1
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Popsuj S, Cohen L, Ward S, Lewis A, Yoshida S, Herrera RA, Cota CD, Stolfi A. CRISPR/Cas9 protocols for disrupting gene function in the non-vertebrate chordate Ciona. Integr Comp Biol 2024:icae108. [PMID: 38982335 DOI: 10.1093/icb/icae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
The evolutionary origins of chordates and their diversification into the three major subphyla of tunicates, vertebrates, and cephalochordates pose myriad questions about the genetic and developmental mechanisms underlying this radiation. Studies in non-vertebrate chordates have refined our model of what the ancestral chordate may have looked like, and have revealed the pre-vertebrate origins of key cellular and developmental traits. Work in the major tunicate laboratory model Ciona has benefitted greatly from the emergence of CRISPR/Cas9 techniques for targeted gene disruption. Here we review some of the important findings made possible by CRISPR in Ciona, and present our latest protocols and recommended practices for plasmid-based, tissue-specific CRISPR/Cas9-mediated mutagenesis.
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Affiliation(s)
- Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lindsey Cohen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Sydney Ward
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Agnes Scott College, Decatur, GA, 30030, USA
| | - Arabella Lewis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Agnes Scott College, Decatur, GA, 30030, USA
| | | | | | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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2
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Sackville MA, Gillis JA, Brauner CJ. The origins of gas exchange and ion regulation in fish gills: evidence from structure and function. J Comp Physiol B 2024:10.1007/s00360-024-01545-5. [PMID: 38530435 DOI: 10.1007/s00360-024-01545-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 03/28/2024]
Abstract
Gill function in gas exchange and ion regulation has played key roles in the evolution of fishes. In this review, we summarize data from the fields of palaeontology, developmental biology and comparative physiology for when and how the gills first acquired these functions. Data from across disciplines strongly supports a stem vertebrate origin for gas exchange structures and function at the gills with the emergence of larger, more active fishes. However, the recent discovery of putative ionocytes in extant cephalochordates and hemichordates suggests that ion regulation at gills might have originated much earlier than gas exchange, perhaps in the ciliated pharyngeal arches in the last common ancestor of deuterostomes. We hypothesize that the ancestral form of ion regulation served a filter-feeding function in the ciliated pharyngeal arches, and was later coopted in vertebrates to regulate extracellular ion and acid-base balance. We propose that future research should explore ionocyte homology and function across extant deuterostomes to test this hypothesis and others in order to determine the ancestral origins of ion regulation in fish gills.
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Affiliation(s)
| | - J Andrew Gillis
- Bay Paul Centre, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Colin J Brauner
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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3
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Pagowski V. A description of the bat star nervous system throughout larval ontogeny. Evol Dev 2024; 26:e12468. [PMID: 38108150 DOI: 10.1111/ede.12468] [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: 08/09/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Larvae represent a distinct life history stage in which animal morphology and behavior contrast strongly to adult organisms. This life history stage is a ubiquitous aspect of animal life cycles, particularly in the marine environment. In many species, the structure and function of the nervous system differ significantly between metamorphosed juveniles and larvae. However, the distribution and diversity of neural cell types in larval nervous systems remains incompletely known. Here, the expression of neurotransmitter and neuropeptide synthesis and transport genes in the bat star Patiria miniata is examined throughout larval development. This characterization of nervous system structure reveals three main neural regions with distinct but overlapping territories. These regions include a densely innervated anterior region, an enteric neural plexus, and neurons associated with the ciliary band. In the ciliary band, cholinergic cells are pervasive while dopaminergic, noradrenergic, and GABAergic cells show regional differences in their localization patterns. Furthermore, the distribution of some neural subtypes changes throughout larval development, suggesting that changes in nervous system structure align with shifting ecological priorities during different larval stages, before the development of the adult nervous system. While past work has described aspects of P. miniata larval nervous system structure, largely focusing on early developmental timepoints, this work provides a comprehensive description of neural cell type localization throughout the extensive larval period.
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Affiliation(s)
- Veronica Pagowski
- Hopkins Marine Station of Stanford University, Pacific Grove, California, USA
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4
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Gao P, Khong HY, Mao W, Chen X, Bao L, Wen X, Xu Y. Tunicates as Sources of High-Quality Nutrients and Bioactive Compounds for Food/Feed and Pharmaceutical Applications: A Review. Foods 2023; 12:3684. [PMID: 37835337 PMCID: PMC10572860 DOI: 10.3390/foods12193684] [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: 09/11/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Tunicates are widely distributed worldwide and are recognized as abundant marine bioresources with many potential applications. In this review, state-of-the-art studies on chemical composition analyses of various tunicate species were summarized; these studies confirmed that tunicates contain nutrients similar to fish (such as abundant cellulose, protein, and ω-3 fatty acid (FA)-rich lipids), indicating their practical and feasible uses for food or animal feed exploration. However, the presence of certain toxic elements should be evaluated in terms of safety. Moreover, recent studies on bioactive substances extracted from tunicates (such as toxins, sphingomyelins, and tunichromes) were analyzed, and their biological properties were comprehensively reviewed, including antimicrobial, anticancer, antioxidant, antidiabetic, and anti-inflammatory activities. In addition, some insights and prospects for the future exploration of tunicates are provided which are expected to guide their further application in the food, animal feed, and pharmaceutical industries. This review is critical to providing a new pathway for converting the common pollution issues of hydroponic nutrients into valuable marine bioresources.
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Affiliation(s)
- Pingping Gao
- Faculty of Applied Sciences, Universiti Teknologi MARA, Sarawak Branch, Kota Samarahan 94300, Malaysia
| | - Heng Yen Khong
- Faculty of Applied Sciences, Universiti Teknologi MARA, Sarawak Branch, Kota Samarahan 94300, Malaysia
| | - Wenhui Mao
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China (Y.X.)
| | - Xiaoyun Chen
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China (Y.X.)
| | - Lingxiang Bao
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China (Y.X.)
| | - Xinru Wen
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China (Y.X.)
| | - Yan Xu
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China (Y.X.)
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5
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Li Y, Dunn FS, Murdock DJE, Guo J, Rahman IA, Cong P. Cambrian stem-group ambulacrarians and the nature of the ancestral deuterostome. Curr Biol 2023:S0960-9822(23)00530-4. [PMID: 37167976 DOI: 10.1016/j.cub.2023.04.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/17/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Deuterostomes are characterized by some of the most widely divergent body plans in the animal kingdom. These striking morphological differences have hindered efforts to predict ancestral characters, with the origin and earliest evolution of the group remaining ambiguous. Several iconic Cambrian fossils have been suggested to be early deuterostomes and hence could help elucidate ancestral character states. However, their phylogenetic relationships are controversial. Here, we describe new, exceptionally preserved specimens of the discoidal metazoan Rotadiscus grandis from the early Cambrian Chengjiang biota of China. These reveal a previously unknown double spiral structure, which we interpret as a chordate-like covering to a coelomopore, located adjacent to a horseshoe-shaped tentacle complex. The tentacles differ in key aspects from those seen in lophophorates and are instead more similar to the tentacular systems of extant pterobranchs and echinoderms. Thus, Rotadiscus exhibits a chimeric combination of ambulacrarian and chordate characters. Phylogenetic analyses recover Rotadiscus and closely related fossil taxa as stem ambulacrarians, filling a significant morphological gap in the deuterostome tree of life. These results allow us to reconstruct the ancestral body plans of major clades of deuterostomes, revealing that key traits of extant forms, such as a post-anal region, gill bars, and a U-shaped gut, evolved through convergence.
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Affiliation(s)
- Yujing Li
- Yunnan Normal University, Kunming 650500, China; Yunnan Key Laboratory for Palaeobiology & MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Institute of Palaeontology, Yunnan University, Kunming 650500, China; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Frances S Dunn
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
| | - Duncan J E Murdock
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
| | - Jin Guo
- Yunnan Key Laboratory for Palaeobiology & MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Institute of Palaeontology, Yunnan University, Kunming 650500, China; Management Committee of the Chengjiang Fossil Site World Heritage, Chengjiang 652599, China
| | - Imran A Rahman
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK; The Natural History Museum, London SW7 5BD, UK.
| | - Peiyun Cong
- Yunnan Key Laboratory for Palaeobiology & MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Institute of Palaeontology, Yunnan University, Kunming 650500, China.
