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Dai Y, Zhong Y, Pan R, Yuan L, Fu Y, Chen Y, Du J, Li M, Wang X, Liu H, Shi C, Liu G, Zhu P, Shimeld S, Zhou X, Li G. Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories. Nat Ecol Evol 2024:10.1038/s41559-024-02469-7. [PMID: 39025981 DOI: 10.1038/s41559-024-02469-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
The common ancestor of all vertebrates had a highly sophisticated nervous system, but questions remain about the evolution of vertebrate neural cell types. The amphioxus, a chordate that diverged before the origin of vertebrates, can inform vertebrate evolution. Here we develop and analyse a single-cell RNA-sequencing dataset from seven amphioxus embryo stages to understand chordate cell type evolution and to study vertebrate neural cell type origins. We identified many new amphioxus cell types, including homologues to the vertebrate hypothalamus and neurohypophysis, rooting the evolutionary origin of these structures. On the basis of ancestor-descendant reconstruction of cell trajectories of the amphioxus and other species, we inferred expression dynamics of transcription factor genes throughout embryogenesis and identified three ancient developmental routes forming chordate neurons. We characterized cell specification at the mechanistic level and generated mutant lines to examine the function of five key transcription factors involved in neural specification. Our results show three developmental origins for the vertebrate nervous system: an anterior FoxQ2-dependent mechanism that is deeply conserved in invertebrates, a less-conserved route leading to more posterior neurons in the vertebrate spinal cord and a mechanism for specifying neuromesoderm progenitors that is restricted to chordates. The evolution of neuromesoderm progenitors may have led to a dramatic shift in posterior neural and mesodermal cell fate decisions and the body elongation process in a stem chordate.
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Affiliation(s)
- Yichen Dai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Yanhong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rongrong Pan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liang Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Yongheng Fu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuwei Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Huimin Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | | | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China.
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
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Burback L, Forner C, Winkler OK, Al-Shamali HF, Ayoub Y, Paquet J, Verghese M. Survival, Attachment, and Healing: An Evolutionary Lens on Interventions for Trauma-Related Dissociation. Psychol Res Behav Manag 2024; 17:2403-2431. [PMID: 38912158 PMCID: PMC11193433 DOI: 10.2147/prbm.s402456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024] Open
Abstract
Purpose Dissociation is a necessary part of our threat response system, common to all animal species, normally temporarily activated under conditions of extreme or inescapable threat. Pathological dissociation, however, continues to occur after the initial threat has passed, in response to reminders or inaccessibility of safety and security. Present across the spectrum of psychiatric diagnoses, recurrent dissociative symptoms are linked to severe trauma exposure, insecure attachment, treatment non-response, and maladaptive coping behaviors such as substance use, suicidality, and self-harm. However, empirical studies testing treatments specific to dissociative processes remain scarce. This narrative review summarizes existing studies and provides theoretical, neurobiological, and evolutionary perspectives on dissociative processes and treatments for pathological dissociation. Methods A systematic search of five databases (MEDLINE, EMBASE, APA PsycINFO, CINAHL plus, Scopus) was conducted on April 13, 2023. Peer-reviewed clinical studies with adult participants, assessing intervention effects on dissociative symptoms, were included. Results were thematically analyzed and summarized. Results Sixty-nine studies were identified, mainly focused on posttraumatic stress disorder, trauma-exposed populations, and borderline personality disorder. Psychotherapy was studied in 72.5% of studies; other interventions included medications and neurostimulation. The majority reported positive outcomes, despite the heterogeneous spectrum of interventions. However, treatment of dissociative symptoms was the primary objective in only a minority. Conclusion Pathological dissociation is a complex phenomenon involving brain and body systems designed for perceiving and responding to severe threats, requiring an individualized approach. A literature is emerging regarding potentially evidence-based treatments to help those impacted by recurrent dissociative symptoms. When contextualized within a neurobiological and evolutionary perspective, these treatments can be understood as facilitating an internal and/or relational sense of safety, resulting in symptom reduction. Further studies are needed to explore effective treatments for dissociative symptoms.
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Affiliation(s)
- Lisa Burback
- Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada
- Neuroscience and Mental Health Institute (NMHI), University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Huda F Al-Shamali
- Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada
| | - Yahya Ayoub
- Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada
| | - Jacquelyn Paquet
- Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada
| | - Myah Verghese
- Department of Neuroscience, University of Alberta, Edmonton, Alberta, Canada
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Grau-Bové X, Subirana L, Meister L, Soubigou A, Neto A, Elek A, Naranjo S, Fornas O, Gomez-Skarmeta JL, Tena JJ, Irimia M, Bertrand S, Sebé-Pedrós A, Escriva H. An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm. Nat Commun 2024; 15:4550. [PMID: 38811547 PMCID: PMC11136973 DOI: 10.1038/s41467-024-48774-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We previously proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a prechordal-plate like territory in amphioxus. Additionally, the transcriptomic profile of somite cell populations supports the homology between specific territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Anaël Soubigou
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Ana Neto
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Oscar Fornas
- Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France.
- Institut universitaire de France (IUF), Paris, France.
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France.
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Wang Y, Lin J, Li W, Ji G, Liu Z. Identification, Expression and Evolutional Analysis of Two cyp19-like Genes in Amphioxus. Animals (Basel) 2024; 14:1140. [PMID: 38672288 PMCID: PMC11047327 DOI: 10.3390/ani14081140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
The mechanism of sex determination and differentiation in animals remains a central focus of reproductive and developmental biology research, and the regulation of sex differentiation in amphioxus remains poorly understood. Cytochrome P450 Family 19 Subfamily A member 1 (CYP19A1) is a crucial sex differentiation gene that catalyzes the conversion of androgens into estrogens. In this study, we identified two aromatase-like genes in amphioxus: cyp19-like1 and cyp19-like2. The cyp19-like1 is more primitive and may represent the ancestral form of cyp19 in zebrafish and other vertebrates, while the cyp19-like2 is likely the result of gene duplication within amphioxus. To gain further insights into the expression level of these two aromatase-like, we examined their expression in different tissues and during different stages of gonad development. While the expression level of the two genes differs in tissues, both are highly expressed in the gonad primordium and are primarily localized to microsomal membrane systems. However, as development proceeds, their expression level decreases significantly. This study enhances our understanding of sex differentiation mechanisms in amphioxus and provides valuable insights into the formation and evolution of sex determination mechanisms in vertebrates.
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Affiliation(s)
| | | | | | | | - Zhenhui Liu
- College of Marine Life Sciences, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (Y.W.); (J.L.); (W.L.); (G.J.)
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Takahashi H, Hisata K, Iguchi R, Kikuchi S, Ogasawara M, Satoh N. scRNA-seq analysis of cells comprising the amphioxus notochord. Dev Biol 2024; 508:24-37. [PMID: 38224933 DOI: 10.1016/j.ydbio.2024.01.003] [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: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/17/2024]
Abstract
Cephalochordates occupy a key phylogenetic position for deciphering the origin and evolution of chordates, since they diverged earlier than urochordates and vertebrates. The notochord is the most prominent feature of chordates. The amphioxus notochord features coin-shaped cells bearing myofibrils. Notochord-derived hedgehog signaling contributes to patterning of the dorsal nerve cord, as in vertebrates. However, properties of constituent notochord cells remain unknown at the single-cell level. We examined these properties using Iso-seq analysis, single-cell RNA-seq analysis, and in situ hybridization (ISH). Gene expression profiles broadly categorize notochordal cells into myofibrillar cells and non-myofibrillar cells. Myofibrillar cells occupy most of the central portion of the notochord, and some cells extend the notochordal horn to both sides of the ventral nerve cord. Some notochord myofibrillar genes are not expressed in myotomes, suggesting an occurrence of myofibrillar genes that are preferentially expressed in notochord. On the other hand, non-myofibrillar cells contain dorsal, lateral, and ventral Müller cells, and all three express both hedgehog and Brachyury. This was confirmed by ISH, although expression of hedgehog in ventral Müller cells was minimal. In addition, dorsal Müller cells express neural transmission-related genes, suggesting an interaction with nerve cord. Lateral Müller cells express hedgehog and other signaling-related genes, suggesting an interaction with myotomes positioned lateral to the notochord. Ventral Müller cells also expressed genes for FGF- and EGF-related signaling, which may be associated with development of endoderm, ventral to the notochord. Lateral Müller cells were intermediate between dorsal/ventral Müller cells. Since vertebrate notochord contributes to patterning and differentiation of ectoderm (nerve cord), mesoderm (somite), and endoderm, this investigation provides evidence that an ancestral or original form of vertebrate notochord is present in extant cephalochordates.
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Affiliation(s)
- Hiroki Takahashi
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Rin Iguchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 262-8522, Japan
| | - Sakura Kikuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 262-8522, Japan.
