the Runx2 GRN underlying bone formation was co-opted from mature cartilage. We discuss how modern molecular genetic experiments, such as comparative transcriptomics, can test this hypothesis directly, meanwhile permitting levels of constraint and adaptation to be evaluated quantitatively. Therefore, comparative transcriptomics may revolutionize understanding of not only the clade-specific evolution of skeletal cells, but also the generation of evolutionary novelties, providing a modern paradigm for the evolutionary process.
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Affiliation(s)
- Patsy Gómez-Picos
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK Canada
| | - B Frank Eames
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK Canada
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191
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Enault S, Muñoz DN, Silva WTAF, Borday-Birraux V, Bonade M, Oulion S, Ventéo S, Marcellini S, Debiais-Thibaud M. Molecular footprinting of skeletal tissues in the catshark Scyliorhinus canicula and the clawed frog Xenopus tropicalis identifies conserved and derived features of vertebrate calcification. Front Genet 2015; 6:283. [PMID: 26442101 PMCID: PMC4584932 DOI: 10.3389/fgene.2015.00283] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/24/2015] [Indexed: 12/22/2022] Open
Abstract
Understanding the evolutionary emergence and subsequent diversification of the vertebrate skeleton requires a comprehensive view of the diverse skeletal cell types found in distinct developmental contexts, tissues, and species. To date, our knowledge of the molecular nature of the shark calcified extracellular matrix, and its relationships with osteichthyan skeletal tissues, remain scarce. Here, based on specific combinations of expression patterns of the Col1a1, Col1a2, and Col2a1 fibrillar collagen genes, we compare the molecular footprint of endoskeletal elements from the chondrichthyan Scyliorhinus canicula and the tetrapod Xenopus tropicalis. We find that, depending on the anatomical location, Scyliorhinus skeletal calcification is associated to cell types expressing different subsets of fibrillar collagen genes, such as high levels of Col1a1 and Col1a2 in the neural arches, high levels of Col2a1 in the tesserae, or associated to a drastic Col2a1 downregulation in the centrum. We detect low Col2a1 levels in Xenopus osteoblasts, thereby revealing that the osteoblastic expression of this gene was significantly reduced in the tetrapod lineage. Finally, we uncover a striking parallel, from a molecular and histological perspective, between the vertebral cartilage calcification of both species and discuss the evolutionary origin of endochondral ossification.
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Affiliation(s)
- Sébastien Enault
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université Montpellier, Centre National de la Recherche Scientifique, IRD, EPHE Montpellier, France
| | - David N Muñoz
- Laboratory of Development and Evolution, Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Willian T A F Silva
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université Montpellier, Centre National de la Recherche Scientifique, IRD, EPHE Montpellier, France
| | - Véronique Borday-Birraux
- Laboratoire EGCE UMR Centre National de la Recherche Scientifique 9191, IRD247, Université Paris Sud Gif-sur-Yvette, France ; Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Morgane Bonade
- Laboratoire EGCE UMR Centre National de la Recherche Scientifique 9191, IRD247, Université Paris Sud Gif-sur-Yvette, France
| | - Silvan Oulion
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université Montpellier, Centre National de la Recherche Scientifique, IRD, EPHE Montpellier, France
| | - Stéphanie Ventéo
- Institute for Neurosciences of Montpellier, Institut National de la Santé et de la Recherche Médicale U1051 Montpellier, France
| | - Sylvain Marcellini
- Laboratory of Development and Evolution, Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université Montpellier, Centre National de la Recherche Scientifique, IRD, EPHE Montpellier, France
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192
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Whittington CM, Griffith OW, Qi W, Thompson MB, Wilson AB. Seahorse Brood Pouch Transcriptome Reveals Common Genes Associated with Vertebrate Pregnancy. Mol Biol Evol 2015; 32:3114-31. [PMID: 26330546 DOI: 10.1093/molbev/msv177] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viviparity (live birth) has evolved more than 150 times in vertebrates, and represents an excellent model system for studying the evolution of complex traits. There are at least 23 independent origins of viviparity in fishes, with syngnathid fishes (seahorses and pipefish) unique in exhibiting male pregnancy. Male seahorses and pipefish have evolved specialized brooding pouches that provide protection, gas exchange, osmoregulation, and limited nutrient provisioning to developing embryos. Pouch structures differ widely across the Syngnathidae, offering an ideal opportunity to study the evolution of reproductive complexity. However, the physiological and genetic changes facilitating male pregnancy are largely unknown. We used transcriptome profiling to examine pouch gene expression at successive gestational stages in a syngnathid with the most complex brood pouch morphology, the seahorse Hippocampus abdominalis. Using a unique time-calibrated RNA-seq data set including brood pouch at key stages of embryonic development, we identified transcriptional changes associated with brood pouch remodeling, nutrient and waste transport, gas exchange, osmoregulation, and immunological protection of developing embryos at conception, development and parturition. Key seahorse transcripts share homology with genes of reproductive function in pregnant mammals, reptiles, and other live-bearing fish, suggesting a common toolkit of genes regulating pregnancy in divergent evolutionary lineages.
