1
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Lagman D, Leon A, Cieminska N, Deng W, Chatzigeorgiou M, Henriet S, Chourrout D. Pax3/7 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory. Dev Biol 2024; 516:207-220. [PMID: 39181419 DOI: 10.1016/j.ydbio.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factor genes expressed during early OE patterning. Among these are two Pax3/7 copies that we named pax37A and pax37B. The vertebrate homologs, PAX3 and PAX7 are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona intestinalis, Pax3/7 plays a role in the development of cells deriving from the neural plate border, including trunk epidermal sensory neurons and tail nerve cord neurons, as well as in the neural tube closure. Here we have investigated the roles of Oikopleura dioica pax37A and pax37B in the development of the OE, by using CRISPR-Cas9 mutant lines and analyzing scRNA-seq data from wild-type animals. We found that pax37B but not pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Trajectory analysis supported a neuroepithelial-like or a preplacodal ectoderm transcriptional signature in these cells. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features. This is supported by a fragmented gene regulatory network involved in their development that also operates in ascidian epidermal neurons.
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Affiliation(s)
- David Lagman
- Michael Sars Centre, University of Bergen, Bergen, NO-5020, Norway; Department of Medical Cell Biology, Uppsala University, Uppsala, SE-75123, Sweden.
| | - Anthony Leon
- Michael Sars Centre, University of Bergen, Bergen, NO-5020, Norway
| | - Nadia Cieminska
- Michael Sars Centre, University of Bergen, Bergen, NO-5020, Norway
| | - Wei Deng
- Michael Sars Centre, University of Bergen, Bergen, NO-5020, Norway
| | | | - Simon Henriet
- Michael Sars Centre, University of Bergen, Bergen, NO-5020, Norway
| | - Daniel Chourrout
- Michael Sars Centre, University of Bergen, Bergen, NO-5020, Norway.
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2
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Stein WD. Orthologs at the Base of the Olfactores Clade. Genes (Basel) 2024; 15:657. [PMID: 38927593 PMCID: PMC11203038 DOI: 10.3390/genes15060657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Tunicate orthologs in the human genome comprise just 84 genes of the 19,872 protein-coding genes and 23 of the 16,528 non-coding genes, yet they stand at the base of the Olfactores clade, which radiated to generate thousands of tunicate and vertebrate species. What were the powerful drivers among these genes that enabled this process? Many of these orthologs are present in gene families. We discuss the biological role of each family and the orthologs' quantitative contribution to the family. Most important was the evolution of a second type of cadherin. This, a Type II cadherin, had the property of detaching the cell containing that cadherin from cells that expressed the Type I class. The set of such Type II cadherins could now detach and move away from their Type I neighbours, a process which would eventually evolve into the formation of the neural crest, "the fourth germ layer", providing a wide range of possibilities for further evolutionary invention. A second important contribution were key additions to the broad development of the muscle and nerve protein and visual perception toolkits. These developments in mobility and vision provided the basis for the development of the efficient predatory capabilities of the Vertebrata.
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Affiliation(s)
- Wilfred D Stein
- Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel
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3
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Calatayud S, Garcia-Risco M, Capdevila M, Cañestro C, Palacios Ò, Albalat R. Modular Evolution and Population Variability of Oikopleura dioica Metallothioneins. Front Cell Dev Biol 2021; 9:702688. [PMID: 34277643 PMCID: PMC8283569 DOI: 10.3389/fcell.2021.702688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/09/2021] [Indexed: 01/29/2023] Open
Abstract
Chordate Oikopleura dioica probably is the fastest evolving metazoan reported so far, and thereby, a suitable system in which to explore the limits of evolutionary processes. For this reason, and in order to gain new insights on the evolution of protein modularity, we have investigated the organization, function and evolution of multi-modular metallothionein (MT) proteins in O. dioica. MTs are a heterogeneous group of modular proteins defined by their cysteine (C)-rich domains, which confer the capacity of coordinating different transition metal ions. O. dioica has two MTs, a bi-modular OdiMT1 consisting of two domains (t-12C and 12C), and a multi-modular OdiMT2 with six t-12C/12C repeats. By means of mass spectrometry and spectroscopy of metal-protein complexes, we have shown that the 12C domain is able to autonomously bind four divalent metal ions, although the t-12C/12C pair –as it is found in OdiMT1– is the optimized unit for divalent metal binding. We have also shown a direct relationship between the number of the t-12C/12C repeats and the metal-binding capacity of the MTs, which means a stepwise mode of functional and structural evolution for OdiMT2. Finally, after analyzing four different O. dioica populations worldwide distributed, we have detected several OdiMT2 variants with changes in their number of t-12C/12C domain repeats. This finding reveals that the number of repeats fluctuates between current O. dioica populations, which provides a new perspective on the evolution of domain repeat proteins.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Mario Garcia-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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4
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Liu AW, Tan Y, Masunaga A, Bliznina A, West C, Plessy C, Luscombe NM. H3S28P Antibody Staining of Okinawan Oikopleura dioica Suggests the Presence of Three Chromosomes. F1000Res 2020; 9:780. [PMID: 33728042 PMCID: PMC7941098 DOI: 10.12688/f1000research.25019.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Oikopleura dioica is a ubiquitous marine zooplankton of biological interest owing to features that include dioecious reproduction, a short life cycle, conserved chordate body plan, and a compact genome. It is an important tunicate model for evolutionary and developmental research, as well as investigations into marine ecosystems. The genome of north Atlantic O. dioica comprises three chromosomes. However, comparisons with the genomes of O. dioica sampled from mainland and southern Japan revealed extensive sequence differences. Moreover, historical studies have reported widely varying chromosome counts. We recently initiated a project to study the genomes of O. dioica individuals collected from the coastline of the Ryukyu (Okinawa) Islands in southern Japan. Given the potentially large extent of genomic diversity, we employed karyological techniques to count individual animals' chromosomes in situ using centromere-specific antibodies directed against H3S28P, a prophase-metaphase cell cycle-specific marker of histone H3. Epifluorescence and confocal images were obtained of embryos and oocytes stained with two commercial anti-H3S28P antibodies (Abcam ab10543 and Thermo Fisher 07-145). The data lead us to conclude that diploid cells from Okinawan O. dioica contain three pairs of chromosomes, in line with the north Atlantic populations. The finding facilitates the telomere-to-telomere assembly of Okinawan O. dioica genome sequences and gives insight into the genomic diversity of O. dioica from different geographical locations. The data deposited in the EBI BioImage Archive provide representative images of the antibodies' staining properties for use in epifluorescent and confocal based fluorescent microscopy.
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Affiliation(s)
- Andrew W. Liu
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, 904-0324, Japan
| | - Yongkai Tan
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, 904-0324, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, 904-0324, Japan
| | - Aleksandra Bliznina
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, 904-0324, Japan
| | - Charlotte West
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, 904-0324, Japan
- Francis Crick Institute, London, NW1 1AT, UK
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, 904-0324, Japan
| | - Nicholas M. Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, 904-0324, Japan
- Francis Crick Institute, London, NW1 1AT, UK
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
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5
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Ferrández-Roldán A, Martí-Solans J, Cañestro C, Albalat R. Oikopleura dioica: An Emergent Chordate Model to Study the Impact of Gene Loss on the Evolution of the Mechanisms of Development. Results Probl Cell Differ 2019; 68:63-105. [PMID: 31598853 DOI: 10.1007/978-3-030-23459-1_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The urochordate Oikopleura dioica is emerging as a nonclassical animal model in the field of evolutionary developmental biology (a.k.a. evo-devo) especially attractive for investigating the impact of gene loss on the evolution of mechanisms of development. This is because this organism fulfills the requirements of an animal model (i.e., has a simple and accessible morphology, a short generation time and life span, and affordable culture in the laboratory and amenable experimental manipulation), but also because O. dioica occupies a key phylogenetic position to understand the diversification and origin of our own phylum, the chordates. During its evolution, O. dioica genome has suffered a drastic process of compaction, becoming the smallest known chordate genome, a process that has been accompanied by exacerbating amount of gene losses. Interestingly, however, despite the extensive gene losses, including entire regulatory pathways essential for the embryonic development of other chordates, O. dioica retains the typical chordate body plan. This unexpected situation led to the formulation of the so-called inverse paradox of evo-devo, that is, when a genetic diversity is able to maintain a phenotypic unity. This chapter reviews the biological features of O. dioica as a model animal, along with the current data on the evolution of its genes and genome. We pay special attention to the numerous examples of gene losses that have taken place during the evolution of this unique animal model, which is helping us to understand to which the limits of evo-devo can be pushed off.
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Affiliation(s)
- Alfonso Ferrández-Roldán
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Martí-Solans
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristian Cañestro
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Ricard Albalat
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain.
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6
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Mikhaleva Y, Skinnes R, Sumic S, Thompson EM, Chourrout D. Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors. Dev Biol 2018; 443:117-126. [DOI: 10.1016/j.ydbio.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/27/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023]
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7
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Torres-Águila NP, Martí-Solans J, Ferrández-Roldán A, Almazán A, Roncalli V, D'Aniello S, Romano G, Palumbo A, Albalat R, Cañestro C. Diatom bloom-derived biotoxins cause aberrant development and gene expression in the appendicularian chordate Oikopleura dioica. Commun Biol 2018; 1:121. [PMID: 30272001 PMCID: PMC6123688 DOI: 10.1038/s42003-018-0127-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022] Open
Abstract
Investigating environmental hazards than could affect appendicularians is of prime ecological interest because they are among the most abundant components of the mesozooplankton. This work shows that embryo development of the appendicularian Oikopleura dioica is compromised by diatom bloom-derived biotoxins, even at concentrations in the same range as those measured after blooms. Developmental gene expression analysis of biotoxin-treated embryos uncovers an aberrant golf ball-like phenotype affecting morphogenesis, midline convergence, and tail elongation. Biotoxins induce a rapid upregulation of defensome genes, and considerable delay and silencing of zygotic transcription of developmental genes. Upon a possible future intensification of blooms associated with ocean warming and acidification, our work puts an alert on the potential impact that an increase of biotoxins may have on marine food webs, and points to defensome genes as molecular biosensors that marine ecologists could use to monitor the genetic stress of natural populations exposed to microalgal blooms.
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Affiliation(s)
- Nuria P Torres-Águila
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Josep Martí-Solans
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Alfonso Ferrández-Roldán
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Alba Almazán
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Vittoria Roncalli
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale 80121, Napoli, Italy
| | - Giovanna Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Anna Palumbo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale 80121, Napoli, Italy
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain.
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain.
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8
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Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty. Nat Commun 2018; 9:1730. [PMID: 29712911 PMCID: PMC5928047 DOI: 10.1038/s41467-018-04136-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/28/2018] [Indexed: 12/03/2022] Open
Abstract
Understanding the emergence of the Animal Kingdom is one of the major challenges of modern evolutionary biology. Many genomic changes took place along the evolutionary lineage that gave rise to the Metazoa. Recent research has revealed the role that co-option of old genes played during this transition, but the contribution of genomic novelty has not been fully assessed. Here, using extensive genome comparisons between metazoans and multiple outgroups, we infer the minimal protein-coding genome of the first animal, in addition to other eukaryotic ancestors, and estimate the proportion of novelties in these ancient genomes. Contrary to the prevailing view, this uncovers an unprecedented increase in the extent of genomic novelty during the origin of metazoans, and identifies 25 groups of metazoan-specific genes that are essential across the Animal Kingdom. We argue that internal genomic changes were as important as external factors in the emergence of animals. Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.
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9
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Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ. De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Sci Rep 2018; 8:5518. [PMID: 29615780 PMCID: PMC5882950 DOI: 10.1038/s41598-018-23749-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 01/17/2023] Open
Abstract
Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.
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Affiliation(s)
- Simon Blanchoud
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Kim Rutherford
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Lisa Zondag
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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10
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Chang WH, Lai AG. A TALE of shrimps: Genome-wide survey of homeobox genes in 120 species from diverse crustacean taxa. F1000Res 2018; 7:71. [PMID: 29899973 PMCID: PMC5968366 DOI: 10.12688/f1000research.13636.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2018] [Indexed: 01/19/2023] Open
Abstract
The homeodomain-containing proteins are an important group of transcription factors found in most eukaryotes including animals, plants and fungi. Homeobox genes are responsible for a wide range of critical developmental and physiological processes, ranging from embryonic development, innate immune homeostasis to whole-body regeneration. With continued fascination on this key class of proteins by developmental and evolutionary biologists, multiple efforts have thus far focused on the identification and characterization of homeobox orthologs from key model organisms in attempts to infer their evolutionary origin and how this underpins the evolution of complex body plans. Despite their importance, the genetic complement of homeobox genes has yet been described in one of the most valuable groups of animals representing economically important food crops. With crustacean aquaculture being a growing industry worldwide, it is clear that systematic and cross-species identification of crustacean homeobox orthologs is necessary in order to harness this genetic circuitry for the improvement of aquaculture sustainability. Using publicly available transcriptome data sets, we identified a total of 4183 putative homeobox genes from 120 crustacean species that include food crop species, such as lobsters, shrimps, crayfish and crabs. Additionally, we identified 717 homeobox orthologs from 6 other non-crustacean arthropods, which include the scorpion, deer tick, mosquitoes and centipede. This high confidence set of homeobox genes will now serve as a key resource to the broader community for future functional and comparative genomics studies.
