1
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Martinez P, Bailly X, Sprecher SG, Hartenstein V. The Acoel nervous system: morphology and development. Neural Dev 2024; 19:9. [PMID: 38907301 PMCID: PMC11191258 DOI: 10.1186/s13064-024-00187-1] [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: 04/15/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
Acoel flatworms have played a relevant role in classical (and current) discussions on the evolutionary origin of bilaterian animals. This is mostly derived from the apparent simplicity of their body architectures. This tenet has been challenged over the last couple of decades, mostly because detailed studies of their morphology and the introduction of multiple genomic technologies have unveiled a complexity of cell types, tissular arrangements and patterning mechanisms that were hidden below this 'superficial' simplicity. One tissue that has received a particular attention has been the nervous system (NS). The combination of ultrastructural and single cell methodologies has revealed unique cellular diversity and developmental trajectories for most of their neurons and associated sensory systems. Moreover, the great diversity in NS architectures shown by different acoels offers us with a unique group of animals where to study key aspects of neurogenesis and diversification od neural systems over evolutionary time.In this review we revisit some recent developments in the characterization of the acoel nervous system structure and the regulatory mechanisms that contribute to their embryological development. We end up by suggesting some promising avenues to better understand how this tissue is organized in its finest cellular details and how to achieve a deeper knowledge of the functional roles that genes and gene networks play in its construction.
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Affiliation(s)
- Pedro Martinez
- Departament de Genètica, Microbiologia I Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.
- ICREA (Institut Català de Recerca I Estudis Avancats), Barcelona, Spain.
| | - Xavier Bailly
- Station Biologique de Roscoff, Multicellular Marine Models (M3) Team, FR2424, CNRS / Sorbonne Université - Place Georges Teissier, Roscoff, 29680, France
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, 10, Ch. Du Musée, Fribourg, 1700, Switzerland
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
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2
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Casas-Rodríguez A, Medrano-Padial C, Jos A, Cameán AM, Campos A, Fonseca E. Characterization of NR1J1 Paralog Responses of Marine Mussels: Insights from Toxins and Natural Activators. Int J Mol Sci 2024; 25:6287. [PMID: 38928005 PMCID: PMC11204112 DOI: 10.3390/ijms25126287] [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: 05/06/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The pregnane X receptor (PXR) is a nuclear hormone receptor that plays a pivotal role in regulating gene expression in response to various ligands, particularly xenobiotics. In this context, the aim of this study was to shed light on the ligand affinity and functions of four NR1J1 paralogs identified in the marine mussel Mytilus galloprovincialis, employing a dual-luciferase reporter assay. To achieve this, the activation patterns of these paralogs in response to various toxins, including freshwater cyanotoxins (Anatoxin-a, Cylindrospermopsin, and Microcystin-LR, -RR, and -YR) and marine algal toxins (Nodularin, Saxitoxin, and Tetrodotoxin), alongside natural compounds (Saint John's Wort, Ursolic Acid, and 8-Methoxypsoralene) and microalgal extracts (Tetraselmis, Isochrysis, LEGE 95046, and LEGE 91351 extracts), were studied. The investigation revealed nuanced differences in paralog response patterns, highlighting the remarkable sensitivity of MgaNR1J1γ and MgaNR1J1δ paralogs to several toxins. In conclusion, this study sheds light on the intricate mechanisms of xenobiotic metabolism and detoxification, particularly focusing on the role of marine mussel NR1J1 in responding to a diverse array of compounds. Furthermore, comparative analysis with human PXR revealed potential species-specific adaptations in detoxification mechanisms, suggesting evolutionary implications. These findings deepen our understanding of PXR-mediated metabolism mechanisms, offering insights into environmental monitoring and evolutionary biology research.
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Affiliation(s)
- Antonio Casas-Rodríguez
- Area of Toxicology, Faculty of Pharmacy, Universidad de Sevilla, Profesor García González n◦2, 41012 Seville, Spain
| | - Concepción Medrano-Padial
- Area of Toxicology, Faculty of Pharmacy, Universidad de Sevilla, Profesor García González n◦2, 41012 Seville, Spain
- Laboratorio de Fitoquímica y Alimentos Saludables (LabFAS), Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Campus Universitario 25, Espinardo, 30100 Murcia, Spain
| | - Angeles Jos
- Area of Toxicology, Faculty of Pharmacy, Universidad de Sevilla, Profesor García González n◦2, 41012 Seville, Spain
| | - Ana M Cameán
- Area of Toxicology, Faculty of Pharmacy, Universidad de Sevilla, Profesor García González n◦2, 41012 Seville, Spain
| | - Alexandre Campos
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
| | - Elza Fonseca
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
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3
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Bowles AMC, Williams TA, Donoghue PCJ, Campbell DA, Williamson CJ. Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land. THE NEW PHYTOLOGIST 2024. [PMID: 38840553 DOI: 10.1111/nph.19860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Douglas A Campbell
- Department of Biology, Mount Allison University, Sackville, NB, E4L 1H3, Canada
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4
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Mantica F, Iñiguez LP, Marquez Y, Permanyer J, Torres-Mendez A, Cruz J, Franch-Marro X, Tulenko F, Burguera D, Bertrand S, Doyle T, Nouzova M, Currie PD, Noriega FG, Escriva H, Arnone MI, Albertin CB, Wotton KR, Almudi I, Martin D, Irimia M. Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Nat Ecol Evol 2024; 8:1140-1153. [PMID: 38622362 DOI: 10.1038/s41559-024-02398-5] [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: 08/02/2023] [Accepted: 03/08/2024] [Indexed: 04/17/2024]
Abstract
Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution.
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Affiliation(s)
- Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Luis P Iñiguez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Marquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josefa Cruz
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Xavier Franch-Marro
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | - Toby Doyle
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Marcela Nouzova
- Institute of Parasitology, CAS, České Budějovice, Czech Republic
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia; Victorian Node, Monash University, Clayton, Victoria, Australia
| | - Fernando G Noriega
- Biology and BSI, Florida International University, Miami, FL, USA
- Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | | | - Caroline B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Karl R Wotton
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Isabel Almudi
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - David Martin
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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5
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Lin RC, Ferreira BT, Yuan YW. The molecular basis of phenotypic evolution: beyond the usual suspects. Trends Genet 2024:S0168-9525(24)00097-0. [PMID: 38704304 DOI: 10.1016/j.tig.2024.04.010] [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: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
It has been well documented that mutations in coding DNA or cis-regulatory elements underlie natural phenotypic variation in many organisms. However, the development of sophisticated functional tools in recent years in a wide range of traditionally non-model systems have revealed many 'unusual suspects' in the molecular bases of phenotypic evolution, including upstream open reading frames (uORFs), cryptic splice sites, and small RNAs. Furthermore, large-scale genome sequencing, especially long-read sequencing, has identified a cornucopia of structural variation underlying phenotypic divergence and elucidated the composition of supergenes that control complex multi-trait polymorphisms. In this review article we highlight recent studies that demonstrate this great diversity of molecular mechanisms producing adaptive genetic variation and the panoply of evolutionary paths leading to the 'grandeur of life'.
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Affiliation(s)
- Rong-Chien Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bianca T Ferreira
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
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6
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Gàlvez-Morante A, Guéguen L, Natsidis P, Telford MJ, Richter DJ. Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions. Genome Biol Evol 2024; 16:evae062. [PMID: 38518756 PMCID: PMC10995720 DOI: 10.1093/gbe/evae062] [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: 01/11/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024] Open
Abstract
Ancestral reconstruction is a widely used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach that allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial data sets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.
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Affiliation(s)
- Alex Gàlvez-Morante
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
| | - Laurent Guéguen
- LBBE, UMR 5558, CNRS, Université Claude Bernard Lyon 1, Villeurbanne 69622, France
| | - Paschalis Natsidis
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Daniel J Richter
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
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7
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Domazet-Lošo M, Široki T, Šimičević K, Domazet-Lošo T. Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages. Nat Commun 2024; 15:2663. [PMID: 38531970 DOI: 10.1038/s41467-024-47017-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The gain and loss of genes fluctuate over evolutionary time in major eukaryotic clades. However, the full profile of these macroevolutionary trajectories is still missing. To give a more inclusive view on the changes in genome complexity across the tree of life, here we recovered the evolutionary dynamics of gene family gain and loss ranging from the ancestor of cellular organisms to 352 eukaryotic species. We show that in all considered lineages the gene family content follows a common evolutionary pattern, where the number of gene families reaches the highest value at a major evolutionary and ecological transition, and then gradually decreases towards extant organisms. This supports theoretical predictions and suggests that the genome complexity is often decoupled from commonly perceived organismal complexity. We conclude that simplification by gene family loss is a dominant force in Phanerozoic genomes of various lineages, probably underpinned by intense ecological specializations and functional outsourcing.
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Affiliation(s)
- Mirjana Domazet-Lošo
- Department of Applied Computing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000, Zagreb, Croatia.
| | - Tin Široki
- Department of Applied Computing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000, Zagreb, Croatia
| | - Korina Šimičević
- Department of Applied Computing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000, Zagreb, Croatia
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
- School of Medicine, Catholic University of Croatia, Ilica 242, HR-10000, Zagreb, Croatia.
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8
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Szathmáry E. Nonadaptive onset of complex multicellularity. Proc Natl Acad Sci U S A 2024; 121:e2401220121. [PMID: 38437572 PMCID: PMC10945832 DOI: 10.1073/pnas.2401220121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Affiliation(s)
- Eörs Szathmáry
- Institute of Evolution, HUN-REN Centre for Ecological Research, Budapest1121, Hungary
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Pöcking82343, Germany
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9
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Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D'Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, Pascual-Anaya J. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nat Ecol Evol 2024; 8:519-535. [PMID: 38216617 DOI: 10.1038/s41559-023-02299-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/04/2023] [Indexed: 01/14/2024]
Abstract
Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity.
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Affiliation(s)
- Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Alan J S Beavan
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Jieyu Shen
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Iori Sato
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- iPS Cell Advanced Characterization and Development Team, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - James W Clark
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Joseph N Keating
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Emily M Carlisle
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Richard P Dearden
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Sam Giles
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Emma Randle
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Robert S Sansom
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - James F Fleming
- Keio University Institute for Advanced Biosciences, Tsuruoka, Japan
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Fumiaki Sugahara
- Division of Biology, Hyogo Medical University, Nishinomiya, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
| | - Cristiano Bertolucci
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Naoki Irie
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Cantas Alev
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Masayuki Hirano
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Jonathan P Rast
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Max D Cooper
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Jordi Paps
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Juan Pascual-Anaya
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan.
- Department of Animal Biology, Faculty of Science, University of Málaga (UMA), Málaga, Spain.
- Edificio de Bioinnovación, Universidad de Málaga, Málaga, Spain.
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10
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Bozdag GO, Szeinbaum N, Conlin PL, Chen K, Fos SM, Garcia A, Penev PI, Schaible GA, Trubl G. Chapter 5: Major Biological Innovations in the History of Life on Earth. ASTROBIOLOGY 2024; 24:S107-S123. [PMID: 38498818 PMCID: PMC11071111 DOI: 10.1089/ast.2021.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/14/2023] [Indexed: 03/20/2024]
Abstract
All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.
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Affiliation(s)
- G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L. Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin–Madison, Wisconsin, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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11
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Bingham EP, Ratcliff WC. A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity. Proc Natl Acad Sci U S A 2024; 121:e2319840121. [PMID: 38315855 PMCID: PMC10873551 DOI: 10.1073/pnas.2319840121] [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: 11/17/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
"Complex multicellularity," conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number of hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here, we propose an alternative, nonadaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. Taken together, we hypothesize that these idiosyncratic lineage-specific evolutionary dynamics play a fundamental role in the long-term divergent evolution of complex multicellularity across the tree of life.
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Affiliation(s)
- Emma P. Bingham
- School of Physics, Georgia Institute of Technology, Atlanta, GA30332
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA30332
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
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12
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Maurer-Alcalá XX, Cote-L’Heureux A, Kosakovsky Pond SL, Katz LA. Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates. PLoS One 2024; 19:e0291688. [PMID: 38271450 PMCID: PMC10810533 DOI: 10.1371/journal.pone.0291688] [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: 03/11/2023] [Accepted: 09/02/2023] [Indexed: 01/27/2024] Open
Abstract
The evolution of lineage-specific gene families remains poorly studied across the eukaryotic tree of life, with most analyses focusing on the recent evolution of de novo genes in model species. Here we explore the origins of lineage-specific genes in ciliates, a ~1 billion year old clade of microeukaryotes that are defined by their division of somatic and germline functions into distinct nuclei. Previous analyses on conserved gene families have shown the effect of ciliates' unusual genome architecture on gene family evolution: extensive genome processing-the generation of thousands of gene-sized somatic chromosomes from canonical germline chromosomes-is associated with larger and more diverse gene families. To further study the relationship between ciliate genome architecture and gene family evolution, we analyzed lineage specific gene families from a set of 46 transcriptomes and 12 genomes representing x species from eight ciliate classes. We assess how the evolution lineage-specific gene families occurs among four groups of ciliates: extensive fragmenters with gene-size somatic chromosomes, non-extensive fragmenters with "large'' multi-gene somatic chromosomes, Heterotrichea with highly polyploid somatic genomes and Karyorelictea with 'paradiploid' somatic genomes. Our analyses demonstrate that: 1) most lineage-specific gene families are found at shallow taxonomic scales; 2) extensive genome processing (i.e., gene unscrambling) during development likely influences the size and number of young lineage-specific gene families; and 3) the influence of somatic genome architecture on molecular evolution is increasingly apparent in older gene families. Altogether, these data highlight the influences of genome architecture on the evolution of lineage-specific gene families in eukaryotes.
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Affiliation(s)
- Xyrus X. Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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13
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Bingham EP, Ratcliff WC. A non-adaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566713. [PMID: 38014282 PMCID: PMC10680650 DOI: 10.1101/2023.11.11.566713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
"Complex multicellularity", conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here we propose an alternative, non-adaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: mutational biases in eukaryotes tend to drive genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. These effects become more severe as organisms evolve larger size and more stringent genetic bottlenecks between generations- both of which are hallmarks of complex multicellularity. Taken together, we hypothesize that it is these idiosyncratic lineage-specific mutational biases, rather than cell-biological innovations within eukaryotes, that underpins the long-term divergent evolution of complex multicellularity across the tree of life.
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Affiliation(s)
- Emma P Bingham
- School of Physics, Georgia Institute of Technology. Atlanta, Georgia 30332, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology. Atlanta, Georgia 30332, USA
| | - William C Ratcliff
- School of Biology, Georgia Institute of Technology. Atlanta, Georgia 30332, USA
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14
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Ruiz-Trillo I, Kin K, Casacuberta E. The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event. Annu Rev Microbiol 2023; 77:499-516. [PMID: 37406343 DOI: 10.1146/annurev-micro-032421-120023] [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] [Indexed: 07/07/2023]
Abstract
The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied.
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Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
- ICREA, Barcelona, Spain
| | - Koryu Kin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
| | - Elena Casacuberta
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
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15
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Merényi Z, Krizsán K, Sahu N, Liu XB, Bálint B, Stajich JE, Spatafora JW, Nagy LG. Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits. Nat Ecol Evol 2023; 7:1221-1231. [PMID: 37349567 PMCID: PMC10406608 DOI: 10.1038/s41559-023-02095-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Fungi are ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. Despite intense interest in their origins, major genomic trends of their evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here we provide a highly resolved genome-wide catalogue of gene family changes across fungal evolution inferred from the genomes of 123 fungi and relatives. We show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and the punctuated emergence of innovation by two main gene duplication events. We find that the gene content of non-Dikarya fungi resembles that of unicellular opisthokonts in many respects, owing to the conservation of protist genes in their genomes. The most rapidly duplicating gene groups included extracellular proteins and transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal history. These results suggest that the genomes of pre-fungal ancestors evolved into the typical filamentous fungal genome by a combination of gradual gene loss, turnover and several large duplication events rather than by abrupt changes. Consequently, the taxonomically defined Fungi represents a genomically non-uniform assemblage of species.
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Affiliation(s)
- Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Budapest, Hungary
| | - Neha Sahu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Jason E Stajich
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary.
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16
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Li JJ, Vasciaveo A, Karagiannis D, Sun Z, Chen X, Socciarelli F, Frankenstein Z, Zou M, Pannellini T, Chen Y, Gardner K, Robinson BD, de Bono J, Abate-Shen C, Rubin MA, Loda M, Sawyers CL, Califano A, Lu C, Shen MM. NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549585. [PMID: 37502956 PMCID: PMC10370123 DOI: 10.1101/2023.07.18.549585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The clinical use of potent androgen receptor (AR) inhibitors has promoted the emergence of novel subtypes of metastatic castration-resistant prostate cancer (mCRPC), including neuroendocrine prostate cancer (CRPC-NE), which is highly aggressive and lethal 1 . These mCRPC subtypes display increased lineage plasticity and often lack AR expression 2-5 . Here we show that neuroendocrine differentiation and castration-resistance in CRPC-NE are maintained by the activity of Nuclear Receptor Binding SET Domain Protein 2 (NSD2) 6 , which catalyzes histone H3 lysine 36 dimethylation (H3K36me2). We find that organoid lines established from genetically-engineered mice 7 recapitulate key features of human CRPC-NE, and can display transdifferentiation to neuroendocrine states in culture. CRPC-NE organoids express elevated levels of NSD2 and H3K36me2 marks, but relatively low levels of H3K27me3, consistent with antagonism of EZH2 activity by H3K36me2. Human CRPC-NE but not primary NEPC tumors expresses high levels of NSD2, consistent with a key role for NSD2 in lineage plasticity, and high NSD2 expression in mCRPC correlates with poor survival outcomes. Notably, CRISPR/Cas9 targeting of NSD2 or expression of a dominant-negative oncohistone H3.3K36M mutant results in loss of neuroendocrine phenotypes and restores responsiveness to the AR inhibitor enzalutamide in mouse and human CRPC-NE organoids and grafts. Our findings indicate that NSD2 inhibition can reverse lineage plasticity and castration-resistance, and provide a potential new therapeutic target for CRPC-NE.
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17
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Santini S, Schenkelaars Q, Jourda C, Duchesne M, Belahbib H, Rocher C, Selva M, Riesgo A, Vervoort M, Leys SP, Kodjabachian L, Le Bivic A, Borchiellini C, Claverie JM, Renard E. The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes. BMC Biol 2023; 21:139. [PMID: 37337252 DOI: 10.1186/s12915-023-01619-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/09/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology-evodevo-and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera. RESULTS We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species. CONCLUSIONS The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.
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Affiliation(s)
- Sébastien Santini
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Quentin Schenkelaars
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Cyril Jourda
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
- CIRAD, UMR PVBMT, La Réunion, France
| | - Marc Duchesne
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Hassiba Belahbib
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Caroline Rocher
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Marjorie Selva
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, SW7 5BD, UK
| | - Michel Vervoort
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Turing Center for Living Systems, Marseille, France
| | - André Le Bivic
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France
| | | | | | - Emmanuelle Renard
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France.
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France.
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18
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Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic Polyadenylation Is an Ancestral Hallmark of Early Development in Animals. Mol Biol Evol 2023; 40:msad137. [PMID: 37288606 PMCID: PMC10284499 DOI: 10.1093/molbev/msad137] [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: 12/02/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.
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Affiliation(s)
- Labib Rouhana
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Fredrik Hugosson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Valeria Dountcheva
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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19
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Barrera-Redondo J, Lotharukpong JS, Drost HG, Coelho SM. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biol 2023; 24:54. [PMID: 36964572 PMCID: PMC10037820 DOI: 10.1186/s13059-023-02895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.
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Affiliation(s)
- Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Jaruwatana Sodai Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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20
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Liang M, Chen W, LaFountain AM, Liu Y, Peng F, Xia R, Bradshaw H, Yuan YW. Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers. Science 2023; 379:576-582. [PMID: 36758083 PMCID: PMC10601778 DOI: 10.1126/science.adf1323] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/06/2022] [Indexed: 02/11/2023]
Abstract
Taxon-specific small RNA loci are widespread in eukaryotic genomes, yet their role in lineage-specific adaptation, phenotypic diversification, and speciation is poorly understood. Here, we report that a speciation locus in monkeyflowers (Mimulus), YELLOW UPPER (YUP), contains an inverted repeat region that produces small interfering RNAs (siRNAs) in a phased pattern. Although the inverted repeat is derived from a partial duplication of a protein-coding gene that is not involved in flower pigmentation, one of the siRNAs targets and represses a master regulator of floral carotenoid pigmentation. YUP emerged with two protein-coding genes that control other aspects of flower coloration as a "superlocus" in a subclade of Mimulus and has contributed to subsequent phenotypic diversification and pollinator-mediated speciation in the descendant species.
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Affiliation(s)
- Mei Liang
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Wenjie Chen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding and Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China
| | - Amy M. LaFountain
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Foen Peng
- Department of Biology, University of Washington, Seattle, WA 98195
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - H.D. Bradshaw
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
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21
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Raicu AM, Kadiyala D, Niblock M, Jain A, Yang Y, Bird KM, Bertholf K, Seenivasan A, Siddiq M, Arnosti DN. The Cynosure of CtBP: Evolution of a Bilaterian Transcriptional Corepressor. Mol Biol Evol 2023; 40:msad003. [PMID: 36625090 PMCID: PMC9907507 DOI: 10.1093/molbev/msad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Evolution of sequence-specific transcription factors clearly drives lineage-specific innovations, but less is known about how changes in the central transcriptional machinery may contribute to evolutionary transformations. In particular, transcriptional regulators are rich in intrinsically disordered regions that appear to be magnets for evolutionary innovation. The C-terminal Binding Protein (CtBP) is a transcriptional corepressor derived from an ancestral lineage of alpha hydroxyacid dehydrogenases; it is found in mammals and invertebrates, and features a core NAD-binding domain as well as an unstructured C-terminus (CTD) of unknown function. CtBP can act on promoters and enhancers to repress transcription through chromatin-linked mechanisms. Our comparative phylogenetic study shows that CtBP is a bilaterian innovation whose CTD of about 100 residues is present in almost all orthologs. CtBP CTDs contain conserved blocks of residues and retain a predicted disordered property, despite having variations in the primary sequence. Interestingly, the structure of the C-terminus has undergone radical transformation independently in certain lineages including flatworms and nematodes. Also contributing to CTD diversity is the production of myriad alternative RNA splicing products, including the production of "short" tailless forms of CtBP in Drosophila. Additional diversity stems from multiple gene duplications in vertebrates, where up to five CtBP orthologs have been observed. Vertebrate lineages show fewer major modifications in the unstructured CTD, possibly because gene regulatory constraints of the vertebrate body plan place specific constraints on this domain. Our study highlights the rich regulatory potential of this previously unstudied domain of a central transcriptional regulator.
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Affiliation(s)
- Ana-Maria Raicu
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
| | - Dhruva Kadiyala
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Madeline Niblock
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | | | - Yahui Yang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Kalynn M Bird
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Kayla Bertholf
- Biochemistry and Molecular Biology Program, College of Wooster
| | - Akshay Seenivasan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Mohammad Siddiq
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - David N Arnosti
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
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22
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Sowa ST, Bosetti C, Galera-Prat A, Johnson MS, Lehtiö L. An Evolutionary Perspective on the Origin, Conservation and Binding Partner Acquisition of Tankyrases. Biomolecules 2022; 12:1688. [PMID: 36421702 PMCID: PMC9688111 DOI: 10.3390/biom12111688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 01/04/2024] Open
Abstract
Tankyrases are poly-ADP-ribosyltransferases that regulate many crucial and diverse cellular processes in humans such as Wnt signaling, telomere homeostasis, mitotic spindle formation and glucose metabolism. While tankyrases are present in most animals, functional differences across species may exist. In this work, we confirm the widespread distribution of tankyrases throughout the branches of multicellular animal life and identify the single-celled choanoflagellates as earliest origin of tankyrases. We further show that the sequences and structural aspects of TNKSs are well-conserved even between distantly related species. We also experimentally characterized an anciently diverged tankyrase homolog from the sponge Amphimedon queenslandica and show that the basic functional aspects, such as poly-ADP-ribosylation activity and interaction with the canonical tankyrase binding peptide motif, are conserved. Conversely, the presence of tankyrase binding motifs in orthologs of confirmed interaction partners varies greatly between species, indicating that tankyrases may have different sets of interaction partners depending on the animal lineage. Overall, our analysis suggests a remarkable degree of conservation for tankyrases, and that their regulatory functions in cells have likely changed considerably throughout evolution.
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Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Chiara Bosetti
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering and InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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23
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Rust J. Phenotype-first hypotheses, spandrels and early metazoan evolution. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:48. [PMID: 36257998 DOI: 10.1007/s40656-022-00531-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Against the neo-Darwinian assumption that genetic factors are the principal source of variation upon which natural selection operates, a phenotype-first hypothesis strikes us as revolutionary because development would seem to constitute an independent source of variability. Richard Watson and his co-authors have argued that developmental memory constitutes one such variety of phenotypic variability. While this version of the phenotype-first hypothesis is especially well-suited for the late metazoan context, where animals have a sufficient history of selection from which to draw, appeals to developmental memory seem less plausible in the evolutionary context of the early metazoans. I provide an interpretation of Stuart Newman's account of deep metazoan phylogenesis that suggests that spandrels are, in addition to developmental memory, an important reservoir of phenotypic variability. I conclude by arguing that Gerd Müller's "side-effect hypothesis" is an illuminating generalization of the proposed non-Watsonian version of the phenotype-first hypothesis.
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Affiliation(s)
- Joshua Rust
- Stetson University, Unit 8250, 104-C Elizabeth Hall, 421 North Woodland Boulevard, DeLand, Florida, 32723, USA.
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24
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Divergent genomic trajectories predate the origin of animals and fungi. Nature 2022; 609:747-753. [PMID: 36002568 PMCID: PMC9492541 DOI: 10.1038/s41586-022-05110-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/14/2022] [Indexed: 12/27/2022]
Abstract
Animals and fungi have radically distinct morphologies, yet both evolved within the same eukaryotic supergroup: Opisthokonta1,2. Here we reconstructed the trajectory of genetic changes that accompanied the origin of Metazoa and Fungi since the divergence of Opisthokonta with a dataset that includes four novel genomes from crucial positions in the Opisthokonta phylogeny. We show that animals arose only after the accumulation of genes functionally important for their multicellularity, a tendency that began in the pre-metazoan ancestors and later accelerated in the metazoan root. By contrast, the pre-fungal ancestors experienced net losses of most functional categories, including those gained in the path to Metazoa. On a broad-scale functional level, fungal genomes contain a higher proportion of metabolic genes and diverged less from the last common ancestor of Opisthokonta than did the gene repertoires of Metazoa. Metazoa and Fungi also show differences regarding gene gain mechanisms. Gene fusions are more prevalent in Metazoa, whereas a larger fraction of gene gains were detected as horizontal gene transfers in Fungi and protists, in agreement with the long-standing idea that transfers would be less relevant in Metazoa due to germline isolation3-5. Together, our results indicate that animals and fungi evolved under two contrasting trajectories of genetic change that predated the origin of both groups. The gradual establishment of two clearly differentiated genomic contexts thus set the stage for the emergence of Metazoa and Fungi.
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25
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Bowles AMC, Paps J, Bechtold U. Water-related innovations in land plants evolved by different patterns of gene cooption and novelty. THE NEW PHYTOLOGIST 2022; 235:732-742. [PMID: 35048381 PMCID: PMC9303528 DOI: 10.1111/nph.17981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/25/2021] [Indexed: 05/26/2023]
Abstract
The origin of land plants and their descendants was marked by the evolution of key adaptations to life in terrestrial environments such as roots, vascular tissue and stomata. Though these innovations are well characterized, the evolution of the genetic toolkit underlying their development and function is poorly understood. We analysed molecular data from 532 species to investigate the evolutionary origin and diversification of genes involved in the development and regulation of these adaptations. We show that novel genes in the first land plants led to the single origin of stomata, but the stomatal closure of seed plants resulted from later gene expansions. By contrast, the major mechanism leading to the origin of vascular tissue was cooption of genes that emerged in the first land plants, enabling continuous water transport throughout the ancestral vascular plant. In turn, new key genes in the ancestors of plants with true leaves and seed plants led to the emergence of roots and lateral roots. The analysis highlights the different modes of evolution that enabled plants to conquer land, suggesting that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history.
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Affiliation(s)
- Alexander M. C. Bowles
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Geographical SciencesUniversity of BristolUniversity RoadBristolBS8 1RLUK
| | - Jordi Paps
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Ulrike Bechtold
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- Present address:
Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
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26
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Wu B, Hao W, Cox MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biol 2022; 20:144. [PMID: 35706021 PMCID: PMC9202105 DOI: 10.1186/s12915-022-01346-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01346-8.
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Affiliation(s)
- Baojun Wu
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
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27
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Santander MD, Maronna MM, Ryan JF, Andrade SCS. The state of Medusozoa genomics: current evidence and future challenges. Gigascience 2022; 11:6586816. [PMID: 35579552 PMCID: PMC9112765 DOI: 10.1093/gigascience/giac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
Medusozoa is a widely distributed ancient lineage that harbors one-third of Cnidaria diversity divided into 4 classes. This clade is characterized by the succession of stages and modes of reproduction during metagenic lifecycles, and includes some of the most plastic body plans and life cycles among animals. The characterization of traditional genomic features, such as chromosome numbers and genome sizes, was rather overlooked in Medusozoa and many evolutionary questions still remain unanswered. Modern genomic DNA sequencing in this group started in 2010 with the publication of the Hydra vulgaris genome and has experienced an exponential increase in the past 3 years. Therefore, an update of the state of Medusozoa genomics is warranted. We reviewed different sources of evidence, including cytogenetic records and high-throughput sequencing projects. We focused on 4 main topics that would be relevant for the broad Cnidaria research community: (i) taxonomic coverage of genomic information; (ii) continuity, quality, and completeness of high-throughput sequencing datasets; (iii) overview of the Medusozoa specific research questions approached with genomics; and (iv) the accessibility of data and metadata. We highlight a lack of standardization in genomic projects and their reports, and reinforce a series of recommendations to enhance future collaborative research.
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Affiliation(s)
- Mylena D Santander
- Correspondence address. Mylena D. Santander, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade São Paulo, 277 Rua do Matão, Cidade Universitária, São Paulo 05508-090, Brazil. E-mail:
| | - Maximiliano M Maronna
- Correspondence address. Maximiliano M. Maronna, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 101 Rua do Matão Cidade Universitária, São Paulo 05508-090, Brazil. E-mail:
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA,Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade São Paulo, 277 Rua do Matão, Cidade Universitária, São Paulo 05508-090, Brazil
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28
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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29
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Holstein TW. The role of cnidarian developmental biology in unraveling axis formation and Wnt signaling. Dev Biol 2022; 487:74-98. [DOI: 10.1016/j.ydbio.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022]
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30
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Repetti SI, Iha C, Uthanumallian K, Jackson CJ, Chen Y, Chan CX, Verbruggen H. Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. THE NEW PHYTOLOGIST 2022; 233:2144-2154. [PMID: 34923642 DOI: 10.1111/nph.17926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the core Chlorophyta and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most prasinophytes and the remainder of the core Chlorophyta. Our results suggest positive selection for genome streamlining in the Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their last common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. Results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising before diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.
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Affiliation(s)
- Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | | | | | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
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31
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Robert NSM, Sarigol F, Zimmermann B, Meyer A, Voolstra CR, Simakov O. Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. BMC Genomics 2022; 23:143. [PMID: 35177000 PMCID: PMC8851819 DOI: 10.1186/s12864-022-08304-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
Background Animal genomes are strikingly conserved in terms of local gene order (microsynteny). While some of these microsyntenies have been shown to be coregulated or to form gene regulatory blocks, the diversity of their genomic and regulatory properties across the metazoan tree of life remains largely unknown. Results Our comparative analyses of 49 animal genomes reveal that the largest gains of synteny occurred in the last common ancestor of bilaterians and cnidarians and in that of bilaterians. Depending on their node of emergence, we further show that novel syntenic blocks are characterized by distinct functional compositions (Gene Ontology terms enrichment) and gene density properties, such as high, average and low gene density regimes. This is particularly pronounced among bilaterian novel microsyntenies, most of which fall into high gene density regime associated with higher gene coexpression levels. Conversely, a majority of vertebrate novel microsyntenies display a low gene density regime associated with lower gene coexpression levels. Conclusions Our study provides first evidence for evolutionary transitions between different modes of microsyntenic block regulation that coincide with key events of metazoan evolution. Moreover, the microsyntenic profiling strategy and interactive online application (Syntenic Density Browser, available at: http://synteny.csb.univie.ac.at/) we present here can be used to explore regulatory properties of microsyntenic blocks and predict their coexpression in a wide-range of animal genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08304-2.
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Affiliation(s)
- Nicolas S M Robert
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
| | - Fatih Sarigol
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Constance, Germany
| | | | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
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32
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Wu YC, Franzenburg S, Ribes M, Pita L. Wounding response in Porifera (sponges) activates ancestral signaling cascades involved in animal healing, regeneration, and cancer. Sci Rep 2022; 12:1307. [PMID: 35079031 PMCID: PMC8789774 DOI: 10.1038/s41598-022-05230-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
Upon injury, the homeostatic balance that ensures tissue function is disrupted. Wound-induced signaling triggers the recovery of tissue integrity and offers a context to understand the molecular mechanisms for restoring tissue homeostasis upon disturbances. Marine sessile animals are particularly vulnerable to chronic wounds caused by grazers that can compromise prey's health. Yet, in comparison to other stressors like warming or acidification, we know little on how marine animals respond to grazing. Marine sponges (Phylum Porifera) are among the earliest-diverging animals and play key roles in the ecosystem; but they remain largely understudied. Here, we investigated the transcriptomic responses to injury caused by a specialist spongivorous opisthobranch (i.e., grazing treatment) or by clipping with a scalpel (i.e., mechanical damage treatment), in comparison to control sponges. We collected samples 3 h, 1 d, and 6 d post-treatment for differential gene expression analysis on RNA-seq data. Both grazing and mechanical damage activated a similar transcriptomic response, including a clotting-like cascade (e.g., with genes annotated as transglutaminases, metalloproteases, and integrins), calcium signaling, and Wnt and mitogen-activated protein kinase signaling pathways. Wound-induced gene expression signature in sponges resembles the initial steps of whole-body regeneration in other animals. Also, the set of genes responding to wounding in sponges included putative orthologs of cancer-related human genes. Further insights can be gained from taking sponge wound healing as an experimental system to understand how ancient genes and regulatory networks determine healthy animal tissues.
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Affiliation(s)
- Yu-Chen Wu
- Research Unit Marine Microbiology, Department Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
| | - Soeren Franzenburg
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts University of Kiel, Kiel, Germany
| | - Marta Ribes
- Department Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Lucía Pita
- Research Unit Marine Microbiology, Department Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
- Department Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain.
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33
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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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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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35
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Mongiardino Koch N. Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci. Mol Biol Evol 2021; 38:4025-4038. [PMID: 33983409 DOI: 10.1101/2021.02.13.431075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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37
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Duruz J, Kaltenrieder C, Ladurner P, Bruggmann R, Martìnez P, Sprecher SG. Acoel Single-Cell Transcriptomics: Cell Type Analysis of a Deep Branching Bilaterian. Mol Biol Evol 2021; 38:1888-1904. [PMID: 33355655 PMCID: PMC8097308 DOI: 10.1093/molbev/msaa333] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bilaterian animals display a wide variety of cell types, organized into defined anatomical structures and organ systems, which are mostly absent in prebilaterian animals. Xenacoelomorpha are an early-branching bilaterian phylum displaying an apparently relatively simple anatomical organization that have greatly diverged from other bilaterian clades. In this study, we use whole-body single-cell transcriptomics on the acoel Isodiametra pulchra to identify and characterize different cell types. Our analysis identifies the existence of ten major cell type categories in acoels all contributing to main biological functions of the organism: metabolism, locomotion and movements, behavior, defense, and development. Interestingly, although most cell clusters express core fate markers shared with other animal clades, we also describe a surprisingly large number of clade-specific marker genes, suggesting the emergence of clade-specific common molecular machineries functioning in distinct cell types. Together, these results provide novel insight into the evolution of bilaterian cell types and open the door to a better understanding of the origins of the bilaterian body plan and their constitutive cell types.
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Affiliation(s)
- Jules Duruz
- Department of Biology, Institute of Zoology, University of Fribourg, Fribourg, Switzerland
| | - Cyrielle Kaltenrieder
- Department of Biology, Institute of Zoology, University of Fribourg, Fribourg, Switzerland
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Rémy Bruggmann
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Pedro Martìnez
- Departament de Genètica, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Institut Català de Recerca i Estudis Avancats (ICREA), Passeig de Lluís Companys, Barcelona, Spain
| | - Simon G Sprecher
- Department of Biology, Institute of Zoology, University of Fribourg, Fribourg, Switzerland
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38
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Piekut T, Wong YY, Walker SE, Smith CL, Gauberg J, Harracksingh AN, Lowden C, Novogradac BB, Cheng HYM, Spencer GE, Senatore A. Early Metazoan Origin and Multiple Losses of a Novel Clade of RIM Presynaptic Calcium Channel Scaffolding Protein Homologs. Genome Biol Evol 2021; 12:1217-1239. [PMID: 32413100 PMCID: PMC7456537 DOI: 10.1093/gbe/evaa097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which, Rab3-interacting molecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channels in vitro via a PDZ domain that binds to the extreme C-termini of the channels at acidic ligand motifs of D/E-D/E/H-WC-COOH, and knockout of RIM in vertebrates and invertebrates disrupts CaV2 channel synaptic localization and synapse function. Here, we describe a previously uncharacterized clade of RIM proteins bearing domain architectures homologous to those of known RIM homologs, but with some notable differences including key amino acids associated with PDZ domain ligand specificity. This novel RIM emerged near the stem lineage of metazoans and underwent extensive losses, but is retained in select animals including the early-diverging placozoan Trichoplax adhaerens, and molluscs. RNA expression and localization studies in Trichoplax and the mollusc snail Lymnaea stagnalis indicate differential regional/tissue type expression, but overlapping expression in single isolated neurons from Lymnaea. Ctenophores, the most early-diverging animals with synapses, are unique among animals with nervous systems in that they lack the canonical RIM, bearing only the newly identified homolog. Through phylogenetic analysis, we find that CaV2 channel D/E-D/E/H-WC-COOH like PDZ ligand motifs were present in the common ancestor of cnidarians and bilaterians, and delineate some deeply conserved C-terminal structures that distinguish CaV1 from CaV2 channels, and CaV1/CaV2 from CaV3 channels.
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Affiliation(s)
| | | | - Sarah E Walker
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Carolyn L Smith
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | | | | | | | | | | | - Gaynor E Spencer
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
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GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life. J Genet Genomics 2021; 48:1122-1129. [PMID: 34538772 DOI: 10.1016/j.jgg.2021.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/21/2021] [Accepted: 03/29/2021] [Indexed: 11/20/2022]
Abstract
The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here, we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into GenOrigin (http://genorigin.chenzxlab.cn/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In GenOrigin, the information such as gene age estimates, annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.
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40
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Jockusch EL, Fisher CR. Something old, something new, something borrowed, something red: the origin of ecologically relevant novelties in Hemiptera. Curr Opin Genet Dev 2021; 69:154-162. [PMID: 34058515 DOI: 10.1016/j.gde.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Comparative transcriptomics, applied in an evolutionary context, has transformed the possibilities for studying phenotypic evolution in non-model taxa. We review recent discoveries about the development of novel, ecologically relevant phenotypes in hemipteran insects. These discoveries highlight the diverse genomic substrates of novelty: 'something old', when novelty results from changes in the regulation of existing genes or gene duplication; 'something new', wherein lineage-restricted genes contribute to the evolution of new phenotypes; and 'something borrowed', showcasing contributions of horizontal gene transfer to the evolution of novelty, including carotenoid synthesis (resulting in 'something red'). These findings show the power and flexibility of comparative transcriptomic approaches for expanding beyond the 'toolkit' model for the evolution of development. We conclude by raising questions about the relationship between new genes and new traits and outlining a research framework for answering them in Hemiptera.
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Affiliation(s)
- Elizabeth L Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd., U-3043, Storrs, CT 06269, USA.
| | - Cera R Fisher
- Cornell University, Department of Entomology, 2126 Comstock Hall, Ithaca, NY 14853, USA
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41
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Wu B, Cox MP. Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi. Environ Microbiol 2021; 23:3251-3264. [PMID: 33939870 PMCID: PMC8360070 DOI: 10.1111/1462-2920.15554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022]
Abstract
Fungi have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Here, we hypothesize that genes shared across all species with the same lifestyle, but absent in genera with alternative lifestyles, are crucial to that lifestyle. By analysing dozens of species within four genera in a fungal order, with each genus following a different lifestyle, we find that genus-specific genes are typically few in number. Notably, not all genus-specific genes appear to derive from de novo birth, with most instead reflecting recurrent loss across the fungi. Importantly, however, a subset of these genus-specific genes are shared by fungi with the same lifestyle in quite different evolutionary orders, thus supporting the view that some genus-specific genes are necessary for specific lifestyles. These lifestyle-specific genes are enriched for key functional classes and often exhibit specialized expression patterns. Genus-specific selection also contributes to lifestyle transitions, and is especially associated with intensity of pathogenesis. Our study, therefore, suggests that fungal adaptation to new lifestyles often requires just a small number of core genes, with gene turnover and positive selection playing complementary roles.
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Affiliation(s)
- Baojun Wu
- Statistics and Bioinformatics Group, School of Fundamental SciencesMassey UniversityPalmerston North4410New Zealand
- Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Murray P. Cox
- Statistics and Bioinformatics Group, School of Fundamental SciencesMassey UniversityPalmerston North4410New Zealand
- Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
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42
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Kuznetsov AV, Vainer VI, Volkova YM, Kartashov LE. Motility disorders and disintegration into separate cells of Trichoplax sp. H2 in the presence of Zn 2+ ions and L-cysteine molecules: A systems approach. Biosystems 2021; 206:104444. [PMID: 34023485 DOI: 10.1016/j.biosystems.2021.104444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 01/01/2023]
Abstract
Placozoa remain an ancient multicellular system with a dynamic body structure where calcium ions carry out a primary role in maintaining the integrity of the entire animal. Zinc ions can compete with calcium ions adsorption. We studied the effect of zinc ions and l-cysteine molecules on the interaction of Trichoplax sp. H2 cells. The regularity of formless motion was diminished in the presence of 20-25 μM of Zn2+ ions leading to the formation of branching animal forms. Locomotor ciliated cells moved chaotically and independently of each other leaving the Trichoplax body and opening a network of fiber cells. Application of 100 μM cysteine resulted in dissociation of the plate into separate cells. The combined chemical treatment shifted the effect in a random sample of animals toward disintegration, i.e. initially leading to disorder of collective cell movement and then to total body fragmentation. Two dissociation patterns of Trichoplax plate as "expanding ring" and "bicycle wheel" were revealed. Analysis of the interaction of Ca2+ and Zn2+ ions with cadherin showed that more than half (54%) of the amino acid residues with which Ca2+ and Zn2+ ions bind are common. The contact interaction of cells covered by the cadherin molecules is important for the coordinated movements of Trichoplax organism, while zinc ions are capable to break junctions between the cells. The involvement of other players, for example, l-cysteine in the regulation of Ca2+-dependent adhesion may be critical leading to the typical dissociation of Trichoplax body like in a calcium-free environment. A hypothesis about the essential role of calcium ions in the emergence of Metazoa ancestor is proposed.
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Affiliation(s)
- A V Kuznetsov
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia.
| | - V I Vainer
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia
| | - Yu M Volkova
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia
| | - L E Kartashov
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia
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43
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Ros-Rocher N, Pérez-Posada A, Leger MM, Ruiz-Trillo I. The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition. Open Biol 2021; 11:200359. [PMID: 33622103 PMCID: PMC8061703 DOI: 10.1098/rsob.200359] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.
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Affiliation(s)
- Núria Ros-Rocher
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Alberto Pérez-Posada
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Centro Andaluz de Biología del Desarrollo (CSIC-Universidad Pablo de Olavide), Carretera de Utrera Km 1, 41013 Sevilla, Andalusia, Spain
| | - Michelle M Leger
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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44
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Zaquin T, Malik A, Drake JL, Putnam HM, Mass T. Evolution of Protein-Mediated Biomineralization in Scleractinian Corals. Front Genet 2021; 12:618517. [PMID: 33633782 PMCID: PMC7902050 DOI: 10.3389/fgene.2021.618517] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian “core biomineralization toolkit.” This “core set” contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians’ ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene.
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Affiliation(s)
- Tal Zaquin
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Jeana L Drake
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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45
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Ruiz-Trillo I, de Mendoza A. Towards understanding the origin of animal development. Development 2020; 147:147/23/dev192575. [PMID: 33272929 DOI: 10.1242/dev.192575] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Almost all animals undergo embryonic development, going from a single-celled zygote to a complex multicellular adult. We know that the patterning and morphogenetic processes involved in development are deeply conserved within the animal kingdom. However, the origins of these developmental processes are just beginning to be unveiled. Here, we focus on how the protist lineages sister to animals are reshaping our view of animal development. Most intriguingly, many of these protistan lineages display transient multicellular structures, which are governed by similar morphogenetic and gene regulatory processes as animal development. We discuss here two potential alternative scenarios to explain the origin of animal embryonic development: either it originated concomitantly at the onset of animals or it evolved from morphogenetic processes already present in their unicellular ancestors. We propose that an integrative study of several unicellular taxa closely related to animals will allow a more refined picture of how the last common ancestor of animals underwent embryonic development.
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Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain .,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Alex de Mendoza
- Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4DQ, UK
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46
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Petit D, Teppa RE, Harduin-Lepers A. A phylogenetic view and functional annotation of the animal β1,3-glycosyltransferases of the GT31 CAZy family. Glycobiology 2020; 31:243-259. [PMID: 32886776 PMCID: PMC8022947 DOI: 10.1093/glycob/cwaa086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 12/28/2022] Open
Abstract
The formation of β1,3-linkages on animal glycoconjugates is catalyzed by a subset of β1,3-glycosyltransferases grouped in the Carbohydrate-Active enZYmes family glycosyltransferase-31 (GT31). This family represents an extremely diverse set of β1,3-N-acetylglucosaminyltransferases [B3GNTs and Fringe β1,3-N-acetylglucosaminyltransferases], β1,3-N-acetylgalactosaminyltransferases (B3GALNTs), β1,3-galactosyltransferases [B3GALTs and core 1 β1,3-galactosyltransferases (C1GALTs)], β1,3-glucosyltransferase (B3GLCT) and β1,3-glucuronyl acid transferases (B3GLCATs or CHs). The mammalian enzymes were particularly well studied and shown to use a large variety of sugar donors and acceptor substrates leading to the formation of β1,3-linkages in various glycosylation pathways. In contrast, there are only a few studies related to other metazoan and lower vertebrates GT31 enzymes and the evolutionary relationships of these divergent sequences remain obscure. In this study, we used bioinformatics approaches to identify more than 920 of putative GT31 sequences in Metazoa, Fungi and Choanoflagellata revealing their deep ancestry. Sequence-based analysis shed light on conserved motifs and structural features that are signatures of all the GT31. We leverage pieces of evidence from gene structure, phylogenetic and sequence-based analyses to identify two major subgroups of GT31 named Fringe-related and B3GALT-related and demonstrate the existence of 10 orthologue groups in the Urmetazoa, the hypothetical last common ancestor of all animals. Finally, synteny and paralogy analysis unveiled the existence of 30 subfamilies in vertebrates, among which 5 are new and were named C1GALT2, C1GALT3, B3GALT8, B3GNT10 and B3GNT11. Altogether, these various approaches enabled us to propose the first comprehensive analysis of the metazoan GT31 disentangling their evolutionary relationships.
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Affiliation(s)
- Daniel Petit
- Glycosylation et différenciation cellulaire, EA 7500, Laboratoire PEIRENE, Université de Limoges, 123 Avenue Albert Thomas, 87060 Limoges Cedex, France
| | - Roxana Elin Teppa
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRA, INSA, 135, Avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Anne Harduin-Lepers
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
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47
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Fonseca E, Machado AM, Vilas-Arrondo N, Gomes-Dos-Santos A, Veríssimo A, Esteves P, Almeida T, Themudo G, Ruivo R, Pérez M, da Fonseca R, Santos MM, Froufe E, Román-Marcote E, Venkatesh B, Castro LFC. Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes. Gen Comp Endocrinol 2020; 295:113527. [PMID: 32526329 DOI: 10.1016/j.ygcen.2020.113527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Nuclear receptors (NRs) are key transcription factors that originated in the common ancestor of metazoans. The vast majority of NRs are triggered by binding to either endogenous (e.g. retinoic acid) or exogenous (e.g. xenobiotics) ligands, and their evolution and expansion is tightly linked to the function of endocrine systems. Importantly, they represent classic targets of physiological exploitation by endocrine disrupting chemicals. The NR gene repertoire in different lineages has been shaped by gene loss, duplication and mutation, denoting a dynamic evolutionary route. As the earliest diverging class of gnathostomes (jawed vertebrates), cartilaginous fishes offer an exceptional opportunity to address the early diversification of NR gene families and the evolution of the endocrine system in jawed vertebrates. Here we provide an exhaustive analysis into the NR gene composition in five elasmobranch (sharks and rays) and two holocephalan (chimaeras) species. For this purpose, we generated also a low coverage draft genome assembly of the chimaera small-eyed rabbitfish, Hydrolagus affinis. We show that cartilaginous fish retain an archetypal NR gene repertoire, similar to that of mammals and coincident with the two rounds of whole genome duplication that occurred in the gnathostome ancestor. Furthermore, novel gene members of the non-canonical NR0B receptors were found in the genomes of this lineage. Our findings provide an essential view into the early diversification of NRs in gnathostomes, paving the way for functional studies.
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Affiliation(s)
- Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Nair Vilas-Arrondo
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain; UVIGO, phD Program "Marine Science, Tehchology and Management" (Do *MAR), Faculty of Biology, University of Vigo, 36200 Vigo, Spain
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - Ana Veríssimo
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, U.Porto, 4485-661 Vairão, Portugal
| | - Pedro Esteves
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; UVIGO, phD Program "Marine Science, Tehchology and Management" (Do *MAR), Faculty of Biology, University of Vigo, 36200 Vigo, Spain
| | - Tereza Almeida
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, U.Porto, 4485-661 Vairão, Portugal
| | - Gonçalo Themudo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Raquel Ruivo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Montse Pérez
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain
| | - Rute da Fonseca
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Denmark
| | - Miguel M Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Esther Román-Marcote
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore.
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal.
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Genes with spiralian-specific protein motifs are expressed in spiralian ciliary bands. Nat Commun 2020; 11:4171. [PMID: 32820176 PMCID: PMC7441323 DOI: 10.1038/s41467-020-17780-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/17/2020] [Indexed: 12/22/2022] Open
Abstract
Spiralia is a large, ancient and diverse clade of animals, with a conserved early developmental program but diverse larval and adult morphologies. One trait shared by many spiralians is the presence of ciliary bands used for locomotion and feeding. To learn more about spiralian-specific traits we have examined the expression of 20 genes with protein motifs that are strongly conserved within the Spiralia, but not detectable outside of it. Here, we show that two of these are specifically expressed in the main ciliary band of the mollusc Tritia (also known as Ilyanassa). Their expression patterns in representative species from five more spiralian phyla—the annelids, nemerteans, phoronids, brachiopods and rotifers—show that at least one of these, lophotrochin, has a conserved and specific role in particular ciliated structures, most consistently in ciliary bands. These results highlight the potential importance of lineage-specific genes or protein motifs for understanding traits shared across ancient lineages. Spiralians have ciliary bands, used for locomotion and feeding, but defining molecular features of these structures are unknown. Here, the authors report a gene, Lophotrochin, that contains a protein domain only found in spiralians, and specifically expressed in diverse ciliary bands across the group, which provides a molecular signature for these structures.
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Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
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Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
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50
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Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing. Nat Commun 2020; 11:3051. [PMID: 32561724 PMCID: PMC7305137 DOI: 10.1038/s41467-020-16801-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/22/2020] [Indexed: 12/30/2022] Open
Abstract
The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.
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