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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Arimoto A, Nishitsuji K, Hisata K, Satoh N, Tagawa K. Transcriptomic evidence for Brachyury expression in the caudal tip region of adult Ptychodera flava (Hemichordata). Dev Growth Differ 2023; 65:470-480. [PMID: 37483093 DOI: 10.1111/dgd.12882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/27/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
Most metazoans have a single copy of the T-box transcription factor gene Brachyury. This gene is expressed in cells of the blastopore of late blastulae and the archenteron invagination region of gastrulae. It appears to be crucial for gastrulation and mesoderm differentiation of embryos. Although this expression pattern is shared by most deuterostomes, Brachyury expression has not been reported in adult stages. Here we show that Brachyury of an indirect developer, the hemichordate acorn worm Ptychodera flava, is expressed not only in embryonic cells, but also in cells of the caudal tip (anus) region of adults. This spatially restricted expression, shown by whole-mount in situ hybridization, was confirmed by Iso-Seq RNA sequencing and single-cell RNA-seq (scRNA-seq) analysis. Iso-Seq analysis showed that gene expression occurs only in the caudal region of adults, but not in anterior regions, including the stomochord. scRNA-seq analysis showed a cluster that contained Brachyury-expressing cells comprising epidermis- and mesoderm-related cells, but which is unlikely to be associated with the nervous system or muscle. Although further investigation is required to examine the roles of Brachyury in adults, this study provides important clues for extending studies on Brachyury expression involved in development of the most posterior region of deuterostomes.
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Affiliation(s)
- Asuka Arimoto
- Marine Biological Laboratory, Blue Innovation Division, Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kuni Tagawa
- Marine Biological Laboratory, Blue Innovation Division, Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
- Faculty of Science and Technology, Maulana Malik Ibrahim State Islamic University of Malang, Kota Malang, Indonesia
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D'Aniello S, Bertrand S, Escriva H. Amphioxus as a model to study the evolution of development in chordates. eLife 2023; 12:e87028. [PMID: 37721204 PMCID: PMC10506793 DOI: 10.7554/elife.87028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023] Open
Abstract
Cephalochordates and tunicates represent the only two groups of invertebrate chordates, and extant cephalochordates - commonly known as amphioxus or lancelets - are considered the best proxy for the chordate ancestor, from which they split around 520 million years ago. Amphioxus has been an important organism in the fields of zoology and embryology since the 18th century, and the morphological and genomic simplicity of cephalochordates (compared to vertebrates) makes amphioxus an attractive model for studying chordate biology at the cellular and molecular levels. Here we describe the life cycle of amphioxus, and discuss the natural histories and habitats of the different species of amphioxus. We also describe their use as laboratory animal models, and discuss the techniques that have been developed to study different aspects of amphioxus.
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Affiliation(s)
- Salvatore D'Aniello
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton DohrnNapoliItaly
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
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Bozzo M, Bellitto D, Amaroli A, Ferrando S, Schubert M, Candiani S. Retinoic Acid and POU Genes in Developing Amphioxus: A Focus on Neural Development. Cells 2023; 12:cells12040614. [PMID: 36831281 PMCID: PMC9953854 DOI: 10.3390/cells12040614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
POU genes are a family of evolutionarily conserved transcription factors with key functions in cell type specification and neurogenesis. In vitro experiments have indicated that the expression of some POU genes is controlled by the intercellular signaling molecule retinoic acid (RA). In this work, we aimed to characterize the roles of RA signaling in the regulation of POU genes in vivo. To do so, we studied POU genes during the development of the cephalochordate amphioxus, an animal model crucial for understanding the evolutionary origins of vertebrates. The expression patterns of amphioxus POU genes were assessed at different developmental stages by chromogenic in situ hybridization and hybridization chain reaction. Expression was further assessed in embryos subjected to pharmacological manipulation of endogenous RA signaling activity. In addition to a detailed description of the effects of these treatments on amphioxus POU gene expression, our survey included the first description of Pou2 and Pou6 expression in amphioxus embryos. We found that Pit-1, Pou2, Pou3l, and Pou6 expression are not affected by alterations of endogenous RA signaling levels. In contrast, our experiments indicated that Brn1/2/4 and Pou4 expression are regulated by RA signaling in the endoderm and the nerve cord, respectively. The effects of the treatments on Pou4 expression in the nerve cord revealed that, in developing amphioxus, RA signaling plays a dual role by (1) providing anteroposterior patterning information to neural cells and (2) specifying neural cell types. This finding is coherent with a terminal selector function of Pou4 for GABAergic neurons in amphioxus and represents the first description of RA-induced changes in POU gene expression in vivo.
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Affiliation(s)
- Matteo Bozzo
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
- Correspondence: (M.B.); (S.C.); Tel.: +39-0103358043 (M.B.); +39-0103358051 (S.C.)
| | - Deianira Bellitto
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Andrea Amaroli
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Sara Ferrando
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Simona Candiani
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
- Correspondence: (M.B.); (S.C.); Tel.: +39-0103358043 (M.B.); +39-0103358051 (S.C.)
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Cheng J, Meistertzheim AL, Leistenschneider D, Philip L, Jacquin J, Escande ML, Barbe V, Ter Halle A, Chapron L, Lartaud F, Bertrand S, Escriva H, Ghiglione JF. Impacts of microplastics and the associated plastisphere on physiological, biochemical, genetic expression and gut microbiota of the filter-feeder amphioxus. ENVIRONMENT INTERNATIONAL 2023; 172:107750. [PMID: 36669287 DOI: 10.1016/j.envint.2023.107750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Oceanic plastic pollution is of major concern to marine organisms, especially filter feeders. However, limited is known about the toxic effects of the weathered microplastics instead of the pristine ones. This study evaluates the effects of weathered polystyrene microplastic on a filter-feeder amphioxus under starvation conditions via its exposure to the microplastics previously deployed in the natural seawater allowing for the development of a mature biofilm (so-called plastisphere). The study focused on the integration of physiological, histological, biochemical, molecular, and microbiota impacts on amphioxus. Overall, specific alterations in gene expression of marker genes were observed to be associated with oxidative stresses and immune systems. Negligible impacts were observed on antioxidant biochemical activities and gut microbiota of amphioxus, while we highlighted the potential transfer of 12 bacterial taxa from the plastisphere to the amphioxus gut microbiota. Moreover, the classical perturbation of body shape detected in control animals under starvation conditions (a slim and curved body) but not for amphioxus exposed to microplastic, indicates that the microorganisms colonizing plastics could serve as a nutrient source for this filter-feeder, commitment with the elevated proportions of goblet cell-like structures after the microplastic exposure. The multidisciplinary approach developed in this study underlined the trait of microplastics that acted as vectors for transporting microorganisms from the plastisphere to amphioxus.
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Affiliation(s)
- Jingguang Cheng
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | | | - David Leistenschneider
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France; SAS Plastic@Sea, Observatoire Océanologique de Banyuls, F-66650, France
| | - Lena Philip
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France; SAS Plastic@Sea, Observatoire Océanologique de Banyuls, F-66650, France
| | - Justine Jacquin
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | - Marie-Line Escande
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057 Evry, France
| | - Alexandra Ter Halle
- Université de Toulouse, CNRS, UMR 5623, Laboratoire des Interactions Moléculaires et Réactivité Chimique et Photochimique (IMRCP), F-31000 Toulouse, France
| | - Leila Chapron
- SAS Plastic@Sea, Observatoire Océanologique de Banyuls, F-66650, France; Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | - Franck Lartaud
- Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Jean-François Ghiglione
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France.
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Morthorst JE, Holbech H, De Crozé N, Matthiessen P, LeBlanc GA. Thyroid-like hormone signaling in invertebrates and its potential role in initial screening of thyroid hormone system disrupting chemicals. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2023; 19:63-82. [PMID: 35581168 PMCID: PMC10083991 DOI: 10.1002/ieam.4632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/30/2022] [Accepted: 05/12/2022] [Indexed: 05/07/2023]
Abstract
This review examines the presence and evolution of thyroid-like systems in selected aquatic invertebrates to determine the potential use of these organisms in screens for vertebrate thyroid hormone axis disrupting chemicals (THADCs). Such a screen might support the phasing out of some vertebrate testing. Although arthropods including crustaceans do not contain a functional thyroid signaling system, elements of such a system exist in the aquatic phyla mollusks, echinoderms, tunicates, and cephalochordates. These phyla can synthesize thyroid hormone, which has been demonstrated in some groups to induce the nuclear thyroid hormone receptor (THR). Thyroid hormone may act in these phyla through interaction with a membrane integrin receptor. Thyroid hormone regulates inter alia metamorphosis but, unlike in vertebrates, this does not occur via receptor activation by the ligands triiodothyronine (T3) and thyroxine (T4). Instead, the unliganded nuclear receptor itself controls metamorphosis in mollusks, echinoderms, and tunicates, whereas the T3 derivative tri-iodothyroacetic acid (TRIAC) acts as a THR ligand in cephalochordates. In view of this, it may be possible to develop an invertebrate-based screen that is sensitive to vertebrate THADCs that interfere with thyroid hormone synthesis or metabolism along with interaction with membrane receptors. The review makes some recommendations for the need to develop an appropriate test method. Integr Environ Assess Manag 2023;19:63-82. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
| | - Henrik Holbech
- Department of BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Noémie De Crozé
- Laboratoire Recherche Environnementale, L'ORÉAL Recherche & InnovationAulnay‐sous‐BoisFrance
| | | | - Gerald A. LeBlanc
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
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11
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Brasó-Vives M, Marlétaz F, Echchiki A, Mantica F, Acemel RD, Gómez-Skarmeta JL, Hartasánchez DA, Le Targa L, Pontarotti P, Tena JJ, Maeso I, Escriva H, Irimia M, Robinson-Rechavi M. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biol 2022; 23:243. [PMID: 36401278 PMCID: PMC9673378 DOI: 10.1186/s13059-022-02808-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome duplications and their developmental complexity. For these reasons, amphioxus are frequently used as an outgroup to study vertebrate genome evolution and Evo-Devo. Aside from whole-genome duplications, genes continuously duplicate on a smaller scale. Small-scale duplicated genes can be found in both amphioxus and vertebrate genomes, while only the vertebrate genomes have duplicated genes product of their 2R whole-genome duplications. Here, we explore the history of small-scale gene duplications in the amphioxus lineage and compare it to small- and large-scale gene duplication history in vertebrates. RESULTS We present a study of the European amphioxus (Branchiostoma lanceolatum) gene duplications thanks to a new, high-quality genome reference. We find that, despite its overall slow molecular evolution, the amphioxus lineage has had a history of small-scale duplications similar to the one observed in vertebrates. We find parallel gene duplication profiles between amphioxus and vertebrates and conserved functional constraints in gene duplication. Moreover, amphioxus gene duplicates show levels of expression and patterns of functional specialization similar to the ones observed in vertebrate duplicated genes. We also find strong conservation of gene synteny between two distant amphioxus species, B. lanceolatum and B. floridae, with two major chromosomal rearrangements. CONCLUSIONS In contrast to their slower molecular and morphological evolution, amphioxus' small-scale gene duplication history resembles that of the vertebrate lineage both in quantitative and in functional terms.