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6
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Adameyko I. Evolutionary origin of the neural tube in basal deuterostomes. Curr Biol 2023; 33:R319-R331. [PMID: 37098338 DOI: 10.1016/j.cub.2023.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The central nervous system (CNS) of chordates, including humans, develops as a hollow tube with ciliated walls containing cerebrospinal fluid. However, most of the animals inhabiting our planet do not use this design and rather build their centralized brains from non-epithelialized condensations of neurons called ganglia, with no traces of epithelialized tubes or liquid-containing cavities. The evolutionary origin of tube-type CNSs stays enigmatic, especially as non-epithelialized ganglionic-type nervous systems dominate the animal kingdom. Here, I discuss recent findings relevant to understanding the potential homologies and scenarios of the origin, histology and anatomy of the chordate neural tube. The nerve cords of other deuterostomes might relate to the chordate neural tube at histological, developmental and cellular levels, including the presence of radial glia, layered stratification, retained epithelial features, morphogenesis via folding and formation of a lumen filled with liquid. Recent findings inspire a new view of hypothetical evolutionary scenarios explaining the tubular epithelialized structure of the CNS. One such idea suggests that early neural tubes were key for improved directional olfaction, which was facilitated by the liquid-containing internal cavity. The later separation of the olfactory portion of the tube led to the formation of the independent olfactory and posterior tubular CNS systems in vertebrates. According to an alternative hypothesis, the thick basiepithelial nerve cords could provide deuterostome ancestors with additional biomechanical support, which later improved by turning the basiepithelial cord into a tube filled with liquid - a hydraulic skeleton.
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Affiliation(s)
- Igor Adameyko
- Center for Brain Research, Medical University of Vienna, Vienna, 1090, Austria; Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 17165, Sweden.
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7
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Nanglu K, Cole SR, Wright DF, Souto C. Worms and gills, plates and spines: the evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development. Biol Rev Camb Philos Soc 2023; 98:316-351. [PMID: 36257784 DOI: 10.1111/brv.12908] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record. Here, we review the available morphological, palaeontological, developmental, and molecular data to establish a framework for exploring the origins of this important and enigmatic group. Recent fossil discoveries strongly support a vermiform ancestor to the group Hemichordata, and a fusiform active swimmer as ancestor to Chordata. The diverse and anatomically bewildering variety of forms among the early echinoderms show evidence of both bilateral and radial symmetry. We consider four characteristics most critical for understanding the form and function of the last common ancestor to Deuterostomia: Hox gene expression patterns, larval morphology, the capacity for biomineralization, and the morphology of the pharyngeal region. We posit a deuterostome last common ancestor with a similar antero-posterior gene regulatory system to that found in modern acorn worms and cephalochordates, a simple planktonic larval form, which was later elaborated in the ambulacrarian lineage, the ability to secrete calcium minerals in a limited fashion, and a pharyngeal respiratory region composed of simple pores. This animal was likely to be motile in adult form, as opposed to the sessile origins that have been historically suggested. Recent debates regarding deuterostome monophyly as well as the wide array of deuterostome-affiliated problematica further suggest the possibility that those features were not only present in the last common ancestor of Deuterostomia, but potentially in the ur-bilaterian. The morphology and development of the early deuterostomes, therefore, underpin some of the most significant questions in the study of metazoan evolution.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Selina R Cole
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - David F Wright
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - Camilla Souto
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,School of Natural Sciences & Mathematics, Stockton University, 101 Vera King Farris Dr, Galloway, NJ, 08205, USA
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8
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Mittal V, Reid RW, Machado DJ, Mashanov V, Janies DA. EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms. BMC Genom Data 2022; 23:75. [PMID: 36274129 PMCID: PMC9590158 DOI: 10.1186/s12863-022-01090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. RESULTS The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. CONCLUSION EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
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Affiliation(s)
- Varnika Mittal
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA.
| | - Robert W Reid
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, 91 Technology Way NE, Winston-Salem, NC, 27101, USA
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
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9
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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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10
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Álvarez-Armada N, Cameron CB, Bauer JE, Rahman IA. Heterochrony and parallel evolution of echinoderm, hemichordate and cephalochordate internal bars. Proc Biol Sci 2022; 289:20220258. [PMID: 35538784 PMCID: PMC9091856 DOI: 10.1098/rspb.2022.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Deuterostomes comprise three phyla with radically different body plans. Phylogenetic bracketing of the living deuterostome clades suggests the latest common ancestor of echinoderms, hemichordates and chordates was a bilaterally symmetrical worm with pharyngeal openings, with these characters lost in echinoderms. Early fossil echinoderms with pharyngeal openings have been described, but their interpretation is highly controversial. Here, we critically evaluate the evidence for pharyngeal structures (gill bars) in the extinct stylophoran echinoderms Lagynocystis pyramidalis and Jaekelocarpus oklahomensis using virtual models based on high-resolution X-ray tomography scans of three-dimensionally preserved fossil specimens. Multivariate analyses of the size, spacing and arrangement of the internal bars in these fossils indicate they are substantially more similar to gill bars in modern enteropneust hemichordates and cephalochordates than to other internal bar-like structures in fossil blastozoan echinoderms. The close similarity between the internal bars of the stylophorans L. pyramidalis and J. oklahomensis and the gill bars of extant chordates and hemichordates is strong evidence for their homology. Differences between these internal bars and bar-like elements of the respiratory systems in blastozoans suggest these structures might have arisen through parallel evolution across deuterostomes, perhaps underpinned by a common developmental genetic mechanism.
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Affiliation(s)
| | - Christopher B Cameron
- Département de sciences biologiques, Université de Montréal C.P. 6128, Succursale Centre-ville, Montréal, QC, Canada H3C 3J7
| | - Jennifer E Bauer
- University of Michigan Museum of Paleontology, Ann Arbor, MI 48109-1085, USA
| | - Imran A Rahman
- The Natural History Museum, London SW7 5BD, UK.,Oxford University Museum of Natural History, Oxford OX1 3PW, UK
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11
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Zamora S, Rahman IA, Sumrall CD, Gibson AP, Thompson JR. Cambrian edrioasteroid reveals new mechanism for secondary reduction of the skeleton in echinoderms. Proc Biol Sci 2022; 289:20212733. [PMID: 35232240 PMCID: PMC8889179 DOI: 10.1098/rspb.2021.2733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Echinoderms are characterized by a distinctive high-magnesium calcite endoskeleton as adults, but elements of this have been drastically reduced in some groups. Herein, we describe a new pentaradial echinoderm, Yorkicystis haefneri n. gen. n. sp., which provides, to our knowledge, the oldest evidence of secondary non-mineralization of the echinoderm skeleton. This material was collected from the Cambrian Kinzers Formation in York (Pennsylvania, USA) and is dated as ca 510 Ma. Detailed morphological observations demonstrate that the ambulacra (i.e. axial region) are composed of flooring and cover plates, but the rest of the body (i.e. extraxial region) is preserved as a dark film and lacks any evidence of skeletal plating. Moreover, X-ray fluorescence analysis reveals that the axial region is elevated in iron. Based on our morphological and chemical data and on taphonomic comparisons with other fossils from the Kinzers Formation, we infer that the axial region was originally calcified, while the extraxial region was non-mineralized. Phylogenetic analyses recover Yorkicystis as an edrioasteroid, indicating that this partial absence of skeleton resulted from a secondary reduction. We hypothesize that skeletal reduction resulted from lack of expression of the skeletogenic gene regulatory network in the extraxial body wall during development. Secondary reduction of the skeleton in Yorkicystis might have allowed for greater flexibility of the body wall.