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Affiliation(s)
- Camilla M Whittington
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Oliver W Griffith
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Centre, University of Zurich, Zurich, Switzerland
| | - Michael B Thompson
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anthony B Wilson
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia Department of Biology, Brooklyn College The Graduate Center, City University of New York
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193
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Abstract
The non-bilaterian animals comprise organisms in the phyla Porifera, Cnidaria, Ctenophora and Placozoa. These early-diverging phyla are pivotal to understanding the evolution of bilaterian animals. After the exponential increase in research in evolutionary development (evo-devo) in the last two decades, these organisms are again in the spotlight of evolutionary biology. In this work, I briefly review some aspects of the developmental biology of nonbilaterians that contribute to understanding the evolution of development and of the metazoans. The evolution of the developmental genetic toolkit, embryonic polarization, the origin of gastrulation and mesodermal cells, and the origin of neural cells are discussed. The possibility that germline and stem cell lineages have the same origin is also examined. Although a considerable number of non-bilaterian species are already being investigated, the use of species belonging to different branches of non-bilaterian lineages and functional experimentation with gene manipulation in the majority of the non-bilaterian lineages will be necessary for further progress in this field.
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Affiliation(s)
- Emilio Lanna
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal da Bahia, Salvador, BA, Brazil
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194
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Martinez-Morales JR. Toward understanding the evolution of vertebrate gene regulatory networks: comparative genomics and epigenomic approaches. Brief Funct Genomics 2015; 15:315-21. [PMID: 26293604 DOI: 10.1093/bfgp/elv032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vertebrates, as most animal phyla, originated >500 million years ago during the Cambrian explosion, and progressively radiated into the extant classes. Inferring the evolutionary history of the group requires understanding the architecture of the developmental programs that constrain the vertebrate anatomy. Here, I review recent comparative genomic and epigenomic studies, based on ChIP-seq and chromatin accessibility, which focus on the identification of functionally equivalent cis-regulatory modules among species. This pioneer work, primarily centered in the mammalian lineage, has set the groundwork for further studies in representative vertebrate and chordate species. Mapping of active regulatory regions across lineages will shed new light on the evolutionary forces stabilizing ancestral developmental programs, as well as allowing their variation to sustain morphological adaptations on the inherited vertebrate body plan.
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195
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The pre-vertebrate origins of neurogenic placodes. Nature 2015; 524:462-5. [PMID: 26258298 DOI: 10.1038/nature14657] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/09/2015] [Indexed: 11/09/2022]
Abstract
The sudden appearance of the neural crest and neurogenic placodes in early branching vertebrates has puzzled biologists for over a century. These embryonic tissues contribute to the development of the cranium and associated sensory organs, which were crucial for the evolution of the vertebrate "new head". A previous study suggests that rudimentary neural crest cells existed in ancestral chordates. However, the evolutionary origins of neurogenic placodes have remained obscure owing to a paucity of embryonic data from tunicates, the closest living relatives to those early vertebrates. Here we show that the tunicate Ciona intestinalis exhibits a proto-placodal ectoderm (PPE) that requires inhibition of bone morphogenetic protein (BMP) and expresses the key regulatory determinant Six1/2 and its co-factor Eya, a developmental process conserved across vertebrates. The Ciona PPE is shown to produce ciliated neurons that express genes for gonadotropin-releasing hormone (GnRH), a G-protein-coupled receptor for relaxin-3 (RXFP3) and a functional cyclic nucleotide-gated channel (CNGA), which suggests dual chemosensory and neurosecretory activities. These observations provide evidence that Ciona has a neurogenic proto-placode, which forms neurons that appear to be related to those derived from the olfactory placode and hypothalamic neurons of vertebrates. We discuss the possibility that the PPE-derived GnRH neurons of Ciona resemble an ancestral cell type, a progenitor to the complex neuronal circuit that integrates sensory information and neuroendocrine functions in vertebrates.
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196
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Musser JM, Wagner GP, Prum RO. Nuclear β-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development. Evol Dev 2015; 17:185-94. [PMID: 25963196 DOI: 10.1111/ede.12123] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Feathers are an evolutionary novelty found in all extant birds. Despite recent progress investigating feather development and a revolution in dinosaur paleontology, the relationship of feathers to other amniote skin appendages, particularly reptile scales, remains unclear. Disagreement arises primarily from the observation that feathers and avian scutate scales exhibit an anatomical placode-defined as an epidermal thickening-in early development, whereas alligator and other avian scales do not. To investigate the homology of feathers and archosaur scales we examined patterns of nuclear β-catenin localization during early development of feathers and different bird and alligator scales. In birds, nuclear β-catenin is first localized to the feather placode, and then exhibits a dynamic pattern of localization in both epidermis and dermis of the feather bud. We found that asymmetric avian scutate scales and alligator scales share similar patterns of nuclear β-catenin localization with feathers. This supports the hypothesis that feathers, scutate scales, and alligator scales are homologous during early developmental stages, and are derived from early developmental stages of an asymmetric scale present in the archosaur ancestor. Furthermore, given that the earliest stage of β-catenin localization in feathers and archosaur scales is also found in placodes of several mammalian skin appendages, including hair and mammary glands, we hypothesize that a common skin appendage placode originated in the common ancestor of all amniotes. We suggest a skin placode should not be defined by anatomical features, but as a local, organized molecular signaling center from which an epidermal appendage develops.
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Affiliation(s)
- Jacob M Musser
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, 21 Sachem St, New Haven, CT 06511, USA.,Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT 06516, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, 21 Sachem St, New Haven, CT 06511, USA.,Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT 06516, USA
| | - Richard O Prum
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, 21 Sachem St, New Haven, CT 06511, USA
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197
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Frank MH, Edwards MB, Schultz ER, McKain MR, Fei Z, Sørensen I, Rose JKC, Scanlon MJ. Dissecting the molecular signatures of apical cell-type shoot meristems from two ancient land plant lineages. THE NEW PHYTOLOGIST 2015; 207:893-904. [PMID: 25900772 DOI: 10.1111/nph.13407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/04/2015] [Indexed: 05/18/2023]
Abstract
Shoot apical meristem (SAM) structure varies markedly within the land plants. The SAMs of many seedless vascular plants contain a conspicuous inverted, pyramidal cell called the apical cell (AC), which is unidentified in angiosperms. In this study, we use transcriptomic sequencing with precise laser microdissections of meristem subdomains to define the molecular signatures of anatomically distinct zones from the AC-type SAMs of a lycophyte (Selaginella moellendorffii) and a monilophyte (Equisetum arvense). The two model species for this study represent vascular plant lineages that diverged > 400 million yr ago. Our data comprise comprehensive molecular signatures for the distinct subdomains within AC-type SAMs, an anatomical anomaly whose functional significance has been debated in the botanical literature for over two centuries. Moreover, our data provide molecular support for distinct gene expression programs between the AC-type SAMs of Selaginella and Equisetum, as compared with the SAM transcriptome of the angiosperm maize. The results are discussed in light of the functional significance and evolutionary success of the AC-type SAM within the embryophytes.
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Affiliation(s)
- Margaret H Frank
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Molly B Edwards
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Eric R Schultz
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Scanlon
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
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198
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Musser JM, Wagner GP. Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called "species signal". JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:588-604. [PMID: 26175303 DOI: 10.1002/jez.b.22636] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/29/2015] [Indexed: 01/01/2023]
Abstract
We elaborate a framework for investigating the evolutionary history of morphological characters. We argue that morphological character trees generated by phylogenetic analysis of transcriptomes provide a useful tool for identifying causal gene expression differences underlying the development and evolution of morphological characters. They also enable rigorous testing of different models of morphological character evolution and origination, including the hypothesis that characters originate via divergence of repeated ancestral characters. Finally, morphological character trees provide evidence that character transcriptomes undergo concerted evolution. We argue that concerted evolution of transcriptomes can explain the so-called "species signal" found in several recent comparative transcriptome studies. The species signal is the phenomenon that transcriptomes cluster by species rather than character type, even though the characters are older than the respective species. We suggest the species signal is a natural consequence of concerted gene expression evolution resulting from mutations that alter gene regulatory network interactions shared by the characters under comparison. Thus, character trees generated from transcriptomes allow us to investigate the variational independence, or individuation, of morphological characters at the level of genetic programs.
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Affiliation(s)
- Jacob M Musser
- Yale Systems Biology Institute, West Haven, Connecticut.,Yale Peabody Museum of Natural History, New Haven, Connecticut.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Günter P Wagner
- Yale Systems Biology Institute, West Haven, Connecticut.,Yale Peabody Museum of Natural History, New Haven, Connecticut.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut.,Department of Obstetrics Gynecology and Reproductive Sciences, Yale Medical School, New Haven, Connecticut.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan
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199
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Gu X. Understanding tissue expression evolution: from expression phylogeny to phylogenetic network. Brief Bioinform 2015; 17:249-54. [PMID: 26141828 DOI: 10.1093/bib/bbv041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Indexed: 01/07/2023] Open
Abstract
Our understanding of tissue expression evolution in multi-cellular model organisms has been considerably advanced with the help of high-throughput technologies from EST, microarray to RNA-seq. Yet, many controversies remained unsolved, ranging from the evolutionary patterns of tissue expressions to expression phylogenetic analysis. Moreover, despite numerous reports published, it is desirable to have a general framework for study of tissue expression evolution. In this article, we first provide an up-to-date and concise review for the study of tissue expression evolution in multi-cellular organisms. While the expression phylogeny of the same tissues sampled from closely or intermediately related species largely reflects the species phylogeny, we demonstrate that phylogenetic network approach may shed some lights for our understanding of the developmental similarity and evolutionary relatedness during the multi-tissue evolution.
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200
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Vu Manh TP, Elhmouzi-Younes J, Urien C, Ruscanu S, Jouneau L, Bourge M, Moroldo M, Foucras G, Salmon H, Marty H, Quéré P, Bertho N, Boudinot P, Dalod M, Schwartz-Cornil I. Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics. Front Immunol 2015; 6:299. [PMID: 26150816 PMCID: PMC4473062 DOI: 10.3389/fimmu.2015.00299] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/25/2015] [Indexed: 12/24/2022] Open
Abstract
Mononuclear phagocytes are organized in a complex system of ontogenetically and functionally distinct subsets, that has been best described in mouse and to some extent in human. Identification of homologous mononuclear phagocyte subsets in other vertebrate species of biomedical, economic, and environmental interest is needed to improve our knowledge in physiologic and physio-pathologic processes, and to design intervention strategies against a variety of diseases, including zoonotic infections. We developed a streamlined approach combining refined cell sorting and integrated comparative transcriptomics analyses which revealed conservation of the mononuclear phagocyte organization across human, mouse, sheep, pigs and, in some respect, chicken. This strategy should help democratizing the use of omics analyses for the identification and study of cell types across tissues and species. Moreover, we identified conserved gene signatures that enable robust identification and universal definition of these cell types. We identified new evolutionarily conserved gene candidates and gene interaction networks for the molecular regulation of the development or functions of these cell types, as well as conserved surface candidates for refined subset phenotyping throughout species. A phylogenetic analysis revealed that orthologous genes of the conserved signatures exist in teleost fishes and apparently not in Lamprey.
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Affiliation(s)
- Thien-Phong Vu Manh
- UM2, Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université , Marseille , France ; U1104, INSERM , Marseille , France ; UMR7280, CNRS , Marseille , France
| | - Jamila Elhmouzi-Younes
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Céline Urien
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Suzana Ruscanu
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Luc Jouneau
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Mickaël Bourge
- IFR87 La Plante et son Environnement, IMAGIF CNRS , Gif-sur-Yvette , France
| | - Marco Moroldo
- CRB GADIE, Génétique Animale et Biologie Intégrative, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Gilles Foucras
- UMR1225, Université de Toulouse, INPT, ENVT , Toulouse , France ; UMR1225, Interactions Hôtes-Agents Pathogènes, INRA , Toulouse , France
| | - Henri Salmon
- UMR1282, Infectiologie et Santé Publique, INRA , Nouzilly , France ; UMR1282, Université François Rabelais de Tours , Tours , France
| | - Hélène Marty
- UMR1282, Infectiologie et Santé Publique, INRA , Nouzilly , France ; UMR1282, Université François Rabelais de Tours , Tours , France
| | - Pascale Quéré
- UMR1282, Infectiologie et Santé Publique, INRA , Nouzilly , France ; UMR1282, Université François Rabelais de Tours , Tours , France
| | - Nicolas Bertho
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Pierre Boudinot
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Marc Dalod
- UM2, Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université , Marseille , France ; U1104, INSERM , Marseille , France ; UMR7280, CNRS , Marseille , France
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