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Affiliation(s)
- Marina Brasó-Vives
- grid.9851.50000 0001 2165 4204Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ferdinand Marlétaz
- grid.83440.3b0000000121901201Department of Genetics, Evolution and Environment (GEE), University College London, London, UK
| | - Amina Echchiki
- grid.9851.50000 0001 2165 4204Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Federica Mantica
- grid.11478.3b0000 0004 1766 3695Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rafael D. Acemel
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - José L. Gómez-Skarmeta
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - Diego A. Hartasánchez
- grid.9851.50000 0001 2165 4204Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lorlane Le Targa
- IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France ,grid.483853.10000 0004 0519 5986IHU-Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France ,grid.483853.10000 0004 0519 5986IHU-Méditerranée Infection, Marseille, France ,grid.4444.00000 0001 2112 9282CNRS, Paris, France
| | - Juan J. Tena
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - Ignacio Maeso
- grid.15449.3d0000 0001 2200 2355Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain ,grid.5841.80000 0004 1937 0247Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Hector Escriva
- grid.462844.80000 0001 2308 1657Biologie Intégrative des Organismes Marins, BIOM, CNRS-Sorbonne University, Banyuls-sur-Mer, France
| | - Manuel Irimia
- grid.11478.3b0000 0004 1766 3695Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Pompeu Fabra University (UPF), Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Barcelona, Spain
| | - Marc Robinson-Rechavi
- grid.9851.50000 0001 2165 4204Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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12
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Exploring tissue morphodynamics using the photoconvertible Kaede protein in amphioxus embryos. PLoS One 2022; 17:e0275193. [PMID: 36166455 PMCID: PMC9514637 DOI: 10.1371/journal.pone.0275193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/12/2022] [Indexed: 12/02/2022] Open
Abstract
Photoconvertible proteins are powerful tools widely used in cellular biology to study cell dynamics and organelles. Over the past decade, photoconvertible proteins have also been used for developmental biology applications to analyze cell lineage and cell fate during embryonic development. One of these photoconvertible proteins called Kaede, from the stony coral Trachyphyllia geoffroyi, undergoes irreversible photoconversion from green to red fluorescence when illuminated with UV light. Undertaking a cell tracing approach using photoconvertible proteins can be challenging when using unconventional animal models. In this protocol, we describe the use of Kaede to track specific cells during embryogenesis of the cephalochordate Branchiostoma lanceolatum. This protocol can be adapted to other unconventional models, especially marine animals.
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Photobiomodulation Therapy through a Novel Flat-Top Hand-Piece Prototype Improves Tissue Regeneration in Amphioxus (Branchiostoma lanceolatum): Proposal of an Ethical Model for Preclinical Screening. PHOTONICS 2022. [DOI: 10.3390/photonics9070503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite the literature providing compelling evidence for the medical efficacy of photobiomodulation (PBM) therapy, its consistency in terms of accuracy and standardization needs improving. Identification of new technology and reliable and ethical biological models is, therefore, a challenge for researchers working on PBM. We tested the reliability of PBM irradiation through a novel delivery probe with a flat-top beam profile on the regenerating amphioxus Branchiostoma lanceolatum. The caudalmost 9 ± 1 myotomes, posterior to the anus, were excised using a sterile lancet. Animals were randomly split into three experimental groups. In the control group, the beam area was bounded with the 635-nm red-light pointer (negligible power, <0.5 mW) and the laser device was coded to irradiate 810 nm and 0 W. In Group laser-1, the beam area was bounded with the same 635-nm red-light pointer and irradiated at 810 nm, 1 W in CW for 60 s, spot-size 1 cm2, 1 W/cm2, 60 J/cm2, and 60 J; irradiation was performed every day for two weeks. In Group laser-2, the beam area was bounded with the same 635-nm red-light pointer and irradiated at 810 nm, 1 W in CW for 60 s, spot-size 1 cm2, 1 W/cm2, 60 J/cm2, and 60 J; irradiation was performed on alternate days for four weeks. We observed that PBM improved the natural wound-healing and regeneration process. The effect was particularly evident for the notochord. Daily irradiation better supported the regenerative process.
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Ma P, Liu X, Xu Z, Liu H, Ding X, Huang Z, Shi C, Liang L, Xu L, Li X, Li G, He Y, Ding Z, Chai C, Wang H, Qiu J, Zhu J, Wang X, Ding P, Zhou S, Yuan Y, Wu W, Wan C, Yan Y, Zhou Y, Zhou QJ, Wang GD, Zhang Q, Xu X, Li G, Zhang S, Mao B, Chen D. Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution. Cell Rep 2022; 39:110979. [PMID: 35732129 DOI: 10.1016/j.celrep.2022.110979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/21/2022] [Accepted: 05/27/2022] [Indexed: 11/03/2022] Open
Abstract
Vertebrate evolution was accompanied by two rounds of whole-genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single-cell sequencing has been widely used to construct the developmental cell atlas of several representative species of vertebrates (human, mouse, zebrafish, and frog) and tunicates (sea squirts). Here, we perform single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated, we constructed a developmental tree for amphioxus cell fate commitment and lineage specification and characterize the underlying key regulators and genetic regulatory networks. The data are publicly available on the online platform AmphioxusAtlas.
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Affiliation(s)
- Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xingyan Liu
- Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing 100190, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaoxu Xu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huimin Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China
| | - Xiangning Ding
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Huang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China; Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China
| | - Langchao Liang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiaolu Li
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Guimei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuqi He
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Zhaoli Ding
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China
| | - Chaochao Chai
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoyu Wang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaying Qiu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiacheng Zhu
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Peiwen Ding
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Wendi Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Cen Wan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Yanan Yan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Yitao Zhou
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China
| | - Qi-Jun Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qiujin Zhang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan District, Xiamen, Fujian 361102, China.
| | - Shihua Zhang
- Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing 100190, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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15
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Meister L, Escriva H, Bertrand S. Functions of the FGF signalling pathway in cephalochordates provide insight into the evolution of the prechordal plate. Development 2022; 149:275365. [PMID: 35575387 PMCID: PMC9188755 DOI: 10.1242/dev.200252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
The fibroblast growth factor (FGF) signalling pathway plays various roles during vertebrate embryogenesis, from mesoderm formation to brain patterning. This diversity of functions relies on the fact that vertebrates possess the largest FGF gene complement among metazoans. In the cephalochordate amphioxus, which belongs to the chordate clade together with vertebrates and tunicates, we have previously shown that the main role of FGF during early development is the control of rostral somite formation. Inhibition of this signalling pathway induces the loss of these structures, resulting in an embryo without anterior segmented mesoderm, as in the vertebrate head. Here, by combining several approaches, we show that the anterior presumptive paraxial mesoderm cells acquire an anterior axial fate when FGF signal is inhibited and that they are later incorporated in the anterior notochord. Our analysis of notochord formation in wild type and in embryos in which FGF signalling is inhibited also reveals that amphioxus anterior notochord presents transient prechordal plate features. Altogether, our results give insight into how changes in FGF functions during chordate evolution might have participated to the emergence of the complex vertebrate head. Summary: FGF signalling inhibition in cephalochordates induces a loss of anteriormost somites. After FGFR inhibition, the presomitic anterior region cells are incorporated in the anterior notochord which transiently present prechordal plate features.
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Affiliation(s)
- Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
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16
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Abstract
The nervous system is a product of evolution. That is, it was constructed through a long series of modifications, within the strong constraints of heredity, and continuously subjected to intense selection pressures. As a result, the organization and functions of the brain are shaped by its history. We believe that this fact, underappreciated in contemporary systems neuroscience, offers an invaluable aid for helping us resolve the brain's mysteries. Indeed, we think that the consideration of evolutionary history ought to take its place alongside other intellectual tools used to understand the brain, such as behavioural experiments, studies of anatomical structure and functional characterization based on recordings of neural activity. In this introduction, we argue for the importance of evolution by highlighting specific examples of ways that evolutionary theory can enhance neuroscience. The rest of the theme issue elaborates this point, emphasizing the conservative nature of neural evolution, the important consequences of specific transitions that occurred in our history, and the ways in which considerations of evolution can shed light on issues ranging from specific mechanisms to fundamental principles of brain organization. This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.
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Affiliation(s)
- Paul Cisek
- Department of Neuroscience, University of Montréal, 2960 chemin de la tour, local 1107 Montréal, QC H3T 1J4 Canada
| | - Benjamin Y Hayden
- Department of Neuroscience, Department of Biomedical Engineering, and Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN 55455, USA
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17
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Somorjai IML, Ehebauer MT, Escrivà H, Garcia-Fernàndez J. JNK Mediates Differentiation, Cell Polarity and Apoptosis During Amphioxus Development by Regulating Actin Cytoskeleton Dynamics and ERK Signalling. Front Cell Dev Biol 2021; 9:749806. [PMID: 34778260 PMCID: PMC8586503 DOI: 10.3389/fcell.2021.749806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
c-Jun N-terminal kinase (JNK) is a multi-functional protein involved in a diverse array of context-dependent processes, including apoptosis, cell cycle regulation, adhesion, and differentiation. It is integral to several signalling cascades, notably downstream of non-canonical Wnt and mitogen activated protein kinase (MAPK) signalling pathways. As such, it is a key regulator of cellular behaviour and patterning during embryonic development across the animal kingdom. The cephalochordate amphioxus is an invertebrate chordate model system straddling the invertebrate to vertebrate transition and is thus ideally suited for comparative studies of morphogenesis. However, next to nothing is known about JNK signalling or cellular processes in this lineage. Pharmacological inhibition of JNK signalling using SP600125 during embryonic development arrests gastrula invagination and causes convergence extension-like defects in axial elongation, particularly of the notochord. Pharynx formation and anterior oral mesoderm derivatives like the preoral pit are also affected. This is accompanied by tissue-specific transcriptional changes, including reduced expression of six3/6 and wnt2 in the notochord, and ectopic wnt11 in neurulating embryos treated at late gastrula stages. Cellular delamination results in accumulation of cells in the gut cavity and a dorsal fin-like protrusion, followed by secondary Caspase-3-mediated apoptosis of polarity-deficient cells, a phenotype only partly rescued by co-culture with the pan-Caspase inhibitor Z-VAD-fmk. Ectopic activation of extracellular signal regulated kinase (ERK) signalling in the neighbours of extruded notochord and neural cells, possibly due to altered adhesive and tensile properties, as well as defects in cellular migration, may explain some phenotypes caused by JNK inhibition. Overall, this study supports conserved functions of JNK signalling in mediating the complex balance between cell survival, apoptosis, differentiation, and cell fate specification during cephalochordate morphogenesis.
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Affiliation(s)
- Ildiko M L Somorjai
- School of Biology, University of St Andrews, St Andrews, United Kingdom.,Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls-sur-Mer, France.,Departament de Genètica, Microbiologia i Estadística, University of Barcelona, Barcelona, Spain
| | | | - Hector Escrivà
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Jordi Garcia-Fernàndez
- Departament de Genètica, Microbiologia i Estadística, University of Barcelona, Barcelona, Spain.,Institut de Biomedicina, University of Barcelona, Barcelona, Spain
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18
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Zou J, Wu X, Shi C, Zhong Y, Zhang L, Yan Q, Su L, Li G. A Potential Method for Rapid Screening of Amphioxus Founder Harboring Germline Mutation and Transgene. Front Cell Dev Biol 2021; 9:702290. [PMID: 34458263 PMCID: PMC8387717 DOI: 10.3389/fcell.2021.702290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Amphioxus is a promising model organism for understanding the origin and evolution of vertebrates due to its basal phylogenetic position among chordates. We here compared the mutation efficacy and mutation type of tail tips and gametes of amphioxus founders injected with Cas9 protein and six different sgRNAs targeting five distinct genes, and revealed a strong correlation for mutation efficacy and a mild correlation for mutation type among the two tissues. In addition, we also observed a positive relationship between gene insertions observed in tail tips and gametes of amphioxus founders injected with Tol2 transposase and two different transgenic constructs. Finally, we showed that amphioxus larvae which had their tail tips cut at the 3-4 gill-slit stage were able to recover within 6 days and developed a normal number of gonads at the adult stage, and that F0 larvae carry similar mutation efficacy and type in the posterior end to that in the tail tips after their metamorphosis. Together, these findings suggest a great potential for obtaining valid amphioxus founders with desired mutations and transgenes at as early as the early larval stage, which will certainly speed up the generation of amphioxus mutants and transgenes and make it more cost- and labor-effective.
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Affiliation(s)
- Jiaqi Zou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaotong Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yanhong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lei Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qiuning Yan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liuru Su
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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19
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Satoh N, Tominaga H, Kiyomoto M, Hisata K, Inoue J, Nishitsuji K. A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum. Front Cell Dev Biol 2021; 9:696875. [PMID: 34336847 PMCID: PMC8321703 DOI: 10.3389/fcell.2021.696875] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Among chordate taxa, the cephalochordates diverged earlier than urochordates and vertebrates; thus, they retain unique, primitive developmental features. In particular, the amphioxus notochord has muscle-like properties, a feature not seen in urochordates or vertebrates. Amphioxus contains two Brachyury genes, Bra1 and Bra2. Bra2 is reportedly expressed in the blastopore, notochord, somites, and tail bud, in contrast to a low level of Bra1 expression only in notochord. To distinguish the expression profiles of the two Brachyury genes at the single-cell level, we carried out single-cell RNA-seq (scRNA-seq) analysis using the amphioxus, Branchiostoma japonicum. This scRNA-seq analysis classified B. japonicum embryonic cells into 15 clusters at developmental stages from midgastrula to early swimming larva. Brachyury was expressed in cells of clusters 4, 5, 8, and 9. We first confirmed that cluster 8 comprises cells that form somites since this cluster specifically expresses four myogenic factor genes. Cluster 9 contains a larger number of cells with high levels of Bra2 expression and a smaller number of cells with Bra1 expression. Simultaneous expression in cluster 9 of tool-kit genes, including FoxA, Goosecoid, and hedgehog, showed that this cluster comprises cells that form the notochord. Expression of Bra2, but not Bra1, in cells of clusters 4 and 5 at the gastrula stage together with expression of Wnt1 and Caudal indicates that clusters 4 and 5 comprise cells of the blastopore, which contiguously form the tail bud. In addition, Hox1, Hox3, and Hox4 were highly expressed in Bra2-expressing clusters 4, 5, 8, and 9 in a temporally coordinated manner, suggesting roles of anterior Hox genes in specification of mesodermal organs, including somites, notochord, and tail bud. This scRNA-seq analysis therefore highlights differences between the two Brachyury genes in relation to embryonic regions in which they are expressed and their levels of expression. Bra2 is the ancestral Brachyury in amphioxus, since expression in the blastopore is shared with other deuterostomes. On the other hand, Bra1 is a duplicate copy and likely evolved a supplementary function in notochord and somite formation in the Branchiostoma lineage.
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Affiliation(s)
- Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hitoshi Tominaga
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Masato Kiyomoto
- Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Chiba, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jun Inoue
- Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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20
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Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.
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21
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Carvalho JE, Lahaye F, Yong LW, Croce JC, Escrivá H, Yu JK, Schubert M. An Updated Staging System for Cephalochordate Development: One Table Suits Them All. Front Cell Dev Biol 2021; 9:668006. [PMID: 34095136 PMCID: PMC8174843 DOI: 10.3389/fcell.2021.668006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
Chordates are divided into three subphyla: Vertebrata, Tunicata, and Cephalochordata. Phylogenetically, the Cephalochordata, more commonly known as lancelets or amphioxus, constitute the sister group of Vertebrata and Tunicata. Lancelets are small, benthic, marine filter feeders, and their roughly three dozen described species are divided into three genera: Branchiostoma, Epigonichthys, and Asymmetron. Due to their phylogenetic position and their stereotypical chordate morphology and genome architecture, lancelets are key models for understanding the evolutionary history of chordates. Lancelets have thus been studied by generations of scientists, with the first descriptions of adult anatomy and developmental morphology dating back to the 19th century. Today, several different lancelet species are used as laboratory models, predominantly for developmental, molecular and genomic studies. Surprisingly, however, a universal staging system and an unambiguous nomenclature for developing lancelets have not yet been adopted by the scientific community. In this work, we characterized the development of the European lancelet (Branchiostoma lanceolatum) using confocal microscopy and compiled a streamlined developmental staging system, from fertilization through larval life, including an unambiguous stage nomenclature. By tracing growth curves of the European lancelet reared at different temperatures, we were able to show that our staging system permitted an easy conversion of any developmental time into a specific stage name. Furthermore, comparisons of embryos and larvae from the European lancelet (B. lanceolatum), the Florida lancelet (Branchiostoma floridae), two Asian lancelets (Branchiostoma belcheri and Branchiostoma japonicum), and the Bahamas lancelet (Asymmetron lucayanum) demonstrated that our staging system could readily be applied to other lancelet species. Although the detailed staging description was carried out on developing B. lanceolatum, the comparisons with other lancelet species thus strongly suggested that both staging and nomenclature are applicable to all extant lancelets. We conclude that this description of embryonic and larval development will be of great use for the scientific community and that it should be adopted as the new standard for defining and naming developing lancelets. More generally, we anticipate that this work will facilitate future studies comparing representatives from different chordate lineages.
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Affiliation(s)
- João E Carvalho
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - François Lahaye
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jenifer C Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Hector Escrivá
- Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
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22
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Caccavale F, Osca D, D’Aniello S, Crocetta F. Molecular taxonomy confirms that the northeastern Atlantic and Mediterranean Sea harbor a single lancelet, Branchiostoma lanceolatum (Pallas, 1774) (Cephalochordata: Leptocardii: Branchiostomatidae). PLoS One 2021; 16:e0251358. [PMID: 33956890 PMCID: PMC8101936 DOI: 10.1371/journal.pone.0251358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/23/2021] [Indexed: 12/02/2022] Open
Abstract
Branchiostomatidae (lancelets or amphioxus) comprises about 30 species, several of which are well-established models in evolutionary development. Our zoological and ecological knowledge of the family is nonetheless limited. Despite evident differences can be found among known populations, the taxonomy of Branchiostoma lanceolatum (type species of the genus Branchiostoma) has never been investigated with modern methods through its range in the northeastern Atlantic and Mediterranean Sea. We address this via a multilocus molecular approach and comparing specimens collected from different European populations. Results obtained here confirm the presence of a single species inhabiting the range between the topotypical localities of B. lanceolatum (Atlantic Ocean) and of its junior synonym B. lubricum (Mediterranean Sea), without evincing geographical structure between populations. This suggests that environment most likely drives the characteristics observed in different geographic areas. The long larval phase and the slow mutation rate in lancelets may have played a key role in the evolutionary history of this iconic species.
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Affiliation(s)
- Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - David Osca
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Fabio Crocetta
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
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23
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Bertrand S, Carvalho JE, Dauga D, Matentzoglu N, Daric V, Yu JK, Schubert M, Escrivá H. The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX). Front Cell Dev Biol 2021; 9:668025. [PMID: 33981708 PMCID: PMC8107275 DOI: 10.3389/fcell.2021.668025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/31/2021] [Indexed: 11/13/2022] Open
Abstract
An ontology is a computable representation of the different parts of an organism and its different developmental stages as well as the relationships between them. The ontology of model organisms is therefore a fundamental tool for a multitude of bioinformatics and comparative analyses. The cephalochordate amphioxus is a marine animal representing the earliest diverging evolutionary lineage of chordates. Furthermore, its morphology, its anatomy and its genome can be considered as prototypes of the chordate phylum. For these reasons, amphioxus is a very important animal model for evolutionary developmental biology studies aimed at understanding the origin and diversification of vertebrates. Here, we have constructed an amphioxus ontology (AMPHX) which combines anatomical and developmental terms and includes the relationships between these terms. AMPHX will be used to annotate amphioxus gene expression patterns as well as phenotypes. We encourage the scientific community to adopt this amphioxus ontology and send recommendations for future updates and improvements.
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Affiliation(s)
- Stephanie Bertrand
- CNRS, Biologie Intégrative des Organismes Marins, Sorbonne Université, Paris, France
| | - João E. Carvalho
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, Paris, France
| | | | | | - Vladimir Daric
- CNRS, Biologie Intégrative des Organismes Marins, Sorbonne Université, Paris, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei City, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Michael Schubert
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, Paris, France
| | - Hector Escrivá
- CNRS, Biologie Intégrative des Organismes Marins, Sorbonne Université, Paris, France
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24
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Aase-Remedios ME, Coll-Lladó C, Ferrier DEK. More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs). Mol Biol Evol 2021; 37:2966-2982. [PMID: 32520990 PMCID: PMC7530620 DOI: 10.1093/molbev/msaa147] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolutionary transition from invertebrates to vertebrates involved extensive gene duplication, but understanding precisely how such duplications contributed to this transition requires more detailed knowledge of specific cases of genes and gene families. Myogenic differentiation (MyoD) has long been recognized as a master developmental control gene and member of the MyoD family of bHLH transcription factors (myogenic regulatory factors [MRFs]) that drive myogenesis across the bilaterians. Phylogenetic reconstructions within this gene family are complicated by multiple instances of gene duplication and loss in several lineages. Following two rounds of whole-genome duplication (2R WGD) at the origin of the vertebrates, the ancestral function of MRFs is thought to have become partitioned among the daughter genes, so that MyoD and Myf5 act early in myogenic determination, whereas Myog and Myf6 are expressed later, in differentiating myoblasts. Comparing chordate MRFs, we find an independent expansion of MRFs in the invertebrate chordate amphioxus, with evidence for a parallel instance of subfunctionalization relative to that of vertebrates. Conserved synteny between chordate MRF loci supports the 2R WGD events as a major force in shaping the evolution of vertebrate MRFs. We also resolve vertebrate MRF complements and organization, finding a new type of vertebrate MRF gene in the process, which allowed us to infer an ancestral two-gene state in the vertebrates corresponding to the early- and late-acting types of MRFs. This necessitates a revision of previous conclusions about the simple one-to-four origin of vertebrate MRFs.
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Affiliation(s)
- Madeleine E Aase-Remedios
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Clara Coll-Lladó
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - David E K Ferrier
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
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25
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Roux N, Logeux V, Trouillard N, Pillot R, Magré K, Salis P, Lecchini D, Besseau L, Laudet V, Romans P. A star is born again: Methods for larval rearing of an emerging model organism, the False clownfish Amphiprion ocellaris. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:376-385. [PMID: 33539680 PMCID: PMC8248105 DOI: 10.1002/jez.b.23028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
As interest increases in ecological, evolutionary, and developmental biology (Eco‐Evo‐Devo), wild species are increasingly used as experimental models. However, we are still lacking a suitable model for marine fish species, as well as coral reef fishes that can be reared at laboratory scales. Extensive knowledge of the life cycle of anemonefishes, and the peculiarities of their biology, make them relevant marine fish models for developmental biology, ecology, and evolutionary sciences. Here, we present standard methods to maintain breeding pairs of the anemonefish Amphiprion ocellaris in captivity, obtain regular good quality spawning, and protocols to ensure larval survival throughout rearing. We provide a detailed description of the anemonefish husbandry system and life prey culturing protocols. Finally, a “low‐volume” rearing protocol useful for the pharmacological treatment of larvae is presented. Such methods are important as strict requirements for large volumes in rearing tanks often inhibit continuous treatments with expensive or rare compounds. This paper describes how to set up a rearing system for anemone fishes at the laboratory scale as this species is becoming a relevant marine fish model to tackle Eco‐Evo‐Devo questions. We detail two rearing methods, one consisting of classical rearing conditions and the other one consisting of low‐volume conditions (500 ml).
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Affiliation(s)
- Natacha Roux
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Valentin Logeux
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Nancy Trouillard
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Rémi Pillot
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Kévin Magré
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Pauline Salis
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France.,EPHE-UPVD-CNRS-USR 3278 CRIOBE BP 1013, PSL Research University, Papetoai, Moorea, French Polynesia
| | - David Lecchini
- EPHE-UPVD-CNRS-USR 3278 CRIOBE BP 1013, PSL Research University, Papetoai, Moorea, French Polynesia.,Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
| | - Laurence Besseau
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Vincent Laudet
- CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France.,Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, Okinawa, Japan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan, Taiwan
| | - Pascal Romans
- CNRS, FR3724, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
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26
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Su L, Shi C, Huang X, Wang Y, Li G. Application of CRISPR/Cas9 Nuclease in Amphioxus Genome Editing. Genes (Basel) 2020; 11:genes11111311. [PMID: 33167309 PMCID: PMC7694359 DOI: 10.3390/genes11111311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
The cephalochordate amphioxus is a promising animal model for studying the origin of vertebrates due to its key phylogenetic position among chordates. Although transcription activator-like effector nucleases (TALENs) have been adopted in amphioxus genome editing, its labor-intensive construction of TALEN proteins limits its usage in many laboratories. Here we reported an application of the CRISPR/Cas9 system, a more amenable genome editing method, in this group of animals. Our data showed that while co-injection of Cas9 mRNAs and sgRNAs into amphioxus unfertilized eggs caused no detectable mutations at targeted loci, injections of Cas9 mRNAs and sgRNAs at the two-cell stage, or of Cas9 protein and sgRNAs before fertilization, can execute efficient disruptions of targeted genes. Among the nine tested sgRNAs (targeting five genes) co-injected with Cas9 protein, seven introduced mutations with efficiency ranging from 18.4% to 90% and four caused specific phenotypes in the injected embryos. We also demonstrated that monomerization of sgRNAs via thermal treatment or modifying the sgRNA structure could increase mutation efficacies. Our study will not only promote application of genome editing method in amphioxus research, but also provide valuable experiences for other organisms in which the CRISPR/Cas9 system has not been successfully applied.
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27
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Pujades C. The multiple functions of hindbrain boundary cells: Tinkering boundaries? Semin Cell Dev Biol 2020; 107:179-189. [DOI: 10.1016/j.semcdb.2020.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 02/01/2023]
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28
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Pergner J, Vavrova A, Kozmikova I, Kozmik Z. Molecular Fingerprint of Amphioxus Frontal Eye Illuminates the Evolution of Homologous Cell Types in the Chordate Retina. Front Cell Dev Biol 2020; 8:705. [PMID: 32850825 PMCID: PMC7417673 DOI: 10.3389/fcell.2020.00705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
The evolution of the vertebrate eye remains so far unresolved. Amphioxus frontal eye pigment cells and photoreceptors were proposed to be homologous to vertebrate photoreceptors and retinal pigmented epithelium, based on ultrastructural morphology and gene expression analysis in B. floridae. Here, we present comparative molecular data using two additional amphioxus species, a closely related B. lanceolatum, and the most divergent A. lucayanum. Taking advantage of a unique set of specific antibodies we characterized photoreceptors and putative interneurons of the frontal eye and investigated its neuronal circuitry. Our results corroborate generally conserved molecular fingerprint among cephalochordate species. Furthermore, we performed pharmacological perturbations and found that the Notch signaling pathway, a key regulator of retina development in vertebrates, is required for correct ratios among frontal eye cell types. In summary, our study provides a valuable insight into cell-type relationships in chordate visual organs and strengthens the previously proposed homology between amphioxus frontal eye and vertebrate eyes.
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Affiliation(s)
- Jiri Pergner
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Anna Vavrova
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Iryna Kozmikova
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Zbynek Kozmik
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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29
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Bi C, Lu N, Huang Z, Chen J, He C, Lu Z. Whole-genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations. Ecol Evol 2020; 10:8210-8224. [PMID: 32788973 PMCID: PMC7417228 DOI: 10.1002/ece3.6527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole-genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long-term population dynamics of Branchiostoma. The inferred ancestral N e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10-9) or third glaciation (mutation rate = 9 × 10-9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.
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Affiliation(s)
- Changwei Bi
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Na Lu
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic AdministrationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Key Laboratory of Special Marine Bio‐resources Sustainable Utilization of Fujian ProvinceFuzhouChina
| | - Junyuan Chen
- Nanjing Institute of Paleontology and GeologyChinese Academy of SciencesNanjingChina
| | - Chunpeng He
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Zuhong Lu
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
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30
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Abstract
The lateral plate mesoderm (LPM) forms the progenitor cells that constitute the heart and cardiovascular system, blood, kidneys, smooth muscle lineage and limb skeleton in the developing vertebrate embryo. Despite this central role in development and evolution, the LPM remains challenging to study and to delineate, owing to its lineage complexity and lack of a concise genetic definition. Here, we outline the processes that govern LPM specification, organization, its cell fates and the inferred evolutionary trajectories of LPM-derived tissues. Finally, we discuss the development of seemingly disparate organ systems that share a common LPM origin. Summary: The lateral plate mesoderm is the origin of several major cell types and organ systems in the vertebrate body plan. How this mesoderm territory emerges and partitions into its downstream fates provides clues about vertebrate development and evolution.
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Affiliation(s)
- Karin D Prummel
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA.,Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Susan Nieuwenhuize
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA.,Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Mosimann
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA .,Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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Yasuoka Y. Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis‐regulatory modules. Dev Growth Differ 2020; 62:279-300. [DOI: 10.1111/dgd.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis RIKEN Center for Integrative Medical Sciences Tsurumi‐ku Japan
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32
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Bozzo M, Candiani S, Schubert M. Whole mount in situ hybridization and immunohistochemistry for studying retinoic acid signaling in developing amphioxus. Methods Enzymol 2020; 637:419-452. [PMID: 32359654 DOI: 10.1016/bs.mie.2020.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Retinoic acid (RA) is a vitamin A-derived signaling molecule acting during development and in the adult. This chapter provides protocols to characterize the role of RA signaling during development of the invertebrate chordate amphioxus. As sister group to all other chordates and characterized by the most vertebrate-like RA signaling system of all invertebrates, amphioxus is an important model for studying the evolution of RA signaling. Focusing on the development of GABAergic neurons in the amphioxus central nervous system, we provide detailed protocols for maintaining and breeding adult animals, for performing pharmacological treatments of embryos and for analyzing the effects of these treatments by whole mount in situ hybridization and immunohistochemistry coupled to confocal microscopy.
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Affiliation(s)
- Matteo Bozzo
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Simona Candiani
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Michael Schubert
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Villefranche-sur-Mer, France.
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33
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Abstract
The cephalochordates amphioxus or lancelets are benthic marine animals representing the earliest divergent evolutionary lineage within chordates. Although amphioxus are present in most of the world's tropical and temperate oceans, only about thirty different species grouped into three different genera, Branchiostoma, Epigonichthys and Asymmetron have been described. In the genus Asymmetron, only two species have been characterized, although for one of them, A. lucayanum, several cryptic lineages exist. In this work we have sequenced and analyzed the mitogenome of an A. lucayanum population previously described in the Red Sea. The phylogenetic study using this complete mitogenome as well as the analysis of COI gene sequences of several individuals of this Red Sea population show that the Red Sea population is a new cryptic species. We propose to call this new species Asymmetron rubrum.
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34
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Pritchard GH, Kedl RM, Hunter CA. The evolving role of T-bet in resistance to infection. Nat Rev Immunol 2020; 19:398-410. [PMID: 30846856 DOI: 10.1038/s41577-019-0145-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The identification of T-bet as a key transcription factor associated with the development of IFNγ-producing CD4+ T cells predicted a crucial role for T-bet in cell-mediated immunity and in resistance to many intracellular infections. This idea was reinforced by initial reports showing that T-bet-deficient mice were more susceptible to pathogens that survived within the lysosomal system of macrophages. However, subsequent studies revealed IFNγ-dependent, T-bet-independent pathways of resistance to diverse classes of microorganisms that occupy other intracellular niches. Consequently, a more complex picture has emerged of how T-bet and the related transcription factor eomesodermin (EOMES) coordinate many facets of the immune response to bona fide pathogens as well as commensals. This article provides an overview of the discovery and evolutionary relationship between T-bet and EOMES and highlights the studies that have uncovered broader functions of T-bet in innate and adaptive immunity and in the development of the effector and memory T cell populations that mediate long-term resistance to infection.
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Affiliation(s)
- Gretchen Harms Pritchard
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross M Kedl
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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35
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You L, Chi J, Huang S, Yu T, Huang G, Feng Y, Sang X, Gao X, Li T, Yue Z, Liu A, Chen S, Xu A. LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5491331. [PMID: 31106360 PMCID: PMC6526094 DOI: 10.1093/database/baz056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Lancelet (amphioxus) represents the most basally divergent extant chordate (cephalochordates) that diverged from the other two chordate lineages (urochordates and vertebrates) more than half a billion years ago. As it occupies a key position in evolution, it is considered as one of the best proxies for understanding the chordate ancestral state. Thus, the construction of a database with multiple lancelet genomes and gene annotation data, including protein domains, is urgently needed to investigate the loss and gain of domains in orthologues among species, especially ancient domain types (non-vertebrate-specific domains) and novel domain combination, which is helpful for providing new insight into the chordate ancestral state and vertebrate evolution. Here, we present an integrated genome database for lancelet, LanceletDB, which provides reference haploid genome sequence and annotation data for lancelet (Branchiostoma belcheri), including gene models and annotation, protein domain types, gene expression pattern in embryogenesis, different expression sequence tag sets and alternative polyadenylation (APA) sites profiled by the sequencing APA sites method. Especially, LanceletDB allows comparison of domain types and combination in orthologues among type species so as to decode the ancient domain types and novel domain combination during evolution. We also integrated the released diploid lancelet genome annotation data (Branchiostoma floridae) to expand LanceletDB and extend its usefulness. These data are available through the search and analysis page, basic local alignment search tool page and genome browser to provide an integrated display.
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Affiliation(s)
- Leiming You
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.,State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Jiaqi Chi
- Department of Oncology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shengfeng Huang
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Ting Yu
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Guangrui Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuchao Feng
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Xiaopu Sang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Xinhui Gao
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Ting'an Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Zirui Yue
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Aijie Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shangwu Chen
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Anlong Xu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.,State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
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36
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Zhang H, Chen S, Shang C, Wu X, Wang Y, Li G. Interplay between Lefty and Nodal signaling is essential for the organizer and axial formation in amphioxus embryos. Dev Biol 2019; 456:63-73. [DOI: 10.1016/j.ydbio.2019.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 01/04/2023]
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37
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de Bakker BS, van den Hoff MJB, Vize PD, Oostra RJ. The Pronephros; a Fresh Perspective. Integr Comp Biol 2019; 59:29-47. [PMID: 30649320 DOI: 10.1093/icb/icz001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Contemporary papers and book chapters on nephrology open with the assumption that human kidney development passes through three morphological stages: pronephros, mesonephros, and metanephros. Current knowledge of the human pronephros, however, appears to be based on only a hand full of human specimens. The ongoing use of variations in the definition of a pronephros hampers the interpretation of study results. Because of the increased interest in the anamniote pronephros as a genetic model for kidney organogenesis we aimed to provide an overview of the literature concerning kidney development and to clarify the existence of a pronephros in human embryos. We performed an extensive literature survey regarding vertebrate renal morphology and we investigated histological sections of human embryos between 2 and 8 weeks of development. To facilitate better understanding of the literature about kidney development, a referenced glossary with short definitions was composed. The most striking difference between pronephros versus meso- and metanephros is found in nephron architecture. The pronephros consists exclusively of non-integrated nephrons with external glomeruli, whereas meso- and metanephros are composed of integrated nephrons with internal glomeruli. Animals whose embryos have comparatively little yolk at their disposal and hence have a free-swimming larval stage do develop a pronephros that is dedicated to survival in aquatic environments. Species in which embryos do not have a free-swimming larval stage have embryos that are supplied with a large amount of yolk or that develop within the body of the parent. In those species the pronephros is usually absent, incompletely developed, and apparently functionless. Non-integrated nephrons were not identified in histological sections of human embryos. Therefore, we conclude that a true pronephros is not detectable in human embryos although the most cranial part of the amniote excretory organ is often confusingly referred to as pronephros. The term pronephros should be avoided in amniotes unless all elements for a functional pronephros are undeniably present.
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Affiliation(s)
- B S de Bakker
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - M J B van den Hoff
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - P D Vize
- Department of Biological Science, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - R J Oostra
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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38
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Abstract
This article proposes that biologically plausible theories of behavior can be constructed by following a method of "phylogenetic refinement," whereby they are progressively elaborated from simple to complex according to phylogenetic data on the sequence of changes that occurred over the course of evolution. It is argued that sufficient data exist to make this approach possible, and that the result can more effectively delineate the true biological categories of neurophysiological mechanisms than do approaches based on definitions of putative functions inherited from psychological traditions. As an example, the approach is used to sketch a theoretical framework of how basic feedback control of interaction with the world was elaborated during vertebrate evolution, to give rise to the functional architecture of the mammalian brain. The results provide a conceptual taxonomy of mechanisms that naturally map to neurophysiological and neuroanatomical data and that offer a context for defining putative functions that, it is argued, are better grounded in biology than are some of the traditional concepts of cognitive science.
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Affiliation(s)
- Paul Cisek
- Department of Neuroscience, University of Montréal, Montréal, Québec, Canada.
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39
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Spawning Induction and Embryo Micromanipulation Protocols in the Amphioxus Branchiostoma lanceolatum. Methods Mol Biol 2019. [PMID: 31552664 DOI: 10.1007/978-1-4939-9732-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
In the last decades, the cephalochordate amphioxus has reached a peculiar place in research laboratories as an excellent animal model to answer Evo/Devo questions. Nevertheless, mainly due to its restricted spawning season and to the small size of its embryos, only a few basic techniques in developmental biology could be used until recently. Fortunately, these last years, and thanks to the development of high-throughput techniques, new technical approaches have been possible, such as comparative transcriptomics and/or genomics. However, classic micromanipulation techniques are still difficult to apply. Here we present simple protocols for the manipulation of amphioxus embryos. First, we present the spawning induction method used with the European amphioxus species Branchiostoma lanceolatum. Second, we explain simple methods to manipulate the developing amphioxus embryo during the first steps of its development (before the hatching stage). These methods open many technical possibilities for future functional studies. Thus, we present here a simple technique to efficiently dechorionate a large number of embryos, we detail a protocol for the dissociation of cells during the first steps of the embryonic development and, finally, we describe micromanipulation approaches for tissue isolation during the gastrula stage.
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40
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Campos-Dávila L, Pérez-Estrada CJ, Rodríguez-Estrella R, Morales-Bojórquez E, Brun-Murillo FG, Balart EF. Seagrass Halodule wrightii as a new habitat for the amphioxus Branchiostoma californiense (Cephalochordata, Branchiostomidae) in the southern Gulf of California, Mexico. Zookeys 2019; 873:113-131. [PMID: 31534388 PMCID: PMC6728395 DOI: 10.3897/zookeys.873.33901] [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] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/17/2019] [Indexed: 01/21/2023] Open
Abstract
The first record of the amphioxus Branchiostomacaliforniense on seagrass patches of Halodulewrightii in the Gulf of California is reported. Sixty individuals (19 males, 18 females, and 23 undifferentiated) were collected in May 2017 at Bahía Balandra, Gulf of California, from subtidal seagrass patches at a depth of 0.5 m at low tide. The length and weight ranged from 15.88–28.44 mm and from 0.01–0.11 g for females and 11.7–27.9 mm and 0.01–0.09 g for males, respectively. The minimum size of sexually mature individuals was 11.70 mm for males and 15.88 mm for females; 62% of the specimens were sexually mature. Analysis of the total length-weight relationship suggested an allometric growth pattern among females, males and undifferentiated individuals, whereas an analysis of the entire sample suggested an isometric growth pattern. Typical and additional morphological characters were used to identify the amphioxi. High morphological variability between individuals was found, suggesting the presence of several morphotypes. Branchiostomacaliforniense had been previously reported as exclusively associated with bare sandy areas, but our study shows that this species can also be found in seagrass patches, using them as breeding and feeding grounds. Thus, seagrass patches are evidenced as suitable habitats for amphioxus.
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Affiliation(s)
- Lucía Campos-Dávila
- Centro de Investigaciones Biológicas del Noroeste, S.C., Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz Baja California Sur, México Centro de Investigaciones Biológicas del Noroeste La Paz Mexico
| | - Claudia J Pérez-Estrada
- Centro de Investigaciones Biológicas del Noroeste, S.C., Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz Baja California Sur, México Centro de Investigaciones Biológicas del Noroeste La Paz Mexico.,Universidad de Cádiz, Departamento de Biología, Estructura y Dinámica de Ecosistemas Acuáticos, Puerto Real, Cádiz, Spain Universidad de Cádiz Puerto Real Spain
| | - Ricardo Rodríguez-Estrella
- Centro de Investigaciones Biológicas del Noroeste, S.C., Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz Baja California Sur, México Centro de Investigaciones Biológicas del Noroeste La Paz Mexico
| | - Enrique Morales-Bojórquez
- Centro de Investigaciones Biológicas del Noroeste, S.C., Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz Baja California Sur, México Centro de Investigaciones Biológicas del Noroeste La Paz Mexico
| | - Fernando G Brun-Murillo
- Universidad de Cádiz, Departamento de Biología, Estructura y Dinámica de Ecosistemas Acuáticos, Puerto Real, Cádiz, Spain Universidad de Cádiz Puerto Real Spain
| | - Eduardo F Balart
- Centro de Investigaciones Biológicas del Noroeste, S.C., Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz Baja California Sur, México Centro de Investigaciones Biológicas del Noroeste La Paz Mexico
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41
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Herrera-Úbeda C, Marín-Barba M, Navas-Pérez E, Gravemeyer J, Albuixech-Crespo B, Wheeler GN, Garcia-Fernàndez J. Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation. BIOLOGY 2019; 8:E61. [PMID: 31450588 PMCID: PMC6784235 DOI: 10.3390/biology8030061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 01/10/2023]
Abstract
Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and Xenopus the expression domain of one of them, Hotairm1, located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in Xenopus, showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution.
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Affiliation(s)
- Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Marta Marín-Barba
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
| | - Enrique Navas-Pérez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Jan Gravemeyer
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Beatriz Albuixech-Crespo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
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42
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Leung B, Shimeld SM. Evolution of vertebrate spinal cord patterning. Dev Dyn 2019; 248:1028-1043. [PMID: 31291046 DOI: 10.1002/dvdy.77] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 12/17/2022] Open
Abstract
The vertebrate spinal cord is organized across three developmental axes, anterior-posterior (AP), dorsal-ventral (DV), and medial-lateral (ML). Patterning of these axes is regulated by canonical intercellular signaling pathways: the AP axis by Wnt, fibroblast growth factor, and retinoic acid (RA), the DV axis by Hedgehog, Tgfβ, and Wnt, and the ML axis where proliferation is controlled by Notch. Developmental time plays an important role in which signal does what and when. Patterning across the three axes is not independent, but linked by interactions between signaling pathway components and their transcriptional targets. Combined this builds a sophisticated organ with many different types of cell in specific AP, DV, and ML positions. Two living lineages share phylum Chordata with vertebrates, amphioxus, and tunicates, while the jawless fish such as lampreys, survive as the most basally divergent vertebrate lineage. Genes and mechanisms shared between lampreys and other vertebrates tell us what predated vertebrates, while those also shared with other chordates tell us what evolved early in chordate evolution. Between these lie vertebrate innovations: genetic and developmental changes linked to evolution of new morphology. These include gene duplications, differences in how signals are received, and new regulatory connections between signaling pathways and their target genes.
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Affiliation(s)
- Brigid Leung
- Department of Zoology, University of Oxford, Oxford, UK
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43
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Aldea D, Subirana L, Keime C, Meister L, Maeso I, Marcellini S, Gomez-Skarmeta JL, Bertrand S, Escriva H. Genetic regulation of amphioxus somitogenesis informs the evolution of the vertebrate head mesoderm. Nat Ecol Evol 2019; 3:1233-1240. [PMID: 31263232 DOI: 10.1038/s41559-019-0933-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 01/13/2023]
Abstract
The evolution of vertebrates from an ancestral chordate was accompanied by the acquisition of a predatory lifestyle closely associated to the origin of a novel anterior structure, the highly specialized head. While the vertebrate head mesoderm is unsegmented, the paraxial mesoderm of the earliest divergent chordate clade, the cephalochordates (amphioxus), is fully segmented in somites. We have previously shown that fibroblast growth factor signalling controls the formation of the most anterior somites in amphioxus; therefore, unravelling the fibroblast growth factor signalling downstream effectors is of crucial importance to shed light on the evolutionary origin of vertebrate head muscles. By using a comparative RNA sequencing approach and genetic functional analyses, we show that several transcription factors, such as Six1/2, Pax3/7 and Zic, act in combination to ensure the formation of three different somite populations. Interestingly, these proteins are orthologous to key regulators of trunk, and not head, muscle formation in vertebrates. Contrary to prevailing thinking, our results suggest that the vertebrate head mesoderm is of visceral and not paraxial origin and support a multistep evolutionary scenario for the appearance of the unsegmented mesoderm of the vertebrates new 'head'.
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Affiliation(s)
- Daniel Aldea
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Celine Keime
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM, U1258, CNRS, UMR7104, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Sylvain Marcellini
- Laboratory of Development and Evolution, Department of Cell Biology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France.
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France.
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Abstract
The BMP signaling pathway has been shown to be involved in different aspects of embryonic development across diverse metazoan phyla. Comparative studies on the roles of the BMP signaling pathway provide crucial insights into the evolution of the animal body plans. In this chapter, we present the general workflow on how to investigate the roles of BMP signaling pathway during amphioxus embryonic development. As amphioxus are basal invertebrate chordates, studies on the BMP signaling pathway in amphioxus could elucidate the functional evolution of BMP pathway in the chordate group. Here, we describe methods for animal husbandry, spawning induction, and manipulation of the BMP signaling pathway during embryonic development through drug inhibitors and recombinant proteins. We also introduce an efficient method of using mesh baskets to handle amphioxus embryos for fluorescence immunostaining and multicolor fluorescence in situ hybridization and to assay the effects of manipulating BMP signaling pathway during amphioxus embryogenesis.
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45
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Pinzón N, Bertrand S, Subirana L, Busseau I, Escrivá H, Seitz H. Functional lability of RNA-dependent RNA polymerases in animals. PLoS Genet 2019; 15:e1007915. [PMID: 30779744 PMCID: PMC6396948 DOI: 10.1371/journal.pgen.1007915] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/01/2019] [Accepted: 12/24/2018] [Indexed: 11/18/2022] Open
Abstract
RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordate Branchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from various Branchiostoma developmental stages. Our results show that Branchiostoma RdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways. RNA interference (RNAi) is a conserved gene regulation system in eukaryotes. In non-animal eukaryotes, it necessitates RNA-dependent RNA polymerases (“RdRPs”). Among animals, only nematodes appear to require RdRPs for RNAi. Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi. Here, we find that RdRPs are much more common in animals than previously thought, but their genes were independently lost in many lineages. Focusing on a species with RdRP genes (a cephalochordate), we found that it does not use them for RNAi. While RNAi is the only known function for eukaryotic RdRPs, our results suggest additional roles. Eukaryotic RdRPs thus have a complex evolutionary history in animals, with frequent independent losses and apparent functional diversification.
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Affiliation(s)
- Natalia Pinzón
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Isabelle Busseau
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Hector Escrivá
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hervé Seitz
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
- * E-mail:
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Yasuoka Y, Tando Y, Kubokawa K, Taira M. Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. ZOOLOGICAL LETTERS 2019; 5:27. [PMID: 31388442 PMCID: PMC6679436 DOI: 10.1186/s40851-019-0143-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/12/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated. RESULTS To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5' upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5' upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5' region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos. CONCLUSIONS On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5' upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate.
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Affiliation(s)
- Yuuri Yasuoka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yukiko Tando
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Kaoru Kubokawa
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: SIRC, Teikyo University, 2-11-1, Itabashi-ku, Tokyo, 173-8605 Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present address: Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551 Japan
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Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 2018; 564:64-70. [PMID: 30464347 PMCID: PMC6292497 DOI: 10.1038/s41586-018-0734-6] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/18/2018] [Indexed: 12/19/2022]
Abstract
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations. Genomic, epigenomic and transcriptomic data derived from the Mediterranean amphioxus (Branchiostoma lanceolatum) provide insights into the evolution of the genomic regulatory landscape of chordates.
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Shi C, Huang J, Chen S, Li G, Wang Y. Generation of two transgenic amphioxus lines using the Tol2 transposon system. J Genet Genomics 2018; 45:513-516. [PMID: 30268359 DOI: 10.1016/j.jgg.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/06/2018] [Accepted: 06/12/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jing Huang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Shixi Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361102, China
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
| | - Yiquan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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Zieger E, Garbarino G, Robert NSM, Yu JK, Croce JC, Candiani S, Schubert M. Retinoic acid signaling and neurogenic niche regulation in the developing peripheral nervous system of the cephalochordate amphioxus. Cell Mol Life Sci 2018; 75:2407-2429. [PMID: 29387904 PMCID: PMC11105557 DOI: 10.1007/s00018-017-2734-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
Abstract
The retinoic acid (RA) signaling pathway regulates axial patterning and neurogenesis in the developing central nervous system (CNS) of chordates, but little is known about its roles during peripheral nervous system (PNS) formation and about how these roles might have evolved. This study assesses the requirement of RA signaling for establishing a functional PNS in the cephalochordate amphioxus, the best available stand-in for the ancestral chordate condition. Pharmacological manipulation of RA signaling levels during embryogenesis reduces the ability of amphioxus larvae to respond to sensory stimulation and alters the number and distribution of ectodermal sensory neurons (ESNs) in a stage- and context-dependent manner. Using gene expression assays combined with immunohistochemistry, we show that this is because RA signaling specifically acts on a small population of soxb1c-expressing ESN progenitors, which form a neurogenic niche in the trunk ectoderm, to modulate ESN production during elongation of the larval body. Our findings reveal an important role for RA signaling in regulating neurogenic niche activity in the larval amphioxus PNS. Although only few studies have addressed this issue so far, comparable RA signaling functions have been reported for neurogenic niches in the CNS and in certain neurogenic placode derivatives of vertebrates. Accordingly, the here-described mechanism is likely a conserved feature of chordate embryonic and adult neural development.
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Affiliation(s)
- Elisabeth Zieger
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Greta Garbarino
- Department of Earth, Environment and Life Sciences (Dipartimento di Scienze della Terra dell'Ambiente e della Vita, DISTAV), University of Genoa, Viale Benedetto XV 5, 16132, Genoa, Italy
| | - Nicolas S M Robert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jenifer C Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Simona Candiani
- Department of Earth, Environment and Life Sciences (Dipartimento di Scienze della Terra dell'Ambiente e della Vita, DISTAV), University of Genoa, Viale Benedetto XV 5, 16132, Genoa, Italy
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France.
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50
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Favarolo MB, López SL. Notch signaling in the division of germ layers in bilaterian embryos. Mech Dev 2018; 154:122-144. [PMID: 29940277 DOI: 10.1016/j.mod.2018.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/08/2018] [Accepted: 06/18/2018] [Indexed: 01/09/2023]
Abstract
Bilaterian embryos are triploblastic organisms which develop three complete germ layers (ectoderm, mesoderm, and endoderm). While the ectoderm develops mainly from the animal hemisphere, there is diversity in the location from where the endoderm and the mesoderm arise in relation to the animal-vegetal axis, ranging from endoderm being specified between the ectoderm and mesoderm in echinoderms, and the mesoderm being specified between the ectoderm and the endoderm in vertebrates. A common feature is that part of the mesoderm segregates from an ancient bipotential endomesodermal domain. The process of segregation is noisy during the initial steps but it is gradually refined. In this review, we discuss the role of the Notch pathway in the establishment and refinement of boundaries between germ layers in bilaterians, with special focus on its interaction with the Wnt/β-catenin pathway.
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Affiliation(s)
- María Belén Favarolo
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Biología Celular y Neurociencias "Prof. E. De Robertis" (IBCN), Facultad de Medicina, Laboratorio de Embriología Molecular "Prof. Dr. Andrés E. Carrasco", Buenos Aires, Argentina
| | - Silvia L López
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Biología Celular y Neurociencias "Prof. E. De Robertis" (IBCN), Facultad de Medicina, Laboratorio de Embriología Molecular "Prof. Dr. Andrés E. Carrasco", Buenos Aires, Argentina.
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