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Affiliation(s)
- Wai Hoong Chang
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Alvina G Lai
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
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11
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Calatayud S, Garcia-Risco M, Rojas NS, Espinosa-Sánchez L, Artime S, Palacios Ò, Cañestro C, Albalat R. Metallothioneins of the urochordate Oikopleura dioica have Cys-rich tandem repeats, large size and cadmium-binding preference. Metallomics 2018; 10:1585-1594. [DOI: 10.1039/c8mt00177d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oikopleura dioica has the longest metallothionein described so far, made of repeats generated by a modular and step-wise evolution.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Mario Garcia-Risco
- Departament de Química
- Facultat de Ciències
- Universitat Autònoma de Barcelona
- E-08193 Cerdanyola del Vallès
- Spain
| | - Natalia S. Rojas
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Lizethe Espinosa-Sánchez
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Sebastián Artime
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Òscar Palacios
- Departament de Química
- Facultat de Ciències
- Universitat Autònoma de Barcelona
- E-08193 Cerdanyola del Vallès
- Spain
| | - Cristian Cañestro
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Ricard Albalat
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
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12
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Kaul-Strehlow S, Urata M, Praher D, Wanninger A. Neuronal patterning of the tubular collar cord is highly conserved among enteropneusts but dissimilar to the chordate neural tube. Sci Rep 2017; 7:7003. [PMID: 28765531 PMCID: PMC5539250 DOI: 10.1038/s41598-017-07052-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/23/2017] [Indexed: 11/09/2022] Open
Abstract
A tubular nervous system is present in the deuterostome groups Chordata (cephalochordates, tunicates, vertebrates) and in the non-chordate Enteropneusta. However, the worm-shaped enteropneusts possess a less complex nervous system featuring only a short hollow neural tube, whereby homology to its chordate counterpart remains elusive. Since the majority of data on enteropneusts stem from the harrimaniid Saccoglossus kowalevskii, putative interspecific variations remain undetected resulting in an unreliable ground pattern that impedes homology assessments. In order to complement the missing data from another enteropneust family, we investigated expression of key neuronal patterning genes in the ptychoderid Balanoglossus misakiensis. The collar cord of B. misakiensis shows anterior Six3/6 and posterior Otx + Engrailed expression, in a region corresponding to the chordate brain. Neuronal Nk2.1/Nk2.2 expression is absent. Interestingly, we found median Dlx and lateral Pax6 expression domains, i.e., a condition that is reversed compared to chordates. Comparative analyses reveal that adult nervous system patterning is highly conserved among the enteropneust families Harrimaniidae, Spengelidae and Ptychoderidae. BmiDlx and BmiPax6 have no corresponding expression domains in the chordate brain, which may be indicative of independent acquisition of a tubular nervous system in Enteropneusta and Chordata.
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Affiliation(s)
- Sabrina Kaul-Strehlow
- Department for Integrative Zoology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria. .,Research Center for Marine Biology, Tohoku University, Asamushi, Aomori, Aomori, 039-3501, Japan. .,Department for Molecular Evolution and Development, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Makoto Urata
- Noto Marine Laboratory, Division of Marine Environmental Studies, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa, 927-0553, Japan
| | - Daniela Praher
- Department for Molecular Evolution and Development, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| | - Andreas Wanninger
- Department for Integrative Zoology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
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Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans. Nat Commun 2017; 8:9. [PMID: 28377584 PMCID: PMC5431905 DOI: 10.1038/s41467-017-00020-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/16/2017] [Indexed: 11/08/2022] Open
Abstract
The phylum Rotifera consists of minuscule, nonsegmented animals with a unique body plan and an unresolved phylogenetic position. The presence of pharyngeal articulated jaws supports an inclusion in Gnathifera nested in the Spiralia. Comparison of Hox genes, involved in animal body plan patterning, can be used to infer phylogenetic relationships. Here, we report the expression of five Hox genes during embryogenesis of the rotifer Brachionus manjavacas and show how these genes define different functional components of the nervous system and not the usual bilaterian staggered expression along the anteroposterior axis. Sequence analysis revealed that the lox5-parapeptide, a key signature in lophotrochozoan and platyhelminthean Hox6/lox5 genes, is absent and replaced by different signatures in Rotifera and Chaetognatha, and that the MedPost gene, until now unique to Chaetognatha, is also present in rotifers. Collectively, our results support an inclusion of chaetognaths in gnathiferans and Gnathifera as sister group to the remaining spiralians. Rotifers are microscopic animals with an unusual, nonsegmented body plan consisting of a head, trunk and foot. Here, Fröbius and Funch investigate the role of Hox genes—which are widely used in animal body plan patterning—in rotifer embryogenesis and find non-canonical expression in the nervous system.
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Abstract
Tunicates, also called urochordates, are an extremely diverse subphylum of the Chordata, a phylum that also contains the vertebrates and cephalochordates. The tunicates seem to have undergone especially rapid evolution: while remaining exclusively marine, they have radiated to occupy habitats ranging from shallow water, to near shore to the open ocean and the deep sea. Furthermore, they have evolved a variety of remarkable reproductive strategies, combining asexual and sexual modes of reproduction that allow for very rapid expansion of populations. An outstanding question is what happened to allow tunicates to evolve so much faster than their nearest relatives, cephalochordates and vertebrates.
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Affiliation(s)
- Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA.
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Abstract
The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
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Heenan P, Zondag L, Wilson MJ. Evolution of the Sox gene family within the chordate phylum. Gene 2016; 575:385-392. [DOI: 10.1016/j.gene.2015.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 12/20/2022]
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Holland LZ. Genomics, evolution and development of amphioxus and tunicates: The Goldilocks principle. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:342-52. [DOI: 10.1002/jez.b.22569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Linda Z. Holland
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California San Diego; La Jolla California 92093-0202 USA
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Cañestro C, Albalat R, Irimia M, Garcia-Fernàndez J. Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Semin Cell Dev Biol 2013; 24:83-94. [DOI: 10.1016/j.semcdb.2012.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 02/06/2023]
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Zhong YF, Holland PWH. HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology. Evol Dev 2013; 13:567-8. [PMID: 23016940 PMCID: PMC3399086 DOI: 10.1111/j.1525-142x.2011.00513.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homeobox gene database (HomeoDB), a manually curated database of homeobox genes and their classification, has been well received since its release in 2008. Here, we report HomeoDB2, an expansion and improvement of the original database that provides greater functionality for the user. HomeoDB2 includes all homeobox loci from 10 animal genomes (human, mouse, chicken, frog, zebrafish, amphioxus, nematode, fruitfly, beetle, honeybee) plus tools for downloading sequences, comparing between species and BLAST searching. HomeoDB2 provides a resource for studying the dynamics of homeobox gene evolution, and is freely accessible at http://www.homeodb.zoo.ox.ac.uk
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Affiliation(s)
- Ying-Fu Zhong
- Department of Zoology, University of Oxford, Oxford, UK.
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20
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Takechi M, Adachi N, Hirai T, Kuratani S, Kuraku S. The Dlx genes as clues to vertebrate genomics and craniofacial evolution. Semin Cell Dev Biol 2013; 24:110-8. [PMID: 23291259 DOI: 10.1016/j.semcdb.2012.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 12/25/2012] [Indexed: 11/25/2022]
Abstract
The group of Dlx genes belongs to the homeobox-containing superfamily, and its members are involved in various morphogenetic processes. In vertebrate genomes, Dlx genes exist as multiple paralogues generated by tandem duplication followed by whole genome duplications. In this review, we provide an overview of the Dlx gene phylogeny with an emphasis on the chordate lineage. Referring to the Dlx gene repertoire, we discuss the establishment and conservation of the nested expression patterns of the Dlx genes in craniofacial development. Despite the accumulating genomic sequence resources in diverse vertebrates, embryological analyses of Dlx gene expression and function remain limited in terms of species diversity. By supplementing our original analysis of shark embryos with previous data from other osteichthyans, such as mice and zebrafish, we support the previous speculation that the nested Dlx expression in the pharyngeal arch is likely a shared feature among all the extant jawed vertebrates. Here, we highlight several hitherto unaddressed issues regarding the evolution and function of Dlx genes, with special reference to the craniofacial development of vertebrates.
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Affiliation(s)
- Masaki Takechi
- Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe 650-0047, Japan
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21
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Hoyle CH. Evolution of neuronal signalling: Transmitters and receptors. Auton Neurosci 2011; 165:28-53. [DOI: 10.1016/j.autneu.2010.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 05/09/2010] [Accepted: 05/18/2010] [Indexed: 11/16/2022]
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Zhong YF, Holland PWH. The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages. BMC Evol Biol 2011; 11:169. [PMID: 21679462 PMCID: PMC3141429 DOI: 10.1186/1471-2148-11-169] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 06/16/2011] [Indexed: 01/04/2023] Open
Abstract
Background Homeobox genes are a large and diverse group of genes, many of which play important roles in transcriptional regulation during embryonic development. Comparison of homeobox genes between species may provide insights into the evolution of developmental mechanisms. Results Here we report an extensive survey of human and mouse homeobox genes based on their most recent genome assemblies, providing the first comprehensive analysis of mouse homeobox genes and updating an earlier survey of human homeobox genes. In total we recognize 333 human homeobox loci comprising 255 probable genes and 78 probable pseudogenes, and 324 mouse homeobox loci comprising 279 probable genes and 45 probable pseudogenes (accessible at http://homeodb.zoo.ox.ac.uk). Comparison to partial genome sequences from other species allows us to resolve which differences are due to gain of genes and which are due to gene losses. Conclusions We find there has been much more homeobox gene loss in the rodent evolutionary lineage than in the primate lineage. While humans have lost only the Msx3 gene, mice have lost Ventx, Argfx, Dprx, Shox, Rax2, LOC647589, Tprx1 and Nanognb. This analysis provides insight into the patterns of homeobox gene evolution in the mammals, and a step towards relating genomic evolution to phenotypic evolution.
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Affiliation(s)
- Ying-fu Zhong
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Cong EH, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Pasquier LD, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Crollius HR, Wincker P, Chourrout D. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 2010; 330:1381-5. [PMID: 21097902 PMCID: PMC3760481 DOI: 10.1126/science.1194167] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.
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Affiliation(s)
- France Denoeud
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Simon Henriet
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Sutada Mungpakdee
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Jean-Marc Aury
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Corinne Da Silva
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Henner Brinkmann
- Département de Biochimie, Université de Montréal, Montréal, Canada
| | - Jana Mikhaleva
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Lisbeth Charlotte Olsen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Claire Jubin
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Cristian Cañestro
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
- Departament de Genètica, Universitat de Barcelona, Spain
| | - Jean-Marie Bouquet
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Gemma Danks
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Bergen Center for Computational Science, University of Bergen, Bergen, Norway
| | - Julie Poulain
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Coen Campsteijn
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Marcin Adamski
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Ismael Cross
- Laboratorio de Genética, Universidad de Cádiz, Cádiz, Spain
| | - Fekadu Yadetie
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Matthieu Muffato
- Dyogen Lab, Institut de Biologie de l’ENS (IBENS), CNRS-UMR8197, Ecole Normale Supérieure,Paris,France
| | - Alexandra Louis
- Dyogen Lab, Institut de Biologie de l’ENS (IBENS), CNRS-UMR8197, Ecole Normale Supérieure,Paris,France
| | - Stephen Butcher
- Department of Biology, University of Iowa, Iowa City, IA 52242–1324, USA
| | - Georgia Tsagkogeorga
- Laboratoire de Paléontologie, Phylogénie et Paléobiologie, Institut des Sciences de l’Evolution, UMR 5554–CNRS, Université Montpellier II, Montpellier, France
| | - Anke Konrad
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Sarabdeep Singh
- Department of Statistics, University of Wyoming, Laramie, WY 82071, USA
| | - Marit Flo Jensen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Evelyne Huynh Cong
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Helen Eikeseth-Otteraa
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Benjamin Noel
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Véronique Anthouard
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Betina M. Porcel
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Rym Kachouri-Lafond
- Institut de Biologie Cellulaire et Moléculaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Atsuo Nishino
- Department of Biological Sciences, Osaka University, Osaka, Japan
| | - Matteo Ugolini
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Hiroki Nishida
- Department of Biological Sciences, Osaka University, Osaka, Japan
| | - Rein Aasland
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Eric Westhof
- Institut de Biologie Cellulaire et Moléculaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Frédéric Delsuc
- Laboratoire de Paléontologie, Phylogénie et Paléobiologie, Institut des Sciences de l’Evolution, UMR 5554–CNRS, Université Montpellier II, Montpellier, France
| | - Hans Lehrach
- Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Richard Reinhardt
- Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jean Weissenbach
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Scott W. Roy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - François Artiguenave
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | | | - J. Robert Manak
- Department of Biology, University of Iowa, Iowa City, IA 52242–1324, USA
| | - Eric M. Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Olivier Jaillon
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Louis Du Pasquier
- Institute of Zoology and Evolutionary Biology, University of Basel, Basel, Switzerland
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique (INRA), Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - David A. Liberles
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242–CNRS/INRA/Université Claude Bernard Lyon 1/Ecole Normale Supérieure, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Hervé Philippe
- Département de Biochimie, Université de Montréal, Montréal, Canada
| | - Boris Lenhard
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Bergen Center for Computational Science, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Hugues Roest Crollius
- Dyogen Lab, Institut de Biologie de l’ENS (IBENS), CNRS-UMR8197, Ecole Normale Supérieure,Paris,France
| | - Patrick Wincker
- Commissariat à l’Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
- CNRS, UMR 8030, Evry, France
- Université d’Evry, Evry, France
| | - Daniel Chourrout
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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Thomas-Chollier M, Ledent V, Leyns L, Vervoort M. A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution. BMC Evol Biol 2010; 10:73. [PMID: 20222951 PMCID: PMC2842273 DOI: 10.1186/1471-2148-10-73] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 03/11/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Hox and the closely-related ParaHox genes, which emerged prior to the divergence between cnidarians and bilaterians, are the most well-known members of the ancient genetic toolkit that controls embryonic development across all metazoans. Fundamental questions relative to their origin and evolutionary relationships remain however unresolved. We investigate here the evolution of metazoan Hox and ParaHox genes using the HoxPred program that allows the identification of Hox genes without the need of phylogenetic tree reconstructions. RESULTS We show that HoxPred provides an efficient and accurate classification of Hox and ParaHox genes in their respective homology groups, including Hox paralogous groups (PGs). We analyzed more than 10,000 sequences from 310 metazoan species, from 6 genome projects and the complete UniProtKB database. The HoxPred program and all results arranged in the Datab'Hox database are freely available at http://cege.vub.ac.be/hoxpred/. Results for the genome-scale studies are coherent with previous studies, and also brings knowledge on the Hox repertoire and clusters for newly-sequenced species. The unprecedented scale of this study and the use of a non-tree-based approach allows unresolved key questions about Hox and ParaHox genes evolution to be addressed. CONCLUSIONS Our analysis suggests that the presence of a single type of Posterior Hox genes (PG9-like) is ancestral to bilaterians, and that new Posterior PGs would have arisen in deuterostomes through independent gene duplications. Four types of Central genes would also be ancestral to bilaterians, with two of them, PG6- and PG7-like that gave rise, in protostomes, to the UbdA- and ftz/Antp/Lox5-type genes, respectively. A fifth type of Central genes (PG8) would have emerged in the vertebrate lineage. Our results also suggest the presence of Anterior (PG1 and PG3), Central and Posterior Hox genes in the cnidarians, supporting an ancestral four-gene Hox cluster. In addition, our data support the relationship of the bilaterian ParaHox genes Gsx and Xlox with PG3, and Cdx with the Central genes. Our study therefore indicates three possible models for the origin of Hox and ParaHox in early metazoans, a two-gene (Anterior/PG3--Central/Posterior), a three-gene (Anterior/PG1, Anterior/PG3 and Central/Posterior), or a four-gene (Anterior/PG1--Anterior/PG3--Central--Posterior) ProtoHox cluster.
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Affiliation(s)
- Morgane Thomas-Chollier
- Laboratoire de Bioinformatique des Génomes et des Réseaux, Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, B-1050 Bruxelles, Belgium.
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Aboobaker A, Blaxter M. The nematode story: Hox gene loss and rapid evolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:101-10. [PMID: 20795325 DOI: 10.1007/978-1-4419-6673-5_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The loss in some taxa of conserved developmental control genes that are present in the vast majority of animal lineages is an understudied phenomenon. It is likely that in those lineages in which loss has occurred it may be a strong signal of the mode, tempo and direction of developmental evolution and thus identify ways of generating morphological novelties. Intuitively we might expect these novelties to be particularly those associated with morphological simplifications. One striking example of this has occurred within the nematodes. It appears that over half the ancestral bilaterian Hox cluster has been lost from the model organism Caenorhabditis elegans and its closest related species. Studying the Hox gene complement of nematodes across the phylum has shown that many, if not all these losses occurred within the phylum. Other nematode clades only distantly related to C. elegans have additional Hox genes orthologous to those present in the ancestral bilaterian but absent from the model nematode. In some of these cases rapid sequence evolution of the homeodomain itself obscures orthology assignment until comparison is made with sequences from multiple nematode clades with slower evolving Hox genes. Across the phylum the homeodomains of the Hox genes that are present are evolving very rapidly. In one particular case the genomic arrangement of two homeodomains suggests a mechanism for gene loss. Studying the function in nematodes of the Hox genes absent from C. elegans awaits further research and the establishment of new nematode models. However, what we do know about Hox gene functions suggests that the genetic circuits within which Hox genes act have changed significantly within C. elegans and its close relatives.
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Affiliation(s)
- Aziz Aboobaker
- Institute of Genetics, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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Chordate roots of the vertebrate nervous system: expanding the molecular toolkit. Nat Rev Neurosci 2009; 10:736-46. [PMID: 19738625 DOI: 10.1038/nrn2703] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate brain is highly complex with millions to billions of neurons. During development, the neural plate border region gives rise to the neural crest, cranial placodes and, in anamniotes, to Rohon-Beard sensory neurons, whereas the boundary region of the midbrain and hindbrain develops organizer properties. Comparisons of developmental gene expression and neuroanatomy between vertebrates and the basal chordate amphioxus, which has only thousands of neurons and lacks a neural crest, most placodes and a midbrain-hindbrain organizer, indicate that these vertebrate features were built on a foundation already present in the ancestral chordate. Recent advances in genomics have provided insights into the elaboration of the molecular toolkit at the invertebrate-vertebrate transition that may have facilitated the evolution of these vertebrate characteristics.
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Aravind L, Anantharaman V, Venancio TM. Apprehending multicellularity: regulatory networks, genomics, and evolution. ACTA ACUST UNITED AC 2009; 87:143-64. [PMID: 19530132 DOI: 10.1002/bdrc.20153] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genomic revolution has provided the first glimpses of the architecture of regulatory networks. Combined with evolutionary information, the "network view" of life processes leads to remarkable insights into how biological systems have been shaped by various forces. This understanding is critical because biological systems, including regulatory networks, are not products of engineering but of historical contingencies. In this light, we attempt a synthetic overview of the natural history of regulatory networks operating in the development and differentiation of multicellular organisms. We first introduce regulatory networks and their organizational principles as can be deduced using ideas from the graph theory. We then discuss findings from comparative genomics to illustrate the effects of lineage-specific expansions, gene-loss, and nonprotein-coding DNA on the architecture of networks. We consider the interaction between expansions of transcription factors, and cis regulatory and more general chromatin state stabilizing elements in the emergence of morphological complexity. Finally, we consider a case study of the Notch subnetwork, which is present throughout Metazoa, to examine how such a regulatory system has been pieced together in evolution from new innovations and pre-existing components that were originally functionally distinct.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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Abstract
Abstract The ParaHox genes comprise three Hox-related homeobox gene families, found throughout the animals. They were first discovered in the invertebrate chordate amphioxus, where they are tightly clustered. In this paper we carry out a comparative review of ParaHox gene cluster organization among the deuterostomes, and discuss how the recently published hagfish ParaHox clusters fit into current theories about the evolution of this group of genes.
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Affiliation(s)
- Rebecca F Furlong
- Department of Zoology, Oxford University, South Parks Road, Oxford OX13PS, UK.
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30
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Abstract
In this chapter, we consider the question of how the ordered clusters of Hox genes arose during evolution. Since ordered Hox clusters are found in all major superphyla, we have to assume that the Hox clusters arose before the Cambrian "explosion" giving rise to all of these taxa. Based on his studies of the bithorax complex (BX-C) in Drosophila Lewis considered the ground state to be the mesothoracic segment (T2) since the deletion of all of the genes of the BX-C leads to a transformation of all segments from T3 to A8/9 (the last abdominal segment) into T2 segments. We define the developmental ground state genetically, by assuming that loss-of-function mutants lead to transformations toward the ground state, whereas gain-of-function mutants lead to homeotic transformations away from the ground state. By this definition, T2 also represents the developmental ground state, if one includes the anterior genes, that is, those of the Antennapedia complex. We have reconstructed the evolution of the Hox cluster on the basis of known genetic mechanisms which involve unequal crossover and lead from an urhox gene, first to an anterior and a posterior gene and subsequently to intermediate genes which are progressively inserted, between the anterior and posterior genes. These intermediate genes are recombinant due to unequal crossover, whereas the anterior and posterior genes are not affected and therefore had the longest time to diverge from the urhox gene. The molecular phylogenetic analysis strongly supports this model. We consider the ground state to be both developmental and evolutionary and to represent the prototypic body segment. It corresponds to T2 and is specified by Antennapedia or Hox6, respectively. Experiments in the mouse also suggest that the ground state is a thoracic segment. Evolution leads from the prototypic segment to segmental divergence in both the anterior and posterior direction. The most anterior head and tail segments are specified by homeobox genes localized outside of the cluster.
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Koop D, Holland LZ. The basal chordate amphioxus as a simple model for elucidating developmental mechanisms in vertebrates. ACTA ACUST UNITED AC 2008; 84:175-87. [DOI: 10.1002/bdrc.20128] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bassham S, Cañestro C, Postlethwait JH. Evolution of developmental roles of Pax2/5/8 paralogs after independent duplication in urochordate and vertebrate lineages. BMC Biol 2008; 6:35. [PMID: 18721460 PMCID: PMC2532684 DOI: 10.1186/1741-7007-6-35] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 08/22/2008] [Indexed: 12/02/2022] Open
Abstract
Background Gene duplication provides opportunities for lineage diversification and evolution of developmental novelties. Duplicated genes generally either disappear by accumulation of mutations (nonfunctionalization), or are preserved either by the origin of positively selected functions in one or both duplicates (neofunctionalization), or by the partitioning of original gene subfunctions between the duplicates (subfunctionalization). The Pax2/5/8 family of important developmental regulators has undergone parallel expansion among chordate groups. After the divergence of urochordate and vertebrate lineages, two rounds of independent gene duplications resulted in the Pax2, Pax5, and Pax8 genes of most vertebrates (the sister group of the urochordates), and an additional duplication provided the pax2a and pax2b duplicates in teleost fish. Separate from the vertebrate genome expansions, a duplication also created two Pax2/5/8 genes in the common ancestor of ascidian and larvacean urochordates. Results To better understand mechanisms underlying the evolution of duplicated genes, we investigated, in the larvacean urochordate Oikopleura dioica, the embryonic gene expression patterns of Pax2/5/8 paralogs. We compared the larvacean and ascidian expression patterns to infer modular subfunctions present in the single pre-duplication Pax2/5/8 gene of stem urochordates, and we compared vertebrate and urochordate expression to infer the suite of Pax2/5/8 gene subfunctions in the common ancestor of olfactores (vertebrates + urochordates). Expression pattern differences of larvacean and ascidian Pax2/5/8 orthologs in the endostyle, pharynx and hindgut suggest that some ancestral gene functions have been partitioned differently to the duplicates in the two urochordate lineages. Novel expression in the larvacean heart may have resulted from the neofunctionalization of a Pax2/5/8 gene in the urochordates. Expression of larvacean Pax2/5/8 in the endostyle, in sites of epithelial remodeling, and in sensory tissues evokes like functions of Pax2, Pax5 and Pax8 in vertebrate embryos, and may indicate ancient origins for these functions in the chordate common ancestor. Conclusion Comparative analysis of expression patterns of chordate Pax2/5/8 duplicates, rooted on the single-copy Pax2/5/8 gene of amphioxus, whose lineage diverged basally among chordates, provides new insights into the evolution and development of the heart, thyroid, pharynx, stomodeum and placodes in chordates; supports the controversial conclusion that the atrial siphon of ascidians and the otic placode in vertebrates are homologous; and backs the notion that Pax2/5/8 functioned in ancestral chordates to engineer epithelial fusions and perforations, including gill slit openings.
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Affiliation(s)
- Susan Bassham
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA.
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Affiliation(s)
- Jean S Deutsch
- Biologie du Développement, UMR 7622, CNRS, 75252 Paris, Cedex 05, France.
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Shook DR, Keller R. Epithelial type, ingression, blastopore architecture and the evolution of chordate mesoderm morphogenesis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2008; 310:85-110. [PMID: 18041055 DOI: 10.1002/jez.b.21198] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chordate embryos show an evolutionary trend in the mechanisms they use to internalize presumptive mesoderm, relying predominantly on invagination in the basal chordates, varying combinations of involution and ingression in the anamniote vertebrates and reptiles, and predominantly on ingression in birds and mammals. This trend is associated with variations in epithelial type and changes in embryonic architecture as well as variations in the type of blastopore formed by an embryo. We also note the surprising conservation of the involution, during gastrulation, of at least a subset of the notochordal cells throughout the chordates, and suggest that this indicates a constraint on morphogenic evolution based on a functional linkage between architecture and patterning. Finally, we propose a model for the evolutionary transitions from gastrulation through a urodele amphibian-type blastopore to gastrulation through a primitive streak, as in chick or mouse.
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Affiliation(s)
- David R Shook
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904-4328, USA.
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Expression of the amphioxus Pit-1 gene (AmphiPOU1F1/Pit-1) exclusively in the developing preoral organ, a putative homolog of the vertebrate adenohypophysis. Brain Res Bull 2008; 75:324-30. [DOI: 10.1016/j.brainresbull.2007.10.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Accepted: 10/17/2007] [Indexed: 01/06/2023]
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Cañestro C, Bassham S, Postlethwait JH. Evolution of the thyroid: Anterior–posterior regionalization of theOikopleura endostyle revealed byOtx,Pax2/5/8, andHox1 expression. Dev Dyn 2008; 237:1490-9. [DOI: 10.1002/dvdy.21525] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TS. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol 2007; 8 Suppl 1:S4. [PMID: 18047696 PMCID: PMC2106839 DOI: 10.1186/gb-2007-8-s1-s4] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around developmental regulatory genes in which an insertion results in the same global expression pattern, irrespective of exact position. These areas coincide with vertebrate chromosomal segments containing identical gene order; a phenomenon known as conserved synteny and thought to be a vestige of evolution. Genomic comparative studies have found large numbers of highly conserved noncoding elements (HCNEs) spanning these and other loci. HCNEs are thought to act as transcriptional enhancers based on the finding that many of those that have been tested direct tissue specific expression in transient or transgenic assays. Although gene order in hox and other gene clusters has long been known to be conserved because of shared regulatory sequences or overlapping transcriptional units, the chromosomal areas found through insertional hotspots contain only one or a few developmental regulatory genes as well as phylogenetically unrelated genes. We have termed these regions genomic regulatory blocks (GRBs), and show that they underlie the phenomenon of conserved synteny through all sequenced vertebrate genomes. After teleost whole genome duplication, a subset of GRBs were retained in two copies, underwent degenerative changes compared with tetrapod loci that exist as single copy, and that therefore can be viewed as representing the ancestral form. We discuss these findings in light of evolution of vertebrate chromosomal architecture and the identification of human disease mutations.
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Affiliation(s)
- Hiroshi Kikuta
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormoehlensgate, 5008 Bergen, Norway
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Holland PWH, Booth HAF, Bruford EA. Classification and nomenclature of all human homeobox genes. BMC Biol 2007; 5:47. [PMID: 17963489 PMCID: PMC2211742 DOI: 10.1186/1741-7007-5-47] [Citation(s) in RCA: 289] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Accepted: 10/26/2007] [Indexed: 12/19/2022] Open
Abstract
Background The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described. Results We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'. Conclusion We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.
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Affiliation(s)
- Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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Søviknes AM, Chourrout D, Glover JC. Development of the caudal nerve cord, motoneurons, and muscle innervation in the appendicularian urochordate Oikopleura dioica. J Comp Neurol 2007; 503:224-43. [PMID: 17492623 DOI: 10.1002/cne.21376] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The development of the caudal nerve cord and muscle innervation in the appendicularian Oikopleura dioica was assessed using differential interference contrast and confocal microscopy, phalloidin staining of actin, and in situ hybridization for the neuronal markers tubulin and choline acetyltransferase (ChAT). The caudal nerve cord first appears as a stream of tubulin mRNA-positive neurons that extends into the tail from the caudal ganglion. By this stage a few actin-rich nerve fibers course longitudinally along the cord. As the tail lengthens, the caudal nerve cord extends and becomes more fasciculated and the neurons cluster at stereotyped longitudinal positions. The number of neurons in the nerve cord reaches a relatively stable maximum of about 29. A subset of neurons in the caudal ganglion and caudal nerve cord expresses ChAT mRNA. These putative motoneurons are distributed along nearly the full extent of the tail in numbers consistent with an independent innervation of each tail muscle cell. The longitudinal series of putative motoneurons is not aligned with the muscle cells, but peripheral nerve fibers extending to the muscle cells are, indicating that motor axons grow along the cord before exiting adjacent to their peripheral target. Muscle innervation occurs roughly coincident with the onset of ChAT mRNA expression. Our results provide the first molecular identification of motoneurons and the first developmental characterization of the motor system in an appendicularian and help set the stage for gene expression studies aimed at understanding the evolution of developmental patterning in this part of the chordate central nervous system.
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Affiliation(s)
- Anne Mette Søviknes
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen High Technology Centre, N-5008 Bergen, Norway
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40
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Ryan JF, Burton PM, Mazza ME, Kwong GK, Mullikin JC, Finnerty JR. The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis. Genome Biol 2007; 7:R64. [PMID: 16867185 PMCID: PMC1779571 DOI: 10.1186/gb-2006-7-7-r64] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Accepted: 07/24/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass predates the evolutionary split between animals, plants, and fungi, many homeobox genes appear unique to animals. The origin of particular homeobox genes may, therefore, be associated with the evolution of particular animal traits. Here we report the first near-complete set of homeodomains from a basal (diploblastic) animal. RESULTS Phylogenetic analyses were performed on 130 homeodomains from the sequenced genome of the sea anemone Nematostella vectensis along with 228 homeodomains from human and 97 homeodomains from Drosophila. The Nematostella homeodomains appear to be distributed among established homeodomain classes in the following fashion: 72 ANTP class; one HNF class; four LIM class; five POU class; 33 PRD class; five SINE class; and six TALE class. For four of the Nematostella homeodomains, there is disagreement between neighbor-joining and Bayesian trees regarding their class membership. A putative Nematostella CUT class gene is also identified. CONCLUSION The homeodomain superclass underwent extensive radiations prior to the evolutionary split between Cnidaria and Bilateria. Fifty-six homeodomain families found in human and/or fruit fly are also found in Nematostella, though seventeen families shared by human and fly appear absent in Nematostella. Homeodomain loss is also apparent in the bilaterian taxa: eight homeodomain families shared by Drosophila and Nematostella appear absent from human (CG13424, EMXLX, HOMEOBRAIN, MSXLX, NK7, REPO, ROUGH, and UNC4), and six homeodomain families shared by human and Nematostella appear absent from fruit fly (ALX, DMBX, DUX, HNF, POU1, and VAX).
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Affiliation(s)
- Joseph F Ryan
- Bioinformatics Program, Boston University, Cummington Street, Boston, MA 02215, USA
- National Human Genome Research Institute, Fishers Lane, Bethesda, MD 20892, USA
| | - Patrick M Burton
- Department of Biology, Boston University, Cummington Street, Boston, MA 02215, USA
| | - Maureen E Mazza
- Department of Biology, Boston University, Cummington Street, Boston, MA 02215, USA
| | - Grace K Kwong
- Department of Biology, Boston University, Cummington Street, Boston, MA 02215, USA
| | - James C Mullikin
- National Human Genome Research Institute, Fishers Lane, Bethesda, MD 20892, USA
| | - John R Finnerty
- Bioinformatics Program, Boston University, Cummington Street, Boston, MA 02215, USA
- Department of Biology, Boston University, Cummington Street, Boston, MA 02215, USA
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41
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Cañestro C, Postlethwait JH. Development of a chordate anterior–posterior axis without classical retinoic acid signaling. Dev Biol 2007; 305:522-38. [PMID: 17397819 DOI: 10.1016/j.ydbio.2007.02.032] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 02/18/2007] [Accepted: 02/26/2007] [Indexed: 11/23/2022]
Abstract
Developmental signaling by retinoic acid (RA) is thought to be an innovation essential for the origin of the chordate body plan. The larvacean urochordate Oikopleura dioica maintains a chordate body plan throughout life, and yet its genome appears to lack genes for RA synthesis, degradation, and reception. This suggests the hypothesis that the RA-machinery was lost during larvacean evolution, and predicts that Oikopleura development has become independent of RA-signaling. This prediction raises the problem that the anterior-posterior organization of a chordate body plan can be developed without the classical morphogenetic role of RA. To address this problem, we performed pharmacological treatments and analyses of developmental molecular markers to investigate whether RA acts in anterior-posterior axial patterning in Oikopleura embryos. Results revealed that RA does not cause homeotic posteriorization in Oikopleura as it does in vertebrates and cephalochordates, and showed that a chordate can develop the phylotypic body plan in the absence of the classical morphogenetic role of RA. A comparison of Oikopleura and ascidian evidence suggests that the lack of RA-induced homeotic posteriorization is a shared derived feature of urochordates. We discuss possible relationships of altered roles of RA in urochordate development to genomic events, such as rupture of the Hox-cluster, in the context of a new understanding of chordate phylogeny.
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Affiliation(s)
- Cristian Cañestro
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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42
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Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis AD, Martindale MQ, Finnerty JR. Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis. PLoS One 2007; 2:e153. [PMID: 17252055 PMCID: PMC1779807 DOI: 10.1371/journal.pone.0000153] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 11/30/2006] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no "true" Hox genes exist in the phylum Cnidaria. METHODOLOGY/PRINCIPAL FINDINGS Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in "dorsoventral" patterning. CONCLUSIONS/SIGNIFICANCE A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today.
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Affiliation(s)
- Joseph F. Ryan
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maureen E. Mazza
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Kevin Pang
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - David Q. Matus
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Andreas D. Baxevanis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark Q. Martindale
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - John R. Finnerty
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
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Abstract
The origins of the Hox gene clusters and their coordinated activities during development have long been of considerable interest to biologists. In a recent paper in Current Biology, the Hox-like genes of two cnidarians are interpreted as evidence that the 'Hox system', sensu stricto, originated after the split from the lineage leading to bilaterian animals and that it was not requisite for complex axial patterning.
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Affiliation(s)
- Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA.
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Candiani S, Oliveri D, Parodi M, Bertini E, Pestarino M. Expression of AmphiPOU-IV in the developing neural tube and epidermal sensory neural precursors in amphioxus supports a conserved role of class IV POU genes in the sensory cells development. Dev Genes Evol 2006; 216:623-33. [PMID: 16773340 DOI: 10.1007/s00427-006-0083-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 05/01/2006] [Indexed: 10/24/2022]
Abstract
POU genes play a prominent role in the nervous system differentiation of several organism models, and in particular, they are involved in the differentiation of sensory neurons in numerous invertebrate and vertebrate species. In the present report, cloning and expression profile of a class IV POU gene in amphioxus was assessed for understanding its role in the sensory systems development. A single class IV gene, AmphiPOU-IV was isolated from the amphioxus Branchiostoma floridae. From a phylogenetic point of view, AmphiPOU-IV appears to be strictly related to the vertebrate one, sharing a high homology ratio especially with all vertebrate POU-IV proteins Brn-3a, Brn-3b, and Brn-3c. AmphiPOU-IV was found in the most anterior neural plate and in scattered ectodermic cells on the flanks of neurula, such ectodermic cells resemble the characteristic morphology and position of AmphiCoe and AmphiTrk developing sensory cells. Later on, the expression was confined in some motoneurons at level of the PMC and in some segmental arranged motoneurons in the hindbrain. Such expression is also maintained in larvae, and a new site of AmphiPOU-IV expression was also found in rostrum and mouth edge epidermal sensory cells of the larva. In conclusion, our data suggest an evolutionary conserved role of POU-IV transcription factors in the specification and differentiation of the sensory system in both vertebrates and invertebrates and underline the importance of amphioxus as linking step between them.
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Affiliation(s)
- Simona Candiani
- Department of Biology, University of Genoa, viale Benedetto XV, 5, Genoa, 16132, Italy
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Castro LFC, Rasmussen SLK, Holland PWH, Holland ND, Holland LZ. A Gbx homeobox gene in amphioxus: insights into ancestry of the ANTP class and evolution of the midbrain/hindbrain boundary. Dev Biol 2006; 295:40-51. [PMID: 16687133 DOI: 10.1016/j.ydbio.2006.03.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Revised: 02/28/2006] [Accepted: 03/01/2006] [Indexed: 11/24/2022]
Abstract
In the vertebrate central nervous system (CNS), mutual antagonism between posteriorly expressed Gbx2 and anteriorly expressed Otx2 positions the midbrain/hindbrain boundary (MHB), but does not induce MHB organizer genes such as En, Pax2/5/8 and Wnt1. In the CNS of the cephalochordate amphioxus, Otx is also expressed anteriorly, but En, Pax2/5/8 and Wnt1 are not expressed near the caudal limit of Otx, raising questions about the existence of an MHB organizer in amphioxus. To investigate the evolutionary origins of the MHB, we cloned the single amphioxus Gbx gene. Fluorescence in situ hybridization showed that, as in vertebrates, amphioxus Gbx and the Hox cluster are on the same chromosome. From analysis of linked genes, we argue that during evolution a single ancestral Gbx gene duplicated fourfold in vertebrates, with subsequent loss of two duplicates. Amphioxus Gbx is expressed in all germ layers in the posterior 75% of the embryo, and in the CNS, the Gbx and Otx domains abut at the boundary between the cerebral vesicle (forebrain/midbrain) and the hindbrain. Thus, the genetic machinery to position the MHB was present in the protochordate ancestors of the vertebrates, but is insufficient for induction of organizer genes. Comparison with hemichordates suggests that anterior Otx and posterior Gbx domains were probably overlapping in the ancestral deuterostome and came to abut at the MHB early in the chordate lineage before MHB organizer properties evolved.
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Affiliation(s)
- L Filipe C Castro
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Delsuc F, Brinkmann H, Chourrout D, Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006; 439:965-8. [PMID: 16495997 DOI: 10.1038/nature04336] [Citation(s) in RCA: 1155] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 10/19/2005] [Indexed: 11/08/2022]
Abstract
Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.
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Affiliation(s)
- Frédéric Delsuc
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada
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Abstract
It has been known that the conservation or diversity of homeobox genes is responsible for the similarity and variability of some of the morphological or physiological characters among different organisms. To gain some insights into the evolutionary pattern of homeobox genes in bilateral animals, we studied the change of the numbers of these genes during the evolution of bilateral animals. We analyzed 2,031 homeodomain sequences compiled from 11 species of bilateral animals ranging from Caenorhabditis elegans to humans. Our phylogenetic analysis using a modified reconciled-tree method suggested that there were at least about 88 homeobox genes in the common ancestor of bilateral animals. About 50-60 genes of them have left at least one descendant gene in each of the 11 species studied, suggesting that about 30-40 genes were lost in a lineage-specific manner. Although similar numbers of ancestral genes have survived in each species, vertebrate lineages gained many more genes by duplication than invertebrate lineages, resulting in more than 200 homeobox genes in vertebrates and about 100 in invertebrates. After these gene duplications, a substantial number of old duplicate genes have also been lost in each lineage. Because many old duplicate genes were lost, it is likely that lost genes had already been differentiated from other groups of genes at the time of gene loss. We conclude that both gain and loss of homeobox genes were important for the evolutionary change of phenotypic characters in bilateral animals.
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Affiliation(s)
- Jongmin Nam
- Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, USA.
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48
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Abstract
Once called the 'Rosetta stone' of developmental biology, the homeobox continues to fascinate both evolutionary and developmental biologists. The birth of the homeotic, or Hox, gene cluster, and its subsequent evolution, has been crucial in mediating the major transitions in metazoan body plan. Comparative genomics studies indicate that the more recently discovered ParaHox and NK clusters were linked to the Hox cluster early in evolution, and that together they constituted a 'megacluster' of homeobox genes that conspicuously contributed to body-plan evolution.
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Affiliation(s)
- Jordi Garcia-Fernàndez
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, España.
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49
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Cañestro C, Bassham S, Postlethwait J. Development of the central nervous system in the larvacean Oikopleura dioica and the evolution of the chordate brain. Dev Biol 2005; 285:298-315. [PMID: 16111672 DOI: 10.1016/j.ydbio.2005.06.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 06/11/2005] [Accepted: 06/17/2005] [Indexed: 11/22/2022]
Abstract
In non-vertebrate chordates, central nervous system (CNS) development has been studied in only two taxa, the Cephalochordata and a single Class (Ascidiacea) of the morphologically diverse Urochordata. To understand development and molecular regionalization of the brain in a different deeply diverging chordate clade, we isolated and determined the expression patterns of orthologs of vertebrate CNS markers (otxa, otxb, otxc, pax6, pax2/5/8a, pax2/5/8b, engrailed, and hox1) in Oikopleura dioica (Subphylum Urochordata, Class Larvacea). The three Oikopleura otx genes are expressed similarly to vertebrate Otx paralogs, demonstrating that trans-homologs converged on similar evolutionary outcomes by independent neo- or subfunctionalization processes during the evolution of the two taxa. This work revealed that the Oikopleura CNS possesses homologs of the vertebrate forebrain, hindbrain, and spinal cord, but not the midbrain. Comparing larvacean gene expression patterns to published results in ascidians disclosed important developmental differences and similarities that suggest mechanisms of development likely present in their last common ancestor. In contrast to ascidians, the lack of a radical reorganization of the CNS as larvaceans become adults allows us to relate embryonic gene expression patterns to three subdivisions of the adult anterior brain. Our study of the Oikopleura brain provides new insights into chordate CNS evolution: first, the absence of midbrain is a urochordate synapomorphy and not a peculiarity of ascidians, perhaps resulting from their drastic CNS metamorphosis; second, there is no convincing evidence for a homolog of a midbrain-hindbrain boundary (MHB) organizer in urochordates; and third, the expression pattern of "MHB-genes" in the urochordate hindbrain suggests that they function in the development of specific neurons rather than in an MHB organizer.
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Affiliation(s)
- Cristian Cañestro
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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50
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Bassham S, Postlethwait JH. The evolutionary history of placodes: a molecular genetic investigation of the larvacean urochordate Oikopleura dioica. Development 2005; 132:4259-72. [PMID: 16120641 DOI: 10.1242/dev.01973] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The evolutionary origin of vertebrate placodes remains controversial because divergent morphologies in urochordates, cephalochordates and vertebrates make it difficult to recognize organs that are clearly homologous to placode-derived features, including the olfactory organ, adenohypophysis, lens, inner ear, lateral line and cranial ganglia. The larvacean urochordate Oikopleura dioica possesses organs that morphologically resemble the vertebrate olfactory organ and adenohypophysis. We tested the hypothesis that orthologs of these vertebrate placodes exist in a larvacean urochordate by analyzing the developmental expression of larvacean homologs of the placode-marking gene families Eya, Pitx and Six. We conclude that extant chordates inherited olfactory and adenohypophyseal placodes from their last common ancestor, but additional independent proliferation and perhaps loss of placode types probably occurred among the three subphyla of Chordata.
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Affiliation(s)
- Susan Bassham
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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