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Affiliation(s)
- Samuel Zamora
- Instituto Geológico y Minero de España (IGME-CSIC), C/Manuel Lasala, 44, 9°B, 50006 Zaragoza, Spain.,Grupo Aragosaurus-IUCA, Área de Paleontología, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Imran A Rahman
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.,Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK
| | - Colin D Sumrall
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996-1526, USA
| | - Adam P Gibson
- Department of Medical Physics and Biomedical Engineering and Institute for Sustainable Heritage, University College London, Gower Street, London WC1E 6BT, UK
| | - Jeffrey R Thompson
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.,UCL Centre for Life's Origins and Evolution, University College London, Gower Street, London WC1E 6BT, UK
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12
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Dunton AD, Göpel T, Ho DH, Burggren W. Form and Function of the Vertebrate and Invertebrate Blood-Brain Barriers. Int J Mol Sci 2021; 22:ijms222212111. [PMID: 34829989 PMCID: PMC8618301 DOI: 10.3390/ijms222212111] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 12/25/2022] Open
Abstract
The need to protect neural tissue from toxins or other substances is as old as neural tissue itself. Early recognition of this need has led to more than a century of investigation of the blood-brain barrier (BBB). Many aspects of this important neuroprotective barrier have now been well established, including its cellular architecture and barrier and transport functions. Unsurprisingly, most research has had a human orientation, using mammalian and other animal models to develop translational research findings. However, cell layers forming a barrier between vascular spaces and neural tissues are found broadly throughout the invertebrates as well as in all vertebrates. Unfortunately, previous scenarios for the evolution of the BBB typically adopt a classic, now discredited 'scala naturae' approach, which inaccurately describes a putative evolutionary progression of the mammalian BBB from simple invertebrates to mammals. In fact, BBB-like structures have evolved independently numerous times, complicating simplistic views of the evolution of the BBB as a linear process. Here, we review BBBs in their various forms in both invertebrates and vertebrates, with an emphasis on the function, evolution, and conditional relevance of popular animal models such as the fruit fly and the zebrafish to mammalian BBB research.
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Affiliation(s)
- Alicia D. Dunton
- Developmental Integrative Biology Group, Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; (T.G.); (W.B.)
- Correspondence:
| | - Torben Göpel
- Developmental Integrative Biology Group, Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; (T.G.); (W.B.)
| | - Dao H. Ho
- Department of Clinical Investigation, Tripler Army Medical Center, Honolulu, HI 96859, USA;
| | - Warren Burggren
- Developmental Integrative Biology Group, Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; (T.G.); (W.B.)
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13
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Matrix Metalloproteinases and Tissue Inhibitors of Metalloproteinases in Echinoderms: Structure and Possible Functions. Cells 2021; 10:cells10092331. [PMID: 34571980 PMCID: PMC8467561 DOI: 10.3390/cells10092331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/13/2023] Open
Abstract
Echinoderms are one of the most ancient groups of invertebrates. The study of their genomes has made it possible to conclude that these animals have a wide variety of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). The phylogenetic analysis shows that the MMPs and TIMPs underwent repeated duplication and active divergence after the separation of Ambulacraria (Echinodermata+Hemichordata) from the Chordata. In this regard the homology of the proteinases and their inhibitors between these groups of animals cannot be established. However, the MMPs of echinoderms and vertebrates have a similar domain structure. Echinoderm proteinases can be structurally divided into three groups-archetypal MMPs, matrilysins, and furin-activatable MMPs. Gelatinases homologous to those of vertebrates were not found in genomes of studied species and are probably absent in echinoderms. The MMPs of echinoderms possess lytic activity toward collagen type I and gelatin and play an important role in the mechanisms of development, asexual reproduction and regeneration. Echinoderms have a large number of genes encoding TIMPs and TIMP-like proteins. TIMPs of these animals, with a few exceptions, have a structure typical for this class of proteins. They contain an NTR domain and 10-12 conservatively located cysteine residues. Repeated duplication and divergence of TIMP genes of echinoderms was probably associated with an increase in the functional importance of the proteins encoded by them in the physiology of the animals.
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Dieris M, Kowatschew D, Korsching SI. Olfactory function in the trace amine-associated receptor family (TAARs) evolved twice independently. Sci Rep 2021; 11:7807. [PMID: 33833329 PMCID: PMC8032801 DOI: 10.1038/s41598-021-87236-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Olfactory receptor families have arisen independently several times during evolution. The origin of taar genes, one of the four major vertebrate olfactory receptor families, is disputed. We performed a phylogenetic analysis making use of 96 recently available genomes, and report that olfactory functionality has arisen twice independently within the TAAR family, once in jawed and once in jawless fish. In lamprey, an ancestral gene expanded to generate a large family of olfactory receptors, while the sister gene in jawed vertebrates did not expand and is not expressed in olfactory sensory neurons. Both clades do not exhibit the defining TAAR motif, and we suggest naming them taar-like receptors (tarl). We have identified the evolutionary origin of both taar and tarl genes in a duplication of the serotonergic receptor 4 that occurred in the most recent common ancestor of vertebrates. We infer two ancestral genes in bony fish (TAAR12, TAAR13) which gave rise to the complete repertoire of mammalian olfactory taar genes and to class II of the taar repertoire of teleost fish. We follow their evolution in seventy-one bony fish genomes and report a high evolutionary dynamic, with many late gene birth events and both early and late gene death events.
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Affiliation(s)
- Milan Dieris
- Institute for Genetics, University At Cologne, Zülpicher Str. 47A, 50674, Cologne, Germany
| | - Daniel Kowatschew
- Institute for Genetics, University At Cologne, Zülpicher Str. 47A, 50674, Cologne, Germany
| | - Sigrun I Korsching
- Institute for Genetics, University At Cologne, Zülpicher Str. 47A, 50674, Cologne, Germany.
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15
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Fodor A, Liu J, Turner L, Swalla BJ. Transitional chordates and vertebrate origins: Tunicates. Curr Top Dev Biol 2021; 141:149-171. [DOI: 10.1016/bs.ctdb.2020.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Nanglu K, Caron JB, Cameron CB. Cambrian Tentaculate Worms and the Origin of the Hemichordate Body Plan. Curr Biol 2020; 30:4238-4244.e1. [PMID: 32857969 DOI: 10.1016/j.cub.2020.07.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/15/2020] [Accepted: 07/27/2020] [Indexed: 11/30/2022]
Abstract
Hemichordate relationships remain contentious due to conflicting molecular results [1-7] and the high degree of morphological disparity between the two hemichordate classes, Enteropneusta and Pterobranchia [8-11]. Additionally, hemichordates have a poor fossil record outside of the Cambrian, with the exception of the collagenous tubes of the pterobranchs (which include graptolites). By the middle Cambrian, tube-dwelling colonial pterobranchs [12, 13] and tube-dwelling enteropneusts coexisted [14, 15], supporting the origin of the hemichordate body plan earlier in the Cambrian without clarifying the morphology of their last common ancestor. Here, we describe a new hemichordate, Gyaltsenglossus senis, based on 33 specimens from the 506-million-year-old Burgess Shale (Odaray Mountain, British Columbia). G. senis has a unique combination of soft anatomical characters found in both extant classes of hemichordates, namely a trimeric-vermiform body plan with an elongate proboscis and six feeding arms with tentacles. The trunk possesses a long through-gut and terminates with a bulbous structure potentially used for locomotion and/or as a temporary anchor. There is no evidence of a secreted tube. Our phylogenetic analyses retrieve this new taxon as a stem-group hemichordate, supporting the hypothesis that a vermiform body plan preceded both tube building and colonial ecologies. This new taxon suggests that a bimodal feeding ecology using tentacles to filter feed and a proboscis to deposit feed may be plesiomorphic in hemichordates. Finally, the presence of a muscular, post-anal attachment structure in all known Cambrian hemichordates supports this feature as an additional hemichordate plesiomorphy critical for understanding early hemichordate evolution.
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Affiliation(s)
- Karma Nanglu
- Department of Paleobiology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560.
| | - Jean-Bernard Caron
- Department of Natural History, Palaeobiology section, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2J7, Canada; Department of Earth Sciences, University of Toronto, Toronto, ON M5S 3B1, Canada
| | - Christopher B Cameron
- Université de Montréal, Département de sciences biologiques, Montréal, QC H2V 2S9, Canada
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17
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Song G, Delroisse J, Schoenaers D, Kim H, Nguyen TC, Horbelt N, Leclère P, Hwang DS, Harrington MJ, Flammang P. Structure and composition of the tunic in the sea pineapple Halocynthia roretzi: A complex cellulosic composite biomaterial. Acta Biomater 2020; 111:290-301. [PMID: 32438110 DOI: 10.1016/j.actbio.2020.04.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 01/01/2023]
Abstract
Biological organisms produce high-performance composite materials, such as bone, wood and insect cuticle, which provide inspiration for the design of novel materials. Ascidians (sea squirts) produce an organic exoskeleton, known as a tunic, which has been studied quite extensively in several species. However, currently, there are still gaps in our knowledge about the detailed structure and composition of this cellulosic biocomposite. Here, we investigate the composition and hierarchical structure of the tough tunic from the species Halocynthia roretzi, through a cross-disciplinary approach combining traditional histology, immunohistochemistry, vibrational spectroscopy, X-ray diffraction, and atomic force and electron microscopies. The picture emerging is that the tunic of H. roretzi is a hierarchically-structured composite of cellulose and proteins with several compositionally and structurally distinct zones. At the surface is a thin sclerotized cuticular layer with elevated composition of protein containing halogenated amino acids and cross-linked via dityrosine linkages. The fibrous layer makes up the bulk of the tunic and is comprised primarily of helicoidally-ordered crystalline cellulose fibres with a lower protein content. The subcuticular zone directly beneath the surface contains much less organized cellulose fibres. Given current efforts to utilize biorenewable cellulose sources for the sustainable production of bio-inspired composites, these insights establish the tunic of H. roretzi as an exciting new archetype for extracting relevant design principles. STATEMENT OF SIGNIFICANCE: Tunicates are the only animals able to produce cellulose. They use this structural polysaccharide to build an exoskeleton called a tunic. Here, we investigate the composition and hierarchical structure of the tough tunic from the sea pineapple Halocynthia roretzi through a multiscale cross-disciplinary approach. The tunic of this species is a composite of cellulose and proteins with two distinct layers. At the surface is a thin sclerotized cuticular layer with a higher protein content containing halogenated amino acids and cross-linked via dityrosine linkages. The fibrous layer makes up the bulk of the tunic and is comprised of well-ordered cellulose fibres with a lower protein content. Given current efforts to utilize cellulose to produce advanced materials, the tunic of the sea pineapple provides a striking model for the design of bio-inspired cellulosic composites.
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Affiliation(s)
- Geonho Song
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, 23 Place du Parc, 7000 Mons, Belgium
| | - Dorian Schoenaers
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, 23 Place du Parc, 7000 Mons, Belgium
| | - Hyungbin Kim
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673
| | - Thai Cuong Nguyen
- Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, 23 Place du Parc, 7000 Mons, Belgium
| | - Nils Horbelt
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany
| | - Philippe Leclère
- Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, 23 Place du Parc, 7000 Mons, Belgium
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673.
| | - Matthew J Harrington
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Research Campus Golm, 14424 Potsdam, Germany; Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, 23 Place du Parc, 7000 Mons, Belgium.
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18
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On the origin of vertebrate body plan: Insights from the endoderm using the hourglass model. Gene Expr Patterns 2020; 37:119125. [PMID: 32599288 DOI: 10.1016/j.gep.2020.119125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/25/2020] [Accepted: 06/21/2020] [Indexed: 11/23/2022]
Abstract
The vertebrate body plan is thought to be derived during the early Cambrian from a worm-like chordate ancestor. While all three germ layers were clearly involved in this innovation, the role of the endoderm remains elusive. According to the hourglass model, the optimal window for investigating the evolution of vertebrate endoderm-derived structures during cephalochordate development is from the Spemann's organizer stage to the opening of the mouth (Stages 1-7, described herein). Regulatory gene expression, examined during these stages, illustrate that the cephalochordate endoderm is patterned into 12 organ primordia. Early vertebrates inherited at least a portion of 6 of these primordia, while the remainder were lost. Of those that were preserved, we demonstrate that the vertebrate symmetric mouth was built on a vestige of the anterior pre-oral pit, that the pre-existing pharyngeal pouch in this chordate ancestor laid the foundation for the new neural crest cell (NCC)-derived vertebrate-type pharyngeal arches, that the thyroid evolved from the posterior endostyle primordim, that the pancreas was derived from the Pdx1-expressing diverticulum primordium, and the small and large intestines originated with the Cdx1-expressing hindgut rudiments. This investigation uncovers the evolutionary foundations of vertebrate endoderm-derived structures, and demonstrates that the number of organ primordia were reduced during evolution.
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19
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Braun K, Leubner F, Stach T. Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea. Cladistics 2020; 36:259-300. [PMID: 34618973 DOI: 10.1111/cla.12405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. "Thaliacea" is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic "Ascidiacea". Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.
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Affiliation(s)
- Katrin Braun
- Vergleichende Zoologie, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, Haus 2, 10115, Berlin, Germany
| | - Fanny Leubner
- Animal Evolution and Biodiversity, J-F-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Thomas Stach
- Molekulare Parasitologie, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, Haus 14, 10115, Berlin, Germany
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20
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Kipryushina YO, Yakovlev KV. Maternal control of early patterning in sea urchin embryos. Differentiation 2020; 113:28-37. [PMID: 32371341 DOI: 10.1016/j.diff.2020.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
Sea urchin development has been studied extensively for more than a century and considered regulative since the first experimental evidence. Further investigations have repeatedly supported this standpoint by revealing the presence of inductive mechanisms that alter cell fate decisions at early cleavage stages and flexibility of development in response to environmental conditions. Some features indicate that sea urchin development is not completely regulative, but actually includes determinative events. In 16-cell embryos, mesomeres and macromeres represent multipotency, while the cell fate of most vegetal micromeres is restricted. It is known that the mature sea urchin eggs are polarized by the asymmetrical distribution of some maternal mRNAs and proteins. Spatially-distributed maternal factors are necessary for the orientation of the primary animal-vegetal axis, which is established by both maternal and zygotic mechanisms later in development. The secondary dorsal-ventral axis is conditionally specified later in development. Dorsal-ventral polarity is very liable during the early cleavages, though more recent data argue that its direction may be oriented by maternal asymmetry. In this review, we focus on the role of maternal factors in initial embryonic patterning during the first cleavages of sea urchin embryos before activation of the embryonic genome.
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Affiliation(s)
- Yulia O Kipryushina
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky St. 17, 690041, Vladivostok, Russia
| | - Konstantin V Yakovlev
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky St. 17, 690041, Vladivostok, Russia; Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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21
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Dolmatov IY, Kalacheva NV, Mekhova ES, Frolova LT. Autotomy and regeneration of the visceral mass in feather stars. ZOOMORPHOLOGY 2020. [DOI: 10.1007/s00435-020-00483-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Baker ME. Steroid receptors and vertebrate evolution. Mol Cell Endocrinol 2019; 496:110526. [PMID: 31376417 DOI: 10.1016/j.mce.2019.110526] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/22/2022]
Abstract
Considering that life on earth evolved about 3.7 billion years ago, vertebrates are young, appearing in the fossil record during the Cambrian explosion about 542 to 515 million years ago. Results from sequence analyses of genomes from bacteria, yeast, plants, invertebrates and vertebrates indicate that receptors for adrenal steroids (aldosterone, cortisol), and sex steroids (estrogen, progesterone, testosterone) also are young, with an estrogen receptor and a 3-ketosteroid receptor first appearing in basal chordates (cephalochordates: amphioxus), which are close ancestors of vertebrates. Duplication and divergence of the 3-ketosteroid receptor yielded an ancestral progesterone receptor and an ancestral corticoid receptor, the common ancestor of the glucocorticoid and mineralocorticoid receptors, in jawless vertebrates (cyclostomes: lampreys, hagfish). This was followed by evolution of an androgen receptor, distinct glucocorticoid and mineralocorticoid receptors and estrogen receptor-α and -β in cartilaginous fishes (Chondrichthyes: sharks). Further evolution of mineralocorticoid signaling occurred with the evolution of aldosterone synthase in lungfish, a forerunner of terrestrial vertebrates. Adrenal and sex steroid receptors are not found in echinoderms and hemichordates, which are ancestors in the lineage of cephalochordates and vertebrates. The evolution of steroid receptors at key nodes in the evolution of vertebrates, in which steroid receptors act as master switches to regulate differentiation, development, reproduction, immune responses, electrolyte homeostasis and stress responses, suggests an important role for steroid receptors in the evolutionary success of vertebrates, considering that the human genome contains about 22,000 genes, which is not much larger than genomes of invertebrates, such as Caenorhabditis elegans (~18,000 genes) and Drosophila (~14,000 genes).
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Affiliation(s)
- Michael E Baker
- Division of Nephrology-Hypertension, Department of Medicine, 0693, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0693, USA.
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23
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He C, Han T, Liao X, Zhou Y, Wang X, Guan R, Tian T, Li Y, Bi C, Lu N, He Z, Hu B, Zhou Q, Hu Y, Lu Z, Chen JY. Phagocytic intracellular digestion in amphioxus ( Branchiostoma). Proc Biol Sci 2019; 285:rspb.2018.0438. [PMID: 29875301 PMCID: PMC6015868 DOI: 10.1098/rspb.2018.0438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/11/2018] [Indexed: 01/10/2023] Open
Abstract
The digestive methods employed by amphioxus (Branchiostoma)—both intracellular phagocytic digestion and extracellular digestion—have been discussed since 1937. Recent studies also show that epithelial cells lining the Branchiostoma digestive tract can express many immune genes. Here, in Branchiostoma belcheri, using a special tissue fixation method, we show that some epithelial cells, especially those lining the large diverticulum protruding from the gut tube, phagocytize food particles directly, and Branchiostoma can rely on this kind of phagocytic intracellular digestion to obtain energy throughout all stages of its life. Gene expression profiles suggest that diverticulum epithelial cells have functional features of both digestive cells and phagocytes. In starved Branchiostoma, these cells accumulate endogenous digestive and hydrolytic enzymes, whereas, when sated, they express many kinds of immune genes in response to stimulation by phagocytized food particles. We also found that the distal hindgut epithelium can phagocytize food particles, but not as many. These results illustrate phagocytic intercellular digestion in Branchiostoma, explain why Branchiostoma digestive tract epithelial cells express typical immune genes and suggest that the main physiological function of the Branchiostoma diverticulum is different from that of the vertebrate liver.
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Affiliation(s)
- Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Xin Liao
- Nanjing Institute of Paleontology and Geology, Nanjing, People's Republic of China.,Guangxi Mangrove Research Center, Beihai, Guangxi, People's Republic of China
| | - Yuxin Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Xiuqiang Wang
- Beihai Marine Science and Economy Park, Beihai, Guangxi, People's Republic of China
| | - Rui Guan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Tian Tian
- Department of Neurobiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yixin Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Changwei Bi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Ziyi He
- Electron Microscopy Research Center, School of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bing Hu
- Electron Microscopy Research Center, School of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Qiang Zhou
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yue Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
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24
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Topper TP, Guo J, Clausen S, Skovsted CB, Zhang Z. A stem group echinoderm from the basal Cambrian of China and the origins of Ambulacraria. Nat Commun 2019; 10:1366. [PMID: 30911013 PMCID: PMC6433856 DOI: 10.1038/s41467-019-09059-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 02/15/2019] [Indexed: 11/21/2022] Open
Abstract
Deuterostomes are a morphologically disparate clade, encompassing the chordates (including vertebrates), the hemichordates (the vermiform enteropneusts and the colonial tube-dwelling pterobranchs) and the echinoderms (including starfish). Although deuterostomes are considered monophyletic, the inter-relationships between the three clades remain highly contentious. Here we report, Yanjiahella biscarpa, a bilaterally symmetrical, solitary metazoan from the early Cambrian (Fortunian) of China with a characteristic echinoderm-like plated theca, a muscular stalk reminiscent of the hemichordates and a pair of feeding appendages. Our phylogenetic analysis indicates that Y. biscarpa is a stem-echinoderm and not only is this species the oldest and most basal echinoderm, but it also predates all known hemichordates, and is among the earliest deuterostomes. This taxon confirms that echinoderms acquired plating before pentaradial symmetry and that their history is rooted in bilateral forms. Yanjiahella biscarpa shares morphological similarities with both enteropneusts and echinoderms, indicating that the enteropneust body plan is ancestral within hemichordates. The early evolution of the deuterostomes is not well resolved. Here, Topper and colleagues investigate the early Cambrian metazoan Yanjiahella biscarpa, concluding that it is a stem echinoderm, is among the oldest known deuterstomes, and supports an ancestral enteropneust body plan in hemichordates.
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Affiliation(s)
- Timothy P Topper
- Shaanxi Key Laboratory of Early Life and Environments, State Key Laboratory of Continental Dynamics and Department of Geology, Northwest University, 710069, Xi'an, China. .,Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 104 05, Stockholm, Sweden. .,Department of Earth Sciences, Durham University, Durham, DH1 3LE, UK.
| | - Junfeng Guo
- School of Earth Science and Resources, Key Laboratory for the study of Focused Magmatism and Giant Ore Deposits, MLR, Chang'an University, 710054, Xi'an, China
| | | | - Christian B Skovsted
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 104 05, Stockholm, Sweden
| | - Zhifei Zhang
- Shaanxi Key Laboratory of Early Life and Environments, State Key Laboratory of Continental Dynamics and Department of Geology, Northwest University, 710069, Xi'an, China
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25
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Inoue J, Satoh N. Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution. Mol Biol Evol 2019; 35:914-924. [PMID: 29319812 PMCID: PMC5888912 DOI: 10.1093/molbev/msy002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fish-like larvae were foundational to the chordate body plan, given the basal placement of free-living lancelets. That body plan probably made it possible for chordate ancestors to swim by beating a tail formed of notochord and bilateral paraxial muscles. In order to investigate the molecular genetic basis of the origin and evolution of paraxial muscle, we deduced the evolutionary histories of 16 contractile protein genes from paraxial muscle, based on genomic data from all five deuterostome lineages, using a newly developed orthology identification pipeline and a species tree. As a result, we found that more than twice as many orthologs of paraxial muscle genes are present in chordates, as in nonchordate deuterostomes (ambulacrarians). Orthologs of paraxial-type actin and troponin C genes are absent in ambulacrarians and most paraxial muscle protein isoforms diversified via gene duplications that occurred in each chordate lineage. Analyses of genes with known expression sites indicated that some isoforms were reutilized in specific muscles of nonvertebrate chordates via gene duplications. As orthologs of most paraxial muscle genes were present in ambulacrarians, in addition to expression patterns of related genes and functions of the two protein isoforms, regulatory mechanisms of muscle genes should also be considered in future studies of the origin of paraxial muscle.
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Affiliation(s)
- Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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Boyko AV, Girich AS, Eliseikina MG, Maslennikov SI, Dolmatov IY. Reference assembly and gene expression analysis of Apostichopus japonicus larval development. Sci Rep 2019; 9:1131. [PMID: 30718912 PMCID: PMC6362246 DOI: 10.1038/s41598-018-37755-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/13/2018] [Indexed: 01/31/2023] Open
Abstract
The transcriptome of the holothurian Apostichopus japonicus was sequenced at four developmental stages-blastula, gastrula, auricularia, pentactula-on an Illumina sequencer. Based on our RNA-seq data and the paired-end reads from 16 libraries obtained by other researchers earlier, we have achieved the currently most complete transcriptome assembly for A. japonicus with the best basic statistical parameters. An analysis of the obtained transcriptome has revealed 174 differentially expressed transcription factors, as well as stage-specific transcription factors that are most promising for further study. In addition, a total of 1,174,999 high-quality single nucleotide polymorphisms have been identified, including 58,932 indels. A GO enrichment analysis of contigs containing polymorphic loci shows the predominance of GO terms associated with immune response. The data obtained by us provide an additional basis for a deeper study of the mechanisms of the planktotrophic-type development in holothurians and can be used in commercial sea cucumber breeding programs.
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Affiliation(s)
- Alexey V Boyko
- National Scientific Centre of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo 17, Vladivostok, 690041, Russia.
- Far Eastern Federal University, Sukhanova 8, Vladivostok, 690950, Russia.
| | - Alexander S Girich
- National Scientific Centre of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo 17, Vladivostok, 690041, Russia
- Far Eastern Federal University, Sukhanova 8, Vladivostok, 690950, Russia
| | - Marina G Eliseikina
- National Scientific Centre of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo 17, Vladivostok, 690041, Russia
| | - Sergey I Maslennikov
- National Scientific Centre of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo 17, Vladivostok, 690041, Russia
- Far Eastern Federal University, Sukhanova 8, Vladivostok, 690950, Russia
| | - Igor Yu Dolmatov
- National Scientific Centre of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo 17, Vladivostok, 690041, Russia
- Far Eastern Federal University, Sukhanova 8, Vladivostok, 690950, Russia
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Li Y, Kocot KM, Tassia MG, Cannon JT, Bernt M, Halanych KM. Mitogenomics Reveals a Novel Genetic Code in Hemichordata. Genome Biol Evol 2019; 11:29-40. [PMID: 30476024 PMCID: PMC6319601 DOI: 10.1093/gbe/evy254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 01/26/2023] Open
Abstract
The diverse array of codon reassignments demonstrate that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced, hindering our understanding of mitochondrial genome evolution within Deuterostomia. In this study, we sequenced four mitochondrial genomes and two transcriptomes, including representatives of both major hemichordate lineages and analyzed together with public available data. Contrary to the current understanding of the mitochondrial genetic code in hemichordates, our comparative analyses suggest that UAA encodes Tyr instead of a "Stop" codon in the pterobranch lineage Cephalodiscidae. We also predict that AAA encodes Lys in pterobranch and enteropneust mitochondrial genomes, contradicting the previous assumption that hemichordates share the same genetic code with echinoderms for which AAA encodes Asn. Thus, we propose a new mitochondrial genetic code for Cephalodiscus and a revised code for enteropneusts. Moreover, our phylogenetic analyses are largely consistent with previous phylogenomic studies. The only exception is the phylogenetic position of the enteropneust Stereobalanus, whose placement as sister to all other described enteropneusts. With broader taxonomic sampling, we provide evidence that evolution of mitochondrial gene order and genetic codes in Hemichordata are more dynamic than previously thought and these findings provide insights into mitochondrial genome evolution within this clade.
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Affiliation(s)
- Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Kevin M Kocot
- Department of Biological Sciences & Alabama Museum of Natural History, The University of Alabama
| | - Michael G Tassia
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Johanna T Cannon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara
| | - Matthias Bernt
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
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Braun K, Stach T. Morphology and evolution of the central nervous system in adult tunicates. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katrin Braun
- Institut für Biologie, Vergleichende Zoologie Humboldt‐Universität zu Berlin Berlin Germany
| | - Thomas Stach
- Institut für Biologie, Molekulare Parasitologie Humboldt‐Universität zu Berlin Berlin Germany
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Lynagh T, Mikhaleva Y, Colding JM, Glover JC, Pless SA. Acid-sensing ion channels emerged over 600 Mya and are conserved throughout the deuterostomes. Proc Natl Acad Sci U S A 2018; 115:8430-8435. [PMID: 30061402 PMCID: PMC6099870 DOI: 10.1073/pnas.1806614115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are proton-gated ion channels broadly expressed in the vertebrate nervous system, converting decreased extracellular pH into excitatory sodium current. ASICs were previously thought to be a vertebrate-specific branch of the DEG/ENaC family, a broadly conserved but functionally diverse family of channels. Here, we provide phylogenetic and experimental evidence that ASICs are conserved throughout deuterostome animals, showing that ASICs evolved over 600 million years ago. We also provide evidence of ASIC expression in the central nervous system of the tunicate, Oikopleura dioica Furthermore, by comparing broadly related ASICs, we identify key molecular determinants of proton sensitivity and establish that proton sensitivity of the ASIC4 isoform was lost in the mammalian lineage. Taken together, these results suggest that contributions of ASICs to neuronal function may also be conserved broadly in numerous animal phyla.
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Affiliation(s)
- Timothy Lynagh
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Yana Mikhaleva
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway
| | - Janne M Colding
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Joel C Glover
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway
- Department of Molecular Medicine, University of Oslo, 0372 Oslo, Norway
| | - Stephan A Pless
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, 2100 Copenhagen, Denmark
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Fan TP, Ting HC, Yu JK, Su YH. Reiterative use of FGF signaling in mesoderm development during embryogenesis and metamorphosis in the hemichordate Ptychodera flava. BMC Evol Biol 2018; 18:120. [PMID: 30075704 PMCID: PMC6091094 DOI: 10.1186/s12862-018-1235-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/26/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Mesoderm is generally considered to be a germ layer that is unique to Bilateria, and it develops into diverse tissues, including muscle, and in the case of vertebrates, the skeleton and notochord. Studies on various deuterostome animals have demonstrated that fibroblast growth factor (FGF) signaling is required for the formation of many mesodermal structures, such as vertebrate somites, from which muscles are differentiated, and muscles in sea urchin embryos, suggesting an ancient role of FGF signaling in muscle development. However, the formation of trunk muscles in invertebrate chordates is FGF-independent, leading to ambiguity about this ancient role in deuterostomes. To further understand the role of FGF signaling during deuterostome evolution, we investigated the development of mesodermal structures during embryogenesis and metamorphosis in Ptychodera flava, an indirect-developing hemichordate that has larval morphology similar to echinoderms and adult body features that are similar to chordates. RESULTS Here we show that genes encoding FGF ligands, FGF receptors and transcription factors that are known to be involved in mesoderm formation and myogenesis are expressed dynamically during embryogenesis and metamorphosis. FGF signaling at the early gastrula stage is required for the specification of the mesodermal cell fate in P. flava. The mesoderm cells are then differentiated stepwise into the hydroporic canal, the pharyngeal muscle and the muscle string; formation of the last two muscular structures are controlled by FGF signaling. Moreover, augmentation of FGF signaling during metamorphosis accelerated the process, facilitating the transformation from cilia-driven swimming larvae into muscle-driven worm-like juveniles. CONCLUSIONS Our data show that FGF signaling is required for mesoderm induction and myogenesis in the P. flava embryo, and it is reiteratively used for the morphological transition during metamorphosis. The dependence of muscle development on FGF signaling in both planktonic larvae and sand-burrowing worms supports its ancestral role in deuterostomes.
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Affiliation(s)
- Tzu-Pei Fan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsiu-Chi Ting
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Yi-Hsien Su
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan. .,Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan.
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Gonzalez P, Jiang JZ, Lowe CJ. The development and metamorphosis of the indirect developing acorn worm Schizocardium californicum (Enteropneusta: Spengelidae). Front Zool 2018; 15:26. [PMID: 29977319 PMCID: PMC6011522 DOI: 10.1186/s12983-018-0270-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/30/2018] [Indexed: 01/08/2023] Open
Abstract
Background Enteropneusts are benthic marine invertebrates that belong to the deuterostome phylum Hemichordata. The two main clades of enteropneusts are defined by differences in early life history strategies. In the Spengelidae and Ptychoderidae, development is indirect via a planktotrophic tornaria larva. In contrast, development in the Harrimanidae is direct without an intervening larval life history stage. Most molecular studies in the development and evolution of the enteropneust adult body plan have been carried out in the harrimanid Saccoglossus kowalevskii. In order to compare these two developmental strategies, we have selected the spengelid enteropneust Schizocardium californicum as a suitable indirect developing species for molecular developmental studies. Here we describe the methods for adult collecting, spawning and larval rearing in Schizocardium californicum, and describe embryogenesis, larval development, and metamorphosis, using light microscopy, immunocytochemistry and confocal microscopy. Results Adult reproductive individuals can be collected intertidally and almost year-round. Spawning can be triggered by heat shock and large numbers of larvae can be reared through metamorphosis under laboratory conditions. Gastrulation begins at 17 h post-fertilization (hpf) and embryos hatch at 26 hpf as ciliated gastrulae. At 3 days post-fertilization (dpf), the tornaria has a circumoral ciliary band, mouth, tripartite digestive tract, protocoel, larval muscles and a simple serotonergic nervous system. The telotroch develops at 5 dpf. In the course of 60 days, the serotonergic nervous system becomes more elaborate, the posterior coeloms develop, and the length of the circumoral ciliary band increases. At the end of the larval stage, larval muscles disappear, gill slits form, and adult muscles develop. Metamorphosis occurs spontaneously when the larva reaches its maximal size (ca. 3 mm), and involves loss and reorganization of larval structures (muscles, nervous system, digestive tract), as well as development of adult structures (adult muscles, tripartite body organization). Conclusions This study will enable future research in S. californicum to address long standing questions related to the evolution of axial patterning mechanisms, germ layer induction, neurogenesis and neural patterning, the mechanisms of metamorphosis, the relationships between larval and adult body plans, and the evolution of metazoan larval forms.
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Affiliation(s)
- Paul Gonzalez
- 1Hopkins Marine Station, Department of Biology, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950 USA
| | - Jeffrey Z Jiang
- 2Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104 USA
| | - Christopher J Lowe
- 1Hopkins Marine Station, Department of Biology, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950 USA
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Wiseman E, Bates L, Dubé A, Carroll DJ. Starfish as a Model System for Analyzing Signal Transduction During Fertilization. Results Probl Cell Differ 2018; 65:49-67. [PMID: 30083915 DOI: 10.1007/978-3-319-92486-1_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
The starfish oocyte and egg offer advantages for use as a model system for signal transduction research. Some of these have been recognized for over a century, including the ease of procuring gametes, in vitro fertilization, and culturing the embryos. New advances, particularly in genomics, have also opened up opportunities for the use of these animals. In this chapter, we give a few examples of the historical use of the starfish for research in cell biology and then describe some new areas in which we believe the starfish can contribute to our understanding of signal transduction-particularly in fertilization.
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Affiliation(s)
- Emily Wiseman
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Lauren Bates
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Altair Dubé
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - David J Carroll
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA.
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The sea cucumber genome provides insights into morphological evolution and visceral regeneration. PLoS Biol 2017; 15:e2003790. [PMID: 29023486 PMCID: PMC5638244 DOI: 10.1371/journal.pbio.2003790] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/11/2017] [Indexed: 11/25/2022] Open
Abstract
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs. Echinoderms, ubiquitous in the marine environment, are important from evolutionary, ecological, and socioeconomic perspectives. Together with chordates and hemichordates, they form the deuterostome clade, making them a crucial node in the study of chordate ancestry. Within echinoderms, class Holothuroidea is unique; its members (the sea cucumbers) display remarkable regenerative abilities and play key roles as sediment bioturbators and symbiotic hosts, and many are prized in the seafood and pharmaceutical industries. The sea cucumber genome therefore has the potential to significantly contribute to our understanding of important evolutionary and biological processes and help enhance aquaculture programs. Here we present a high-quality genome sequence for the economically important species Apostichopus japonicus. Through comparative analyses, we identified 763 echinoderm-specific gene families enriched in genes encoding membrane proteins, ion channels, and signal transduction proteins. Marker genes associated with the notochord and gill slits were also found, providing valuable insight into the origin of chordates. The reduced number and low expression levels of biomineralization genes reflect the skeletal degeneration seen in sea cucumbers. Importantly, 2 gene families appeared to be expanded in A. japonicus and may play crucial roles in its heightened regenerative potential. Together, findings from the sea cucumber genome provide important and novel insights into echinoderm and deuterostome biology.
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Franchi N, Ballarin L. Immunity in Protochordates: The Tunicate Perspective. Front Immunol 2017; 8:674. [PMID: 28649250 PMCID: PMC5465252 DOI: 10.3389/fimmu.2017.00674] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/24/2017] [Indexed: 11/13/2022] Open
Abstract
Tunicates are the closest relatives of vertebrates, and their peculiar phylogenetic position explains the increasing interest toward tunicate immunobiology. They are filter-feeding organisms, and this greatly influences their defense strategies. The majority of the studies on tunicate immunity were carried out in ascidians. The tunic acts as a first barrier against pathogens and parasites. In addition, the oral siphon and the pharynx represent two major, highly vascularized, immune organs, where circulating hemocytes can sense non-self material and trigger immune responses that, usually, lead to inflammation and phagocytosis. Inflammation involves the recruitment of circulating cytotoxic, phenoloxidase (PO)-containing cells in the infected area, where they degranulate as a consequence of non-self recognition and release cytokines, complement factors, and the enzyme PO. The latter, acting on polyphenol substrata, produces cytotoxic quinones, which polymerize to melanin, and reactive oxygen species, which induce oxidative stress. Both the alternative and the lectin pathways of complement activation converge to activate C3: C3a and C3b are involved in the recruitment of hemocytes and in the opsonization of foreign materials, respectively. The interaction of circulating professional phagocytes with potentially pathogenic foreign material can be direct or mediated by opsonins, either complement dependent or complement independent. Together with cytotoxic cells, phagocytes are active in the encapsulation of large materials. Cells involved in immune responses, collectively called immunocytes, represent a large fraction of hemocytes, and the presence of a cross talk between cytotoxic cells and phagocytes, mediated by secreted humoral factors, was reported. Lectins play a pivotal role as pattern-recognition receptors and opsonizing agents. In addition, variable region-containing chitin-binding proteins, identified in the solitary ascidian Ciona intestinalis, control the settlement and colonization of bacteria in the gut.
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Affiliation(s)
- Nicola Franchi
- Department of Biology, University of Padova, Padova, Italy
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Gillis JA, Tidswell ORA. The Origin of Vertebrate Gills. Curr Biol 2017; 27:729-732. [PMID: 28190727 PMCID: PMC5344677 DOI: 10.1016/j.cub.2017.01.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 11/27/2022]
Abstract
Pharyngeal gills are a fundamental feature of the vertebrate body plan [1]. However, the evolutionary history of vertebrate gills has been the subject of a long-standing controversy [2-8]. It is thought that gills evolved independently in cyclostomes (jawless vertebrates-lampreys and hagfish) and gnathostomes (jawed vertebrates-cartilaginous and bony fishes), based on their distinct embryonic origins: the gills of cyclostomes derive from endoderm [9-12], while gnathostome gills were classically thought to derive from ectoderm [10, 13]. Here, we demonstrate by cell lineage tracing that the gills of a cartilaginous fish, the little skate (Leucoraja erinacea), are in fact endodermally derived. This finding supports the homology of gills in cyclostomes and gnathostomes, and a single origin of pharyngeal gills prior to the divergence of these two ancient vertebrate lineages.
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Affiliation(s)
- J Andrew Gillis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK; Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
| | - Olivia R A Tidswell
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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Koop D, Cisternas P, Morris VB, Strbenac D, Yang JYH, Wray GA, Byrne M. Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan. BMC DEVELOPMENTAL BIOLOGY 2017; 17:4. [PMID: 28193178 PMCID: PMC5307799 DOI: 10.1186/s12861-017-0145-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 01/26/2017] [Indexed: 12/27/2022]
Abstract
BACKGROUND The molecular mechanisms underlying the development of the unusual echinoderm pentameral body plan and their likeness to mechanisms underlying the development of the bilateral plans of other deuterostomes are of interest in tracing body plan evolution. In this first study of the spatial expression of genes associated with Nodal and BMP2/4 signalling during the transition to pentamery in sea urchins, we investigate Heliocidaris erythrogramma, a species that provides access to the developing adult rudiment within days of fertilization. RESULTS BMP2/4, and the putative downstream genes, Six1/2, Eya, Tbx2/3 and Msx were expressed in the earliest morphological manifestation of pentamery during development, the five hydrocoele lobes. The formation of the vestibular ectoderm, the specialized region overlying the left coelom that forms adult ectoderm, involved the expression of putative Nodal target genes Chordin, Gsc and BMP2/4 and putative BMP2/4 target genes Dlx, Msx and Tbx. The expression of Nodal, Lefty and Pitx2 in the right ectoderm, and Pitx2 in the right coelom, was as previously observed in other sea urchins. CONCLUSION That genes associated with Nodal and BMP2/4 signalling are expressed in the hydrocoele lobes, indicates that they have a role in the developmental transition to pentamery, contributing to our understanding of how the most unusual body plan in the Bilateria may have evolved. We suggest that the Nodal and BMP2/4 signalling cascades might have been duplicated or split during the evolution to pentamery.
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Affiliation(s)
- Demian Koop
- School of Medical Science and Bosch Institute, The University of Sydney, Sydney, NSW 2006 Australia
| | - Paula Cisternas
- School of Medical Science and Bosch Institute, The University of Sydney, Sydney, NSW 2006 Australia
| | - Valerie B. Morris
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Dario Strbenac
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006 Australia
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006 Australia
| | - Gregory A. Wray
- Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA
| | - Maria Byrne
- School of Medical Science and Bosch Institute, The University of Sydney, Sydney, NSW 2006 Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
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Abstract
Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates. Despite this previous lack of coverage, interest in hemichordates has piqued in the past couple of decades, as they are critical to understanding the evolution of chordates–as acorn worms likely resemble the deuterostome ancestor more closely than any other extant animal. This review provides an overview of our current knowledge of hemichordates, focusing specifically on their global biodiversity, geographic distribution, and taxonomy. Using information available in the World Register of Marine Species and published literature, we assembled a list of 130 described, extant species. The majority (83%) of these species are enteropneusts, and more taxonomic descriptions are forthcoming. Ptychoderidae contained the greatest number of species (41 species), closely followed by Harrimaniidae (40 species), of the recognized hemichordate families. Hemichordates are found throughout the world’s oceans, with the highest reported numbers by regions with marine labs and diligent taxonomic efforts (e.g. North Pacific and North Atlantic). Pterobranchs are abundant in Antarctica, but have also been found at lower latitudes. We consider this a baseline report and expect new species of Hemichordata will continue to be discovered and described as new marine habitats are characterized and explored.
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Affiliation(s)
- Michael G. Tassia
- Department of Biology, University of Washington, Seattle, WA, United States of America
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Johanna T. Cannon
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, United States of America
- Department of Zoology, Naturhistoriska riksmuseet, Stockholm, SE-104 05, Sweden
| | - Charlotte E. Konikoff
- Department of Biology, University of Washington, Seattle, WA, United States of America
| | - Noa Shenkar
- Department of Biology, University of Washington, Seattle, WA, United States of America
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Zoology, George S. Wise Faculty of Life Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Kenneth M. Halanych
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Billie J. Swalla
- Department of Biology, University of Washington, Seattle, WA, United States of America
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- * E-mail:
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Gavilán B, Perea-Atienza E, Martínez P. Xenacoelomorpha: a case of independent nervous system centralization? Philos Trans R Soc Lond B Biol Sci 2016; 371:20150039. [PMID: 26598722 DOI: 10.1098/rstb.2015.0039] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Centralized nervous systems (NSs) and complex brains are among the most important innovations in the history of life on our planet. In this context, two related questions have been formulated: How did complex NSs arise in evolution, and how many times did this occur? As a step towards finding an answer, we describe the NS of several representatives of the Xenacoelomorpha, a clade whose members show different degrees of NS complexity. This enigmatic clade is composed of three major taxa: acoels, nemertodermatids and xenoturbellids. Interestingly, while the xenoturbellids seem to have a rather 'simple' NS (a nerve net), members of the most derived group of acoel worms clearly have ganglionic brains. This interesting diversity of NS architectures (with different degrees of compaction) provides a unique system with which to address outstanding questions regarding the evolution of brains and centralized NSs. The recent sequencing of xenacoelomorph genomes gives us a privileged vantage point from which to analyse neural evolution, especially through the study of key gene families involved in neurogenesis and NS function, such as G protein-coupled receptors, helix-loop-helix transcription factors and Wnts. We finish our manuscript proposing an adaptive scenario for the origin of centralized NSs (brains).
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Affiliation(s)
- Brenda Gavilán
- Departament de Genètica, Universitat de Barcelona, Avinguda Diagonal, 643, Barcelona 08028, Spain
| | - Elena Perea-Atienza
- Departament de Genètica, Universitat de Barcelona, Avinguda Diagonal, 643, Barcelona 08028, Spain
| | - Pedro Martínez
- Departament de Genètica, Universitat de Barcelona, Avinguda Diagonal, 643, Barcelona 08028, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, Barcelona 08010, Spain
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Rahman IA, Zamora S, Falkingham PL, Phillips JC. Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome. Proc Biol Sci 2016; 282:20151964. [PMID: 26511049 DOI: 10.1098/rspb.2015.1964] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy.
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Affiliation(s)
- Imran A Rahman
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
| | - Samuel Zamora
- Instituto Geológico y Minero de España, C/Manuel Lasala, 44 - 9° B, Zaragoza 50006, Spain
| | - Peter L Falkingham
- School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Jeremy C Phillips
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
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40
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Hemichordate models. Curr Opin Genet Dev 2016; 39:71-78. [DOI: 10.1016/j.gde.2016.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/28/2016] [Accepted: 05/30/2016] [Indexed: 11/23/2022]
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Braun K, Stach T. Comparative study of serotonin-like immunoreactivity in the branchial basket, digestive tract, and nervous system in tunicates. ZOOMORPHOLOGY 2016. [DOI: 10.1007/s00435-016-0317-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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42
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Campagna D, Gasparini F, Franchi N, Vitulo N, Ballin F, Manni L, Valle G, Ballarin L. Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri. BMC Genomics 2016; 17:275. [PMID: 27038623 PMCID: PMC4818882 DOI: 10.1186/s12864-016-2598-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/16/2016] [Indexed: 12/15/2022] Open
Abstract
Background We performed an analysis of the transcriptome during the blastogenesis of the chordate Botryllus schlosseri, focusing in particular on genes involved in cell death by apoptosis. The tunicate B. schlosseri is an ascidian forming colonies characterized by the coexistence of three blastogenetic generations: filter-feeding adults, buds on adults, and budlets on buds. Cyclically, adult tissues undergo apoptosis and are progressively resorbed and replaced by their buds originated by asexual reproduction. This is a feature of colonial tunicates, the only known chordates that can reproduce asexually. Results Thanks to a newly developed web-based platform (http://botryllus.cribi.unipd.it), we compared the transcriptomes of the mid-cycle, the pre-take-over, and the take-over phases of the colonial blastogenetic cycle. The platform is equipped with programs for comparative analysis and allows to select the statistical stringency. We enriched the genome annotation with 11,337 new genes; 581 transcripts were resolved as complete open reading frames, translated in silico into amino acid sequences and then aligned onto the non-redundant sequence database. Significant differentially expressed genes were classified within the gene ontology categories. Among them, we recognized genes involved in apoptosis activation, de-activation, and regulation. Conclusions With the current work, we contributed to the improvement of the first released B. schlosseri genome assembly and offer an overview of the transcriptome changes during the blastogenetic cycle, showing up- and down-regulated genes. These results are important for the comprehension of the events underlying colony growth and regression, cell proliferation, colony homeostasis, and competition among different generations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2598-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Davide Campagna
- CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Fabio Gasparini
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Nicola Franchi
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Nicola Vitulo
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Department of Biotechnology, University of Verona, Verona, Italy
| | - Francesca Ballin
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
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Karakostis K, Zanella-Cléon I, Immel F, Guichard N, Dru P, Lepage T, