1
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Hulett RE, Rivera-López C, Gehrke AR, Gompers A, Srivastava M. A wound-induced differentiation trajectory for neurons. Proc Natl Acad Sci U S A 2024; 121:e2322864121. [PMID: 38976727 PMCID: PMC11260127 DOI: 10.1073/pnas.2322864121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/03/2024] [Indexed: 07/10/2024] Open
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully functional new organs, including new brains, de novo. The regeneration of a new brain requires the formation of diverse neural cell types and their assembly into an organized structure with correctly wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neural subpopulations, however, how these transcriptional programs are initiated in response to injury remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia, to study wound-induced transcriptional regulatory events that lead to the production of neurons and subsequently a functional brain. Footprinting analysis using chromatin accessibility data on a chromosome-scale genome assembly revealed that binding sites for the Nuclear Factor Y (NFY) transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal function. Single-cell transcriptome analysis combined with functional studies identified soxC+ stem cells as a putative progenitor population for multiple neural subtypes. Further, we found that wound-induced soxC expression is likely under direct transcriptional control by NFY, uncovering a mechanism for the initiation of a neural differentiation pathway by early wound-induced binding of a transcriptional regulator.
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Affiliation(s)
- Ryan E. Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA02138
| | - Andrew R. Gehrke
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Annika Gompers
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
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2
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Lerosey-Aubril R, Ortega-Hernández J. A long-headed Cambrian soft-bodied vertebrate from the American Great Basin region. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240350. [PMID: 39050723 PMCID: PMC11267725 DOI: 10.1098/rsos.240350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
The fossil record suggests that chordates might have been minor components of marine ecosystems during the first major diversification of animal life in the Cambrian. Vertebrates are represented by a handful of rare soft-bodied stem-lineage taxa known from Konservat-Lagerstätten, including Myllokunmingia and Yunnanozoon from the Stage 3 of South China, and Emmonsaspis and Metaspriggina from Stage 4-Drumian deposits of northeast USA and British Columbia. Here, we describe the first soft-bodied vertebrate from the American Great Basin, a region home to a dozen Cambrian Konservat-Lagerstätten. Found in the Drumian Marjum Formation of Utah, Nuucichthys rhynchocephalus gen. et sp. nov. is characterized by a finless torpedo-shaped body that includes a snout-like anterior head bearing anterolateral eyes, approximately 25 thick myomeres, a large branchial chamber with a keel and approximately seven putative dorsal bars and a spiniform caudal process. Using Bayesian inference, our analysis recovers Nuucichthys within the vertebrate stem, closer to the crown than Pikaia, Yunnanozoon and Myllokunmingia, where it forms a polytomy with its Laurentian relatives, Emmonsaspis and Metaspriggina, and a scion consisting of conodonts and crown-group vertebrates. Based on the eye orientation and absence of fins, we tentatively reconstruct Nuucichthys as a pelagic organism with limited swimming abilities (planktonektic).
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Affiliation(s)
- Rudy Lerosey-Aubril
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA02138, USA
| | - Javier Ortega-Hernández
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA02138, USA
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3
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Lin CY, Marlétaz F, Pérez-Posada A, Martínez-García PM, Schloissnig S, Peluso P, Conception GT, Bump P, Chen YC, Chou C, Lin CY, Fan TP, Tsai CT, Gómez Skarmeta JL, Tena JJ, Lowe CJ, Rank DR, Rokhsar DS, Yu JK, Su YH. Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution. PLoS Biol 2024; 22:e3002661. [PMID: 38829909 PMCID: PMC11175523 DOI: 10.1371/journal.pbio.3002661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ferdinand Marlétaz
- Center for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alberto Pérez-Posada
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | | | - Paul Peluso
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Paul Bump
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Cindy Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Pei Fan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chang-Tai Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - José Luis Gómez Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Christopher J. Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
| | - David R. Rank
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Daniel S. Rokhsar
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Molecular Genetics Unit, Okinawa Institute for Science and Technology, Onna, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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4
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Mörsdorf D, Knabl P, Genikhovich G. Highly conserved and extremely evolvable: BMP signalling in secondary axis patterning of Cnidaria and Bilateria. Dev Genes Evol 2024; 234:1-19. [PMID: 38472535 PMCID: PMC11226491 DOI: 10.1007/s00427-024-00714-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
Bilateria encompass the vast majority of the animal phyla. As the name states, they are bilaterally symmetric, that is with a morphologically clear main body axis connecting their anterior and posterior ends, a second axis running between their dorsal and ventral surfaces, and with a left side being roughly a mirror image of their right side. Bone morphogenetic protein (BMP) signalling has widely conserved functions in the formation and patterning of the second, dorso-ventral (DV) body axis, albeit to different extents in different bilaterian species. Whilst initial findings in the fruit fly Drosophila and the frog Xenopus highlighted similarities amongst these evolutionarily very distant species, more recent analyses featuring other models revealed considerable diversity in the mechanisms underlying dorsoventral patterning. In fact, as phylogenetic sampling becomes broader, we find that this axis patterning system is so evolvable that even its core components can be deployed differently or lost in different model organisms. In this review, we will try to highlight the diversity of ways by which BMP signalling controls bilaterality in different animals, some of which do not belong to Bilateria. Future research combining functional analyses and modelling is bound to give us some understanding as to where the limits to the extent of the evolvability of BMP-dependent axial patterning may lie.
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Affiliation(s)
- David Mörsdorf
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
| | - Paul Knabl
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria.
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5
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Robertson HE, Sebé-Pedrós A, Saudemont B, Loe-Mie Y, Zakrzewski AC, Grau-Bové X, Mailhe MP, Schiffer P, Telford MJ, Marlow H. Single cell atlas of Xenoturbella bocki highlights limited cell-type complexity. Nat Commun 2024; 15:2469. [PMID: 38503762 PMCID: PMC10951248 DOI: 10.1038/s41467-024-45956-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
Phylogenetic analyses over the last two decades have united a few small, and previously orphan clades, the nematodermatids, acoels and xenoturbelids, into the phylum Xenacoelomorpha. Some phylogenetic analyses support a sister relationship between Xenacoelomorpha and Ambulacraria (Xenambulacraria), while others suggest that Xenacoelomorpha may be sister to the rest of the Bilateria (Nephrozoa). An understanding of the cell type complements of Xenacoelomorphs is essential to assessing these alternatives as well as to our broader understanding of bilaterian cell type evolution. Employing whole organism single-cell RNA-seq in the marine xenacoelomorph worm Xenoturbella bocki, we show that Xenambulacrarian nerve nets share regulatory features and a peptidergic identity with those found in cnidarians and protostomes and more broadly share muscle and gland cell similarities with other metazoans. Taken together, these data are consistent with broad homologies of animal gland, muscle, and neurons as well as more specific affinities between Xenoturbella and acoel gut and epidermal tissues, consistent with the monophyly of Xenacoelomorpha.
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Affiliation(s)
- Helen E Robertson
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Anne-C Zakrzewski
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marie-Pierre Mailhe
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Philipp Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Institute of Zoology, Section Developmental Biology, University of Cologne, Köln, Wormlab, Germany
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA.
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.
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6
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Lacalli T. The Cambrian fossil Pikaia, and the origin of chordate somites. EvoDevo 2024; 15:1. [PMID: 38302988 PMCID: PMC10832150 DOI: 10.1186/s13227-024-00222-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
The Middle Cambrian fossil Pikaia has a regular series of vertical bands that, assuming chordate affinities, can be interpreted as septa positioned between serial myotomes. Whether Pikaia has a notochord and nerve cord is less certain, as the dorsal organ, which has no obvious counterpart in living chordates, is the only clearly defined axial structure extending the length of the body. Without a notochord to serve as a reference point, the location of the nerve cord is then conjectural, which begs the question of how a dorsal neural center devoted to somite innervation would first have arisen from a more diffuse ancestral plexus of intraepithelial nerves. This question is examined using hemichordates as a reference point, first for the information they provide on the organization of the ancestral deuterostome nervous system, and second, extending the analysis of E. E. Ruppert, to explain why neural infoldings like the enteropneust collar cord would first have evolved. Both implicate the medial surface of the anterior-most part of the metacoel as the likely site for the evolution of the first somites. The analysis highlights the importance of the somatobranchial condition in chordates, meaning the linkage between the anterior trunk, hox1 expression, and the beginning of the gill series and somites. This feature is arguably a valid criterion by which to assess extinct taxa from the Cambrian that resemble chordates (e.g., vetulicolians and yunnanozoans), but may be unrelated to them. In a more speculative vein, the nature of the dorsal organ is discussed, including the possibility that it is an expanded neural tube combining neural and support functions in one structure.
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Affiliation(s)
- Thurston Lacalli
- Biology Department, University of Victoria, Victoria, V8W-3N5, Canada.
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7
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Ma CY, Chen Y, Zhan X, Dong YW. Tracing the evolution of tissue inhibitor of metalloproteinases in Metazoa with the Pteria penguin genome. iScience 2024; 27:108579. [PMID: 38161420 PMCID: PMC10755359 DOI: 10.1016/j.isci.2023.108579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 09/13/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024] Open
Abstract
Tissue inhibitors of metalloproteinase (TIMPs) play a pivotal role in regulating extracellular matrix (ECM) dynamics and have been extensively studied in vertebrates. However, understanding their evolution across invertebrate phyla is limited. Utilizing the high-quality Pteria penguin genome, we conducted phylogenomic orthology analyses across metazoans, revealing the emergence and distribution of the TIMP gene family. Our findings show that TIMP repertoires originated during eumetazoan radiation, experiencing independent duplication events in different clades, resulting in varied family sizes. Particularly, Pteriomorphia bivalves within Mollusca exhibited the most significant expansion and displayed the most diverse TIMP repertoires among metazoans. These expansions were attributed to multiple gene duplication events, potentially driven by the demands for functional diversification related to multiple adaptive traits, contributing to the adaptation of Pteriomorphia bivalves as stationary filter feeders. In this context, Pteriomorphia bivalves offer a promising model for studying invertebrate TIMP evolution.
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Affiliation(s)
- Chao-Yi Ma
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
- Academy of the Future Ocean, Ocean University of China, Qingdao 266100, P.R. China
| | - Yi Chen
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, P.R. China
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, P.R. China
| | - Xin Zhan
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, P.R. China
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, P.R. China
| | - Yun-Wei Dong
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
- Academy of the Future Ocean, Ocean University of China, Qingdao 266100, P.R. China
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8
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol 2024; 42:139-147. [PMID: 37081138 PMCID: PMC10791578 DOI: 10.1038/s41587-023-01753-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Computer Science, ETH, Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Department of Computer Science, University College London, London, UK.
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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9
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Bump P, Lubeck L. Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis. Integr Comp Biol 2023; 63:999-1009. [PMID: 37188638 PMCID: PMC10714908 DOI: 10.1093/icb/icad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/25/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023] Open
Abstract
Over the past decade, single-cell RNA-sequencing (scRNA-seq) has made it possible to study the cellular diversity of a broad range of organisms. Technological advances in single-cell isolation and sequencing have expanded rapidly, allowing the transcriptomic profile of individual cells to be captured. As a result, there has been an explosion of cell type atlases created for many different marine invertebrate species from across the tree of life. Our focus in this review is to synthesize current literature on marine invertebrate scRNA-seq. Specifically, we provide perspectives on key insights from scRNA-seq studies, including descriptive studies of cell type composition, how cells respond in dynamic processes such as development and regeneration, and the evolution of new cell types. Despite these tremendous advances, there also lie several challenges ahead. We discuss the important considerations that are essential when making comparisons between experiments, or between datasets from different species. Finally, we address the future of single-cell analyses in marine invertebrates, including combining scRNA-seq data with other 'omics methods to get a fuller understanding of cellular complexities. The full diversity of cell types across marine invertebrates remains unknown and understanding this diversity and evolution will provide rich areas for future study.
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Affiliation(s)
- Paul Bump
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Lauren Lubeck
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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10
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Kapli P, Kotari I, Telford MJ, Goldman N, Yang Z. DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies. Syst Biol 2023; 72:1119-1135. [PMID: 37366056 PMCID: PMC10627555 DOI: 10.1093/sysbio/syad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 06/28/2023] Open
Abstract
Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here, we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies.
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Affiliation(s)
- Paschalia Kapli
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Ioanna Kotari
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, 1210, Austria
| | - Maximilian J Telford
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Nick Goldman
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ziheng Yang
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
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11
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Smith MR. Evolution: Assembling the deuterostome body plan. Curr Biol 2023; 33:R691-R694. [PMID: 37339599 DOI: 10.1016/j.cub.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Starfish, graptolites and humans look as different as can be, yet are more closely related to each other than to any other phylum. Disc-shaped Cambrian fossils join the dots between these disparate body plans to plot out their evolutionary origins.
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Affiliation(s)
- Martin R Smith
- Department of Earth Sciences, Durham University, Mountjoy Site, Durham DH1 3LE, UK.
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12
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Schuster HC, Hirth F. Phylogenetic tracing of midbrain-specific regulatory sequences suggests single origin of eubilaterian brains. SCIENCE ADVANCES 2023; 9:eade8259. [PMID: 37224241 PMCID: PMC10208574 DOI: 10.1126/sciadv.ade8259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 04/18/2023] [Indexed: 05/26/2023]
Abstract
Conserved cis-regulatory elements (CREs) control Engrailed-, Pax2-, and dachshund-related gene expression networks directing the formation and function of corresponding midbrain circuits in arthropods and vertebrates. Polarized outgroup analyses of 31 sequenced metazoan genomes representing all animal clades reveal the emergence of Pax2- and dachshund-related CRE-like sequences in anthozoan Cnidaria. The full complement, including Engrailed-related CRE-like sequences, is only detectable in spiralians, ecdysozoans, and chordates that have a brain; they exhibit comparable genomic locations and extensive nucleotide identities that reveal the presence of a conserved core domain, all of which are absent in non-neural genes and, together, distinguish them from randomly assembled sequences. Their presence concurs with a genetic boundary separating the rostral from caudal nervous systems, demonstrated for the metameric brains of annelids, arthropods, and chordates and the asegmental cycloneuralian and urochordate brain. These findings suggest that gene regulatory networks for midbrain circuit formation evolved within the lineage that led to the common ancestor of protostomes and deuterostomes.
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Affiliation(s)
- Helen C. Schuster
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, and Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
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Hulett RE, Gehrke AR, Gompers A, Rivera-López C, Srivastava M. A wound-induced differentiation trajectory for neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540286. [PMID: 37214981 PMCID: PMC10197691 DOI: 10.1101/2023.05.10.540286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully-functional new organs, de novo . The regeneration of a new brain requires the formation of diverse neuronal cell types and their assembly into an organized structure and correctly-wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neuronal subpopulations, however how these transcriptional programs are initiated upon amputation remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia , to study wound-induced transcriptional regulatory events that lead to the production of neurons. Footprinting analysis using chromatin accessibility data on an improved genome assembly revealed that binding sites for the NFY transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal functional. Single-cell transcriptome analysis combined with functional studies identified sox4 + stem cells as the likely progenitor population for multiple neuronal subtypes. Further, we found that wound-induced sox4 expression is likely under direct transcriptional control by NFY, uncovering a mechanism for how early wound-induced binding of a transcriptional regulator results in the initiation of a neuronal differentiation pathway. Highlights A new chromosome-scale assembly for Hofstenia enables comprehensive analysis of transcription factor binding during regeneration NFY motifs become dynamically bound by 1hpa in regenerating tail fragments, particularly in the loci of neural genes A sox4 + neural-specialized stem cell is identified using scRNA-seq sox4 is wound-induced and required for differentiation of multiple neural cell types NFY regulates wound-induced expression of sox4 during regeneration.
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Hulett RE, Kimura JO, Bolaños DM, Luo YJ, Rivera-López C, Ricci L, Srivastava M. Acoel single-cell atlas reveals expression dynamics and heterogeneity of adult pluripotent stem cells. Nat Commun 2023; 14:2612. [PMID: 37147314 PMCID: PMC10163032 DOI: 10.1038/s41467-023-38016-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
Adult pluripotent stem cell (aPSC) populations underlie whole-body regeneration in many distantly-related animal lineages, but how the underlying cellular and molecular mechanisms compare across species is unknown. Here, we apply single-cell RNA sequencing to profile transcriptional cell states of the acoel worm Hofstenia miamia during postembryonic development and regeneration. We identify cell types shared across stages and their associated gene expression dynamics during regeneration. Functional studies confirm that the aPSCs, also known as neoblasts, are the source of differentiated cells and reveal transcription factors needed for differentiation. Subclustering of neoblasts recovers transcriptionally distinct subpopulations, the majority of which are likely specialized to differentiated lineages. One neoblast subset, showing enriched expression of the histone variant H3.3, appears to lack specialization. Altogether, the cell states identified in this study facilitate comparisons to other species and enable future studies of stem cell fate potentials.
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Affiliation(s)
- Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - D Marcela Bolaños
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
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15
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Li Y, Dunn FS, Murdock DJE, Guo J, Rahman IA, Cong P. Cambrian stem-group ambulacrarians and the nature of the ancestral deuterostome. Curr Biol 2023:S0960-9822(23)00530-4. [PMID: 37167976 DOI: 10.1016/j.cub.2023.04.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/17/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Deuterostomes are characterized by some of the most widely divergent body plans in the animal kingdom. These striking morphological differences have hindered efforts to predict ancestral characters, with the origin and earliest evolution of the group remaining ambiguous. Several iconic Cambrian fossils have been suggested to be early deuterostomes and hence could help elucidate ancestral character states. However, their phylogenetic relationships are controversial. Here, we describe new, exceptionally preserved specimens of the discoidal metazoan Rotadiscus grandis from the early Cambrian Chengjiang biota of China. These reveal a previously unknown double spiral structure, which we interpret as a chordate-like covering to a coelomopore, located adjacent to a horseshoe-shaped tentacle complex. The tentacles differ in key aspects from those seen in lophophorates and are instead more similar to the tentacular systems of extant pterobranchs and echinoderms. Thus, Rotadiscus exhibits a chimeric combination of ambulacrarian and chordate characters. Phylogenetic analyses recover Rotadiscus and closely related fossil taxa as stem ambulacrarians, filling a significant morphological gap in the deuterostome tree of life. These results allow us to reconstruct the ancestral body plans of major clades of deuterostomes, revealing that key traits of extant forms, such as a post-anal region, gill bars, and a U-shaped gut, evolved through convergence.
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Affiliation(s)
- Yujing Li
- Yunnan Normal University, Kunming 650500, China; Yunnan Key Laboratory for Palaeobiology & MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Institute of Palaeontology, Yunnan University, Kunming 650500, China; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Frances S Dunn
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
| | - Duncan J E Murdock
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
| | - Jin Guo
- Yunnan Key Laboratory for Palaeobiology & MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Institute of Palaeontology, Yunnan University, Kunming 650500, China; Management Committee of the Chengjiang Fossil Site World Heritage, Chengjiang 652599, China
| | - Imran A Rahman
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK; The Natural History Museum, London SW7 5BD, UK.
| | - Peiyun Cong
- Yunnan Key Laboratory for Palaeobiology & MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Institute of Palaeontology, Yunnan University, Kunming 650500, China.
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16
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Marlétaz F, Couloux A, Poulain J, Labadie K, Da Silva C, Mangenot S, Noel B, Poustka AJ, Dru P, Pegueroles C, Borra M, Lowe EK, Lhomond G, Besnardeau L, Le Gras S, Ye T, Gavriouchkina D, Russo R, Costa C, Zito F, Anello L, Nicosia A, Ragusa MA, Pascual M, Molina MD, Chessel A, Di Carlo M, Turon X, Copley RR, Exposito JY, Martinez P, Cavalieri V, Ben Tabou de Leon S, Croce J, Oliveri P, Matranga V, Di Bernardo M, Morales J, Cormier P, Geneviève AM, Aury JM, Barbe V, Wincker P, Arnone MI, Gache C, Lepage T. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. CELL GENOMICS 2023; 3:100295. [PMID: 37082140 PMCID: PMC10112332 DOI: 10.1016/j.xgen.2023.100295] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 12/24/2022] [Accepted: 03/06/2023] [Indexed: 04/22/2023]
Abstract
Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement.
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Affiliation(s)
- Ferdinand Marlétaz
- Center for Life’s Origin & Evolution, Department of Genetics, Evolution, & Environment, University College London, WC1 6BT London, UK
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Sophie Mangenot
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Albert J. Poustka
- Evolution and Development Group, Max-Planck-Institut für Molekulare Genetik, 14195 Berlin, Germany
- Dahlem Center for Genome Research and Medical Systems Biology (Environmental and Phylogenomics Group), 12489 Berlin, Germany
| | - Philippe Dru
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Cinta Pegueroles
- Institute for Research on Biodiversity (IRBio), Department of Genetics, Microbiology, and Statistics, University of Barcelona, 08028 Barcelona, Spain
| | - Marco Borra
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Elijah K. Lowe
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Guy Lhomond
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Lydia Besnardeau
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Stéphanie Le Gras
- Plateforme GenomEast, IGBMC, CNRS UMR7104, INSERM U1258, Université de Strasbourg, 67404 Illirch Cedex, France
| | - Tao Ye
- Plateforme GenomEast, IGBMC, CNRS UMR7104, INSERM U1258, Université de Strasbourg, 67404 Illirch Cedex, France
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, 904-0495 Onna-son, Japan
| | - Roberta Russo
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Caterina Costa
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Francesca Zito
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Letizia Anello
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Aldo Nicosia
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Marta Pascual
- Institute for Research on Biodiversity (IRBio), Department of Genetics, Microbiology, and Statistics, University of Barcelona, 08028 Barcelona, Spain
| | - M. Dolores Molina
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
| | - Aline Chessel
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
| | - Marta Di Carlo
- Institute for Biomedical Research and Innovation (CNR), 90146 Palermo, Italy
| | - Xavier Turon
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB, CSIC), 17300 Blanes, Spain
| | - Richard R. Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Jean-Yves Exposito
- Laboratoire de Biologie Tissulaire et d’Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Institut de Biologie et Chimie des Protéines, Université Lyon 1, 69367 Lyon, France
| | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), 08028 Barcelona, Spain
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Smadar Ben Tabou de Leon
- Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, 31095 Haifa, Israel
| | - Jenifer Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Paola Oliveri
- Center for Life’s Origin & Evolution, Department of Genetics, Evolution, & Environment, University College London, WC1 6BT London, UK
| | - Valeria Matranga
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Maria Di Bernardo
- Consiglio Nazionale delle Ricerche, Istituto di Farmacologia Traslazionale, 90146 Palermo, Italy
| | - Julia Morales
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, CNRS, Sorbonne Université, 29680 Roscoff, France
| | - Patrick Cormier
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, CNRS, Sorbonne Université, 29680 Roscoff, France
| | - Anne-Marie Geneviève
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, 66650 Banyuls/Mer, France
| | - Jean Marc Aury
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Christian Gache
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Thierry Lepage
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
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17
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Martí-Solans J, Børve A, Bump P, Hejnol A, Lynagh T. Peripheral and central employment of acid-sensing ion channels during early bilaterian evolution. eLife 2023; 12:e81613. [PMID: 36821351 PMCID: PMC9949801 DOI: 10.7554/elife.81613] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/08/2023] [Indexed: 02/24/2023] Open
Abstract
Nervous systems are endowed with rapid chemosensation and intercellular signaling by ligand-gated ion channels (LGICs). While a complex, bilaterally symmetrical nervous system is a major innovation of bilaterian animals, the employment of specific LGICs during early bilaterian evolution is poorly understood. We therefore questioned bilaterian animals' employment of acid-sensing ion channels (ASICs), LGICs that mediate fast excitatory responses to decreases in extracellular pH in vertebrate neurons. Our phylogenetic analysis identified an earlier emergence of ASICs from the overarching DEG/ENaC (degenerin/epithelial sodium channel) superfamily than previously thought and suggests that ASICs were a bilaterian innovation. Our broad examination of ASIC gene expression and biophysical function in each major bilaterian lineage of Xenacoelomorpha, Protostomia, and Deuterostomia suggests that the earliest bilaterian ASICs were probably expressed in the periphery, before being incorporated into the brain as it emerged independently in certain deuterostomes and xenacoelomorphs. The loss of certain peripheral cells from Ecdysozoa after they separated from other protostomes likely explains their loss of ASICs, and thus the absence of ASICs from model organisms Drosophila and Caenorhabditis elegans. Thus, our use of diverse bilaterians in the investigation of LGIC expression and function offers a unique hypothesis on the employment of LGICs in early bilaterian evolution.
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Affiliation(s)
| | - Aina Børve
- Department of Biological Sciences, University of BergenBergenNorway
| | - Paul Bump
- Hopkins Marine Station, Department of Biology, Stanford UniversityPacific GroveUnited States
| | - Andreas Hejnol
- Department of Biological Sciences, University of BergenBergenNorway
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18
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Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa. Nat Commun 2023; 14:710. [PMID: 36765060 PMCID: PMC9918546 DOI: 10.1038/s41467-023-36152-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
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19
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Nielsen C. Hydrodynamics in early animal evolution. Biol Rev Camb Philos Soc 2023; 98:376-385. [PMID: 36216338 DOI: 10.1111/brv.12909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Choanoflagellates and sponges feed by filtering microscopic particles from water currents created by the flagella of microvillar collar complexes situated on the cell bodies of the solitary or colonial choanoflagellates and on the choanocytes in sponges. The filtering mechanism has been known for more than a century, but only recently has the filtering process been studied in detail and also modelled, so that a detailed picture of the water currents has been obtained. In the solitary and most of the colonial choanoflagellates, the water flows freely around the cells, but in some forms, the cells are arranged in an open meshwork through which the water can be pumped. In the sponges, the choanocytes are located in choanocyte chambers (or choanocyte areas) with separate incurrent and excurrent canals/pores located in a larger body, which enables a fixed pattern of water currents through the collar complexes. Previous theories for the origin of sponges show evolutionary stages with choanocyte chambers without any opening or with only one opening, which makes separation of incurrent and excurrent impossible, and such stages must have been unable to feed. Therefore a new theory is proposed, which shows a continuous evolutionary lineage in which all stages are able to feed by means of the collar complexes.
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Affiliation(s)
- Claus Nielsen
- Natural History Museum of Denmark (University of Copenhagen), Zoological Museum, Universitetsparken 15, DK-2990, Copenhagen, Denmark
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20
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Juravel K, Porras L, Höhna S, Pisani D, Wörheide G. Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny. PLoS One 2023; 18:e0282444. [PMID: 36952565 PMCID: PMC10035847 DOI: 10.1371/journal.pone.0282444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
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Affiliation(s)
- Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Luis Porras
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Höhna
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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21
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Read2Tree: scalable and accurate phylogenetic trees from raw reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.18.488678. [PMID: 36561179 PMCID: PMC9774205 DOI: 10.1101/2022.04.18.488678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate-the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolution. Applied to Coronaviridae samples, Read2Tree accurately classified highly diverse animal samples and near-identical SARS-CoV-2 sequences on a single tree-thereby exhibiting remarkable breadth and depth. The speed, accuracy, and versatility of Read2Tree enables comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- present address: F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, 4070, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, ETH, 8092 Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, University College London, London WC1E 6BT, UK
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E, UK
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22
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Mulhair PO, McCarthy CGP, Siu-Ting K, Creevey CJ, O'Connell MJ. Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life. Curr Biol 2022; 32:5180-5188.e3. [PMID: 36356574 DOI: 10.1016/j.cub.2022.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/09/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum1,2,3,4,5,6 or within Deuterostomia, sister to Ambulacraria.7,8,9,10,11 Although their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. Recent studies have questioned whether Deuterostomia should be considered monophyletic at all.10,12,13 Hidden paralogy and poor phylogenetic signal present a major challenge for reconstructing species phylogenies.14,15,16,17,18 Here, we assess whether these issues have contributed to the conflict over the placement of Xenacoelomorpha. We reanalyzed published datasets, enriching for orthogroups whose gene trees support well-resolved clans elsewhere in the animal tree.16 We find that most genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy and low phylogenetic signal affect the ability to reconstruct branching patterns at deep nodes in the animal tree. We demonstrate that removing orthogroups that cannot recapitulate incontestable relationships alters the final topology that is inferred, while simultaneously improving the fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our set of filtered orthogroups. At a time when we are progressing toward sequencing all life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modeled adequately.19.
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Affiliation(s)
- Peter O Mulhair
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Charley G P McCarthy
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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23
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Fliniaux I, Marchand G, Molinaro C, Decloquement M, Martoriati A, Marin M, Bodart JF, Harduin-Lepers A, Cailliau K. Diversity of sialic acids and sialoglycoproteins in gametes and at fertilization. Front Cell Dev Biol 2022; 10:982931. [PMID: 36340022 PMCID: PMC9630641 DOI: 10.3389/fcell.2022.982931] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/10/2022] [Indexed: 09/22/2023] Open
Abstract
Sialic acids are a family of 9-carbon monosaccharides with particular physicochemical properties. They modulate the biological functions of the molecules that carry them and are involved in several steps of the reproductive process. Sialoglycoproteins participate in the balance between species recognition and specificity, and the mechanisms of these aspects remain an issue in gametes formation and binding in metazoan reproduction. Sialoglycoproteins form a specific coat at the gametes surface and specific polysialylated chains are present on marine species oocytes. Spermatozoa are submitted to critical sialic acid changes in the female reproductive tract facilitating their migration, their survival through the modulation of the female innate immune response, and the final oocyte-binding event. To decipher the role of sialic acids in gametes and at fertilization, the dynamical changes of enzymes involved in their synthesis and removal have to be further considered.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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24
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Liu Y, Carlisle E, Zhang H, Yang B, Steiner M, Shao T, Duan B, Marone F, Xiao S, Donoghue PCJ. Saccorhytus is an early ecdysozoan and not the earliest deuterostome. Nature 2022; 609:541-546. [PMID: 35978194 DOI: 10.1038/s41586-022-05107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/13/2022] [Indexed: 11/09/2022]
Abstract
The early history of deuterostomes, the group composed of the chordates, echinoderms and hemichordates1, is still controversial, not least because of a paucity of stem representatives of these clades2-5. The early Cambrian microscopic animal Saccorhytus coronarius was interpreted as an early deuterostome on the basis of purported pharyngeal openings, providing evidence for a meiofaunal ancestry6 and an explanation for the temporal mismatch between palaeontological and molecular clock timescales of animal evolution6-8. Here we report new material of S. coronarius, which is reconstructed as a millimetric and ellipsoidal meiobenthic animal with spinose armour and a terminal mouth but no anus. Purported pharyngeal openings in support of the deuterostome hypothesis6 are shown to be taphonomic artefacts. Phylogenetic analyses indicate that S. coronarius belongs to total-group Ecdysozoa, expanding the morphological disparity and ecological diversity of early Cambrian ecdysozoans.
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Affiliation(s)
- Yunhuan Liu
- School of Earth Science and Resources, Chang'an University, Xi'an, China
| | - Emily Carlisle
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Huaqiao Zhang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Ben Yang
- MNR Key Laboratory of Stratigraphy and Palaeontology, Institute of Geology, Chinese Academy of Geological Sciences, Beijing, China
| | - Michael Steiner
- College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Tiequan Shao
- School of Earth Science and Resources, Chang'an University, Xi'an, China
| | - Baichuan Duan
- Key Laboratory of Marine Geology and Metallogeny, First Institute of Oceanography, Ministry of Natural Resource, Qingdao, China
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA.
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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25
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Martynov AV, Korshunova TA. Renewed perspectives on the sedentary-pelagic last common bilaterian ancestor. CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Various evaluations of the last common bilaterian ancestor (lcba) currently suggest that it resembled either a microscopic, non-segmented motile adult; or, on the contrary, a complex segmented adult motile urbilaterian. These fundamental inconsistencies remain largely unexplained. A majority of multidisciplinary data regarding sedentary adult ancestral bilaterian organization is overlooked. The sedentary-pelagic model is supported now by a number of novel developmental, paleontological and molecular phylogenetic data: (1) data in support of sedentary sponges, in the adult stage, as sister to all other Metazoa; (2) a similarity of molecular developmental pathways in both adults and larvae across sedentary sponges, cnidarians, and bilaterians; (3) a cnidarian-bilaterian relationship, including a unique sharing of a bona fide Hox-gene cluster, of which the evolutionary appearance does not connect directly to a bilaterian motile organization; (4) the presence of sedentary and tube-dwelling representatives of the main bilaterian clades in the early Cambrian; (5) an absence of definite taxonomic attribution of Ediacaran taxa reconstructed as motile to any true bilaterian phyla; (6) a similarity of tube morphology (and the clear presence of a protoconch-like apical structure of the Ediacaran sedentary Cloudinidae) among shells of the early Cambrian, and later true bilaterians, such as semi-sedentary hyoliths and motile molluscs; (7) recent data that provide growing evidence for a complex urbilaterian, despite a continuous molecular phylogenetic controversy. The present review compares the main existing models and reconciles the sedentary model of an urbilaterian and the model of a larva-like lcba with a unified sedentary(adult)-pelagic(larva) model of the lcba.
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Affiliation(s)
- Alexander V. Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia,
| | - Tatiana A. Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334 Moscow, Russia
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26
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Comparisons of cell proliferation and cell death from tornaria larva to juvenile worm in the hemichordate Schizocardium californicum. EvoDevo 2022; 13:13. [PMID: 35668535 PMCID: PMC9169294 DOI: 10.1186/s13227-022-00198-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/13/2022] [Indexed: 12/06/2022] Open
Abstract
Background There are a wide range of developmental strategies in animal phyla, but most insights into adult body plan formation come from direct-developing species. For indirect-developing species, there are distinct larval and adult body plans that are linked together by metamorphosis. Some outstanding questions in the development of indirect-developing organisms include the extent to which larval tissue undergoes cell death during the process of metamorphosis and when and where the tissue that will give rise to the adult originates. How do the processes of cell division and cell death redesign the body plans of indirect developers? In this study, we present patterns of cell proliferation and cell death during larval body plan development, metamorphosis, and adult body plan formation, in the hemichordate Schizocardium californium (Cameron and Perez in Zootaxa 3569:79–88, 2012) to answer these questions. Results We identified distinct patterns of cell proliferation between larval and adult body plan formation of S. californicum. We found that some adult tissues proliferate during the late larval phase prior to the start of overt metamorphosis. In addition, using an irradiation and transcriptomic approach, we describe a genetic signature of proliferative cells that is shared across the life history states, as well as markers that are unique to larval or juvenile states. Finally, we observed that cell death is minimal in larval stages but begins with the onset of metamorphosis. Conclusions Cell proliferation during the development of S. californicum has distinct patterns in the formation of larval and adult body plans. However, cell death is very limited in larvae and begins during the onset of metamorphosis and into early juvenile development in specific domains. The populations of cells that proliferated and gave rise to the larvae and juveniles have a genetic signature that suggested a heterogeneous pool of proliferative progenitors, rather than a set-aside population of pluripotent cells. Taken together, we propose that the gradual morphological transformation of S. californicum is mirrored at the cellular level and may be more representative of the development strategies that characterize metamorphosis in many metazoan animals. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-022-00198-1.
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27
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Álvarez-Armada N, Cameron CB, Bauer JE, Rahman IA. Heterochrony and parallel evolution of echinoderm, hemichordate and cephalochordate internal bars. Proc Biol Sci 2022; 289:20220258. [PMID: 35538784 PMCID: PMC9091856 DOI: 10.1098/rspb.2022.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Deuterostomes comprise three phyla with radically different body plans. Phylogenetic bracketing of the living deuterostome clades suggests the latest common ancestor of echinoderms, hemichordates and chordates was a bilaterally symmetrical worm with pharyngeal openings, with these characters lost in echinoderms. Early fossil echinoderms with pharyngeal openings have been described, but their interpretation is highly controversial. Here, we critically evaluate the evidence for pharyngeal structures (gill bars) in the extinct stylophoran echinoderms Lagynocystis pyramidalis and Jaekelocarpus oklahomensis using virtual models based on high-resolution X-ray tomography scans of three-dimensionally preserved fossil specimens. Multivariate analyses of the size, spacing and arrangement of the internal bars in these fossils indicate they are substantially more similar to gill bars in modern enteropneust hemichordates and cephalochordates than to other internal bar-like structures in fossil blastozoan echinoderms. The close similarity between the internal bars of the stylophorans L. pyramidalis and J. oklahomensis and the gill bars of extant chordates and hemichordates is strong evidence for their homology. Differences between these internal bars and bar-like elements of the respiratory systems in blastozoans suggest these structures might have arisen through parallel evolution across deuterostomes, perhaps underpinned by a common developmental genetic mechanism.
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Affiliation(s)
| | - Christopher B Cameron
- Département de sciences biologiques, Université de Montréal C.P. 6128, Succursale Centre-ville, Montréal, QC, Canada H3C 3J7
| | - Jennifer E Bauer
- University of Michigan Museum of Paleontology, Ann Arbor, MI 48109-1085, USA
| | - Imran A Rahman
- The Natural History Museum, London SW7 5BD, UK.,Oxford University Museum of Natural History, Oxford OX1 3PW, UK
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28
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Xiong Q, Wan ATY, Liu X, Fung CSH, Xiao X, Malainual N, Hou J, Wang L, Wang M, Yang KY, Cui Y, Leung ELH, Nong W, Shin SK, Au SWN, Jeong KY, Chew FT, Hui JHL, Leung TF, Tungtrongchitr A, Zhong N, Liu Z, Tsui SKW. Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations. Mol Biol Evol 2022; 39:6582989. [PMID: 35535514 PMCID: PMC9113151 DOI: 10.1093/molbev/msac097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing ∼1–2% of all allergic diseases globally; however, their evolutionary origin and diverse lifestyles including reversible parasitism have not been illustrated at the genomic level, which hampers allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the diversification of astigmatic mites. In monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, and then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases. Gene diversification after tandem duplications provides many genetic resources for adaptation to sensing environmental signals, digestion, and detoxification in rapidly changing household environments. Many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UDP glucuronosyltransferases and several important fungal cell wall lytic enzymes, which enable detoxification and digestive functions and provide perfect drug targets for pest control. This comparative study sheds light on the divergent evolution and quick adaptation to human household environments of astigmatic mites and provides insights into the genetic adaptations and even control of human household pests.
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Affiliation(s)
- Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Xiaoyu Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Cathy Sin-Hang Fung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Xiaojun Xiao
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Nat Malainual
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
| | - Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Yubao Cui
- Department of Clinical Laboratory, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Elaine Lai-Han Leung
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Soo-Kyung Shin
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | | | - Kyoung Yong Jeong
- Institute of Allergy, Department of Internal Medicine, College of Medicine, Yonsei University, Seoul, Korea
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jerome Ho-Lam Hui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Ting-Fan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong
| | - Anchalee Tungtrongchitr
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhigang Liu
- Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong
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29
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Schmidt-Ott U, Yoon Y. Evolution and loss of ß-catenin and TCF-dependent axis specification in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100877. [PMID: 35104659 PMCID: PMC9133022 DOI: 10.1016/j.cois.2022.100877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Mechanisms and evolution of primary axis specification in insects are discussed in the context of the roles of ß-catenin and TCF in polarizing metazoan embryos. Three hypotheses are presented. First, insects with sequential segmentation and posterior growth use cell-autonomous mechanisms for establishing embryo polarity via the nuclear ratio of ß-catenin and TCF. Second, TCF homologs establish competence for anterior specification. Third, the evolution of simultaneous segmentation mechanisms, also known as long-germ development, resulted in primary axis specification mechanisms that are independent of ß-catenin but reliant on TCF, a condition that preceded the frequent replacement of anterior determinants in long germ insects.
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Affiliation(s)
- Urs Schmidt-Ott
- University of Chicago, Dept. of Organismal Biology and Anatomy, 1027 East 57th Street, Chicago, IL 60637, USA.
| | - Yoseop Yoon
- University of California, Irvine, Dept. of Microbiology and Molecular Genetics, School of Medicine, 811 Health Sciences Rd., Med Sci B262, CA 92617, USA
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30
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Srivastava M. Studying development, regeneration, stem cells, and more in the acoel Hofstenia miamia. Curr Top Dev Biol 2022; 147:153-172. [PMID: 35337448 DOI: 10.1016/bs.ctdb.2022.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Acoel worms represent an enigmatic lineage of animals (Acoelomorpha) that has danced around the tree of animal life. Morphology-based classification placed them as flatworms (Phylum Platyhelminthes), with much of their biology being interpreted as a variation on what is observed in better-studied members of that phylum. However, molecular phylogenies suggest that acoels belong to a clade (Xenacoelomorpha) that could be a sister group to other animals with bilateral symmetry (Bilateria) or could belong within deuterostomes, closely related to a group that includes sea stars (Ambulacraria). This change in phylogenetic position has led to renewed interest in the biology of acoels, which can now offer insights into the evolution of many bilaterian traits. The acoel Hofstenia miamia has emerged as a powerful new research organism that enables mechanistic studies of xenacoelomorph biology, especially of developmental and regenerative processes. This article explains the motivation for developing Hofstenia as a new model system, describes Hofstenia biology, highlights the tools and resources that make Hofstenia a good research organism, and considers the questions that Hofstenia is well-positioned to answer. Finally, looking to the future, this article serves as an invitation to new and established scientists to join the growing community of researchers studying this exciting model system.
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Affiliation(s)
- Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States.
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31
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Abstract
Hemichordates have long been recognized as a critical group for addressing hypotheses of chordate origins. Historically this was due to anatomical traits that resembled those of chordates, most strikingly the dorsolateral gill slits. As molecular data and phylogenetic analyses were found to support a close phylogenetic relationship between hemichordates and chordates within the deuterostomes, interest was revived in hemichordates. In particular, Saccoglossus kowalevskii has been developed as a molecular model to represent hemichordate developmental biology. Herein, we highlight the considerations when choosing a particular species to study and the challenges we encountered when developing S. kowalevskii. We discuss our findings and how method and tool development enabled them, and how we envision expanding our repertoire of molecular tools in the future. Establishing a new model organism comes with many obstacles-from identifying a reliable season to collect animals, to developing modern molecular techniques. The Saccoglossus research community has benefited greatly from the collaborations and teamwork established over the years. As a result, Saccoglossus is well positioned to contribute to a new century of evolutionary developmental (evo-devo) research.
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32
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Ballesteros JA, Santibáñez-López CE, Baker CM, Benavides LR, Cunha TJ, Gainett G, Ontano AZ, Setton EVW, Arango CP, Gavish-Regev E, Harvey MS, Wheeler WC, Hormiga G, Giribet G, Sharma PP. Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida. Mol Biol Evol 2022; 39:6522129. [PMID: 35137183 PMCID: PMC8845124 DOI: 10.1093/molbev/msac021] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Carlos E Santibáñez-López
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biology, Western Connecticut State University, Danbury, CT, 06810, USA
| | - Caitlin M Baker
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Ligia R Benavides
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Tauana J Cunha
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Andrew Z Ontano
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Claudia P Arango
- Office for Research, Griffith University, Nathan, Queensland, 4111, Australia
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Mark S Harvey
- Collections & Research, Western Australian Museum, Welshpool, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western, Crawley, Western Australia, 6009, Australia; Australia
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Monroig Ó, Shu-Chien A, Kabeya N, Tocher D, Castro L. Desaturases and elongases involved in long-chain polyunsaturated fatty acid biosynthesis in aquatic animals: From genes to functions. Prog Lipid Res 2022; 86:101157. [DOI: 10.1016/j.plipres.2022.101157] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/17/2021] [Accepted: 01/22/2022] [Indexed: 01/01/2023]
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Bozzo M, Costa S, Obino V, Bachetti T, Marcenaro E, Pestarino M, Schubert M, Candiani S. Functional Conservation and Genetic Divergence of Chordate Glycinergic Neurotransmission: Insights from Amphioxus Glycine Transporters. Cells 2021; 10:cells10123392. [PMID: 34943900 PMCID: PMC8699752 DOI: 10.3390/cells10123392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022] Open
Abstract
Glycine is an important neurotransmitter in vertebrates, performing both excitatory and inhibitory actions. Synaptic levels of glycine are tightly controlled by the action of two glycine transporters, GlyT1 and GlyT2, located on the surface of glial cells and neurons, respectively. Only limited information is available on glycinergic neurotransmission in invertebrates, and the evolution of glycinergic neurotransmission is poorly understood. Here, by combining phylogenetic and gene expression analyses, we characterized the glycine transporter complement of amphioxus, an important invertebrate model for studying the evolution of chordates. We show that amphioxus possess three glycine transporter genes. Two of these (GlyT2.1 and GlyT2.2) are closely related to GlyT2 of vertebrates, whereas the third (GlyT) is a member of an ancestral clade of deuterostome glycine transporters. GlyT2.2 expression is predominantly non-neural, whereas GlyT and GlyT2.1 are widely expressed in the amphioxus nervous system and are differentially expressed, respectively, in neurons and glia. Vertebrate glycinergic neurons express GlyT2 and glia GlyT1, suggesting that the evolution of the chordate glycinergic system was accompanied by a paralog-specific inversion of gene expression. Despite this genetic divergence between amphioxus and vertebrates, we found strong evidence for conservation in the role glycinergic neurotransmission plays during larval swimming, the implication being that the neural networks controlling the rhythmic movement of chordate bodies may be homologous.
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Affiliation(s)
- Matteo Bozzo
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
- Correspondence: (M.B.); (S.C.); Tel.: +39-010-335-8043 (M.B.); +39-010-335-8051 (S.C.)
| | - Simone Costa
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Valentina Obino
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
| | - Tiziana Bachetti
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Emanuela Marcenaro
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
| | - Mario Pestarino
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France;
| | - Simona Candiani
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
- Correspondence: (M.B.); (S.C.); Tel.: +39-010-335-8043 (M.B.); +39-010-335-8051 (S.C.)
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Transgenesis in the acoel worm Hofstenia miamia. Dev Cell 2021; 56:3160-3170.e4. [PMID: 34752780 DOI: 10.1016/j.devcel.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 12/27/2022]
Abstract
The acoel worm Hofstenia miamia, which can replace tissue lost to injury via differentiation of a population of stem cells, has emerged as a new research organism for studying regeneration. To enhance the depth of mechanistic studies in this system, we devised a protocol for microinjection into embryonic cells that resulted in stable transgene integration into the genome and generated animals with tissue-specific fluorescent transgene expression in epidermis, gut, and muscle. We demonstrate that transgenic Hofstenia are amenable to the isolation of specific cell types, investigations of regeneration, tracking of photoconverted molecules, and live imaging. Further, our stable transgenic lines revealed insights into the biology of Hofstenia, including a high-resolution three-dimensional view of cell morphology and the organization of muscle as a cellular scaffold for other tissues. Our work positions Hofstenia as a powerful system with multiple toolkits for mechanistic investigations of development, whole-body regeneration, and stem cell biology.
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What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata. DIVERSITY 2021. [DOI: 10.3390/d13110568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.
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Moroz LL, Nikitin MA, Poličar PG, Kohn AB, Romanova DY. Evolution of glutamatergic signaling and synapses. Neuropharmacology 2021; 199:108740. [PMID: 34343611 PMCID: PMC9233959 DOI: 10.1016/j.neuropharm.2021.108740] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
Glutamate (Glu) is the primary excitatory transmitter in the mammalian brain. But, we know little about the evolutionary history of this adaptation, including the selection of l-glutamate as a signaling molecule in the first place. Here, we used comparative metabolomics and genomic data to reconstruct the genealogy of glutamatergic signaling. The origin of Glu-mediated communications might be traced to primordial nitrogen and carbon metabolic pathways. The versatile chemistry of L-Glu placed this molecule at the crossroad of cellular biochemistry as one of the most abundant metabolites. From there, innovations multiplied. Many stress factors or injuries could increase extracellular glutamate concentration, which led to the development of modular molecular systems for its rapid sensing in bacteria and archaea. More than 20 evolutionarily distinct families of ionotropic glutamate receptors (iGluRs) have been identified in eukaryotes. The domain compositions of iGluRs correlate with the origins of multicellularity in eukaryotes. Although L-Glu was recruited as a neuro-muscular transmitter in the early-branching metazoans, it was predominantly a non-neuronal messenger, with a possibility that glutamatergic synapses evolved more than once. Furthermore, the molecular secretory complexity of glutamatergic synapses in invertebrates (e.g., Aplysia) can exceed their vertebrate counterparts. Comparative genomics also revealed 15+ subfamilies of iGluRs across Metazoa. However, most of this ancestral diversity had been lost in the vertebrate lineage, preserving AMPA, Kainate, Delta, and NMDA receptors. The widespread expansion of glutamate synapses in the cortical areas might be associated with the enhanced metabolic demands of the complex brain and compartmentalization of Glu signaling within modular neuronal ensembles.
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Affiliation(s)
- Leonid L Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Mikhail A Nikitin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Pavlin G Poličar
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Faculty of Computer and Information Science, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Andrea B Kohn
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA
| | - Daria Y Romanova
- Cellular Neurobiology of Learning Lab, Institute of Higher Nervous Activity and Neurophysiology, Moscow, 117485, Russia.
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Abstract
There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.
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Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jordi Paps
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
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Kimura JO, Ricci L, Srivastava M. Embryonic development in the acoel Hofstenia miamia. Development 2021; 148:270768. [PMID: 34196362 DOI: 10.1242/dev.188656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
Acoels are marine worms that belong to the phylum Xenacoelomorpha, a deep-diverging bilaterian lineage. This makes acoels an attractive system for studying the evolution of major bilaterian traits. Thus far, acoel development has not been described in detail at the morphological and transcriptomic levels in a species in which functional genetic studies are possible. We present a set of developmental landmarks for embryogenesis in the highly regenerative acoel Hofstenia miamia. We generated a developmental staging atlas from zygote to hatched worm based on gross morphology, with accompanying bulk transcriptome data. Hofstenia embryos undergo a stereotyped cleavage program known as duet cleavage, which results in two large vegetal pole 'macromeres' and numerous small animal pole 'micromeres'. These macromeres become internalized as micromere progeny proliferate and move vegetally. We also noted a second, previously undescribed, cell-internalization event at the animal pole, following which we detected major body axes and tissues corresponding to all three germ layers. Our work on Hofstenia embryos provides a resource for mechanistic investigations of acoel development, which will yield insights into the evolution of bilaterian development and regeneration.
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Affiliation(s)
- Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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Aboitiz F, Montiel JF. The Enigmatic Reissner's Fiber and the Origin of Chordates. Front Neuroanat 2021; 15:703835. [PMID: 34248511 PMCID: PMC8261243 DOI: 10.3389/fnana.2021.703835] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/03/2021] [Indexed: 12/02/2022] Open
Abstract
Reissner’s fiber (RF) is a secreted filament that floats in the neural canal of chordates. Since its discovery in 1860, there has been no agreement on its primary function, and its strong conservation across chordate species has remained a mystery for comparative neuroanatomists. Several findings, including the chemical composition and the phylogenetic history of RF, clinical observations associating RF with the development of the neural canal, and more recent studies suggesting that RF is needed to develop a straight vertebral column, may shed light on the functions of this structure across chordates. In this article, we will briefly review the evidence mentioned above to suggest a role of RF in the origin of fundamental innovations of the chordate body plan, especially the elongation of the neural tube and maintenance of the body axis. We will also mention the relevance of RF for medical conditions like hydrocephalus, scoliosis of the vertebral spine and possibly regeneration of the spinal cord.
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Affiliation(s)
- Francisco Aboitiz
- Departamento de Psiquiatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro Interdisciplinario de Neurociencias, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan F Montiel
- Centro de Investigación Biomédica, Facultad de Medicina, Universidad Diego Portales, Santiago, Chile
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Molecular evidence for a single origin of ultrafiltration-based excretory organs. Curr Biol 2021; 31:3629-3638.e2. [PMID: 34166606 DOI: 10.1016/j.cub.2021.05.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/14/2021] [Accepted: 05/26/2021] [Indexed: 01/14/2023]
Abstract
Excretion is an essential physiological process, carried out by all living organisms, regardless of their size or complexity.1-3 Both protostomes (e.g., flies and flatworms) and deuterostomes (e.g., humans and sea urchins) possess specialized excretory organs serving that purpose. Those organs exhibit an astonishing diversity, ranging from units composed of just few distinct cells (e.g., protonephridia) to complex structures, built by millions of cells of multiple types with divergent morphology and function (e.g., vertebrate kidneys).4,5 Although some molecular similarities between the development of kidneys of vertebrates and the regeneration of the protonephridia of flatworms have been reported,6,7 the molecular underpinnings of the development of excretory organs have never been systematically studied in a comparative context.4 Here, we show that a set of transcription factors (eya, six1/2, pou3, sall, lhx1/5, and osr) and structural proteins (nephrin, kirre, and zo1) is expressed in the excretory organs of a phoronid, brachiopod, annelid, onychophoran, priapulid, and hemichordate that represent major protostome lineages and non-vertebrate deuterostomes. We demonstrate that the molecular similarity observed in the vertebrate kidney and flatworm protonephridia6,7 is also seen in the developing excretory organs of those animals. Our results show that all types of ultrafiltration-based excretory organs are patterned by a conserved set of developmental genes, an observation that supports their homology. We propose that the last common ancestor of protostomes and deuterostomes already possessed an ultrafiltration-based organ that later gave rise to the vast diversity of extant excretory organs, including both proto- and metanephridia.
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Burzyńska P, Sobala ŁF, Mikołajczyk K, Jodłowska M, Jaśkiewicz E. Sialic Acids as Receptors for Pathogens. Biomolecules 2021; 11:831. [PMID: 34199560 PMCID: PMC8227644 DOI: 10.3390/biom11060831] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
Carbohydrates have long been known to mediate intracellular interactions, whether within one organism or between different organisms. Sialic acids (Sias) are carbohydrates that usually occupy the terminal positions in longer carbohydrate chains, which makes them common recognition targets mediating these interactions. In this review, we summarize the knowledge about animal disease-causing agents such as viruses, bacteria and protozoa (including the malaria parasite Plasmodium falciparum) in which Sias play a role in infection biology. While Sias may promote binding of, e.g., influenza viruses and SV40, they act as decoys for betacoronaviruses. The presence of two common forms of Sias, Neu5Ac and Neu5Gc, is species-specific, and in humans, the enzyme converting Neu5Ac to Neu5Gc (CMAH, CMP-Neu5Ac hydroxylase) is lost, most likely due to adaptation to pathogen regimes; we discuss the research about the influence of malaria on this trait. In addition, we present data suggesting the CMAH gene was probably present in the ancestor of animals, shedding light on its glycobiology. We predict that a better understanding of the role of Sias in disease vectors would lead to more effective clinical interventions.
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Affiliation(s)
| | | | | | | | - Ewa Jaśkiewicz
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland; (P.B.); (Ł.F.S.); (K.M.); (M.J.)
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Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nat Commun 2021; 12:1783. [PMID: 33741994 PMCID: PMC7979703 DOI: 10.1038/s41467-021-22074-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/24/2021] [Indexed: 11/08/2022] Open
Abstract
Resolving the relationships between the major lineages in the animal tree of life is necessary to understand the origin and evolution of key animal traits. Sponges, characterized by their simple body plan, were traditionally considered the sister group of all other animal lineages, implying a gradual increase in animal complexity from unicellularity to complex multicellularity. However, the availability of genomic data has sparked tremendous controversy as some phylogenomic studies support comb jellies taking this position, requiring secondary loss or independent origins of complex traits. Here we show that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models. Testing on real datasets, we show a great improvement in model-fit that attenuates branching artefacts induced by systematic error. We reanalyse key datasets and show that partitioned phylogenomics does not support comb jellies as sister to other animals at either the supermatrix or partition-specific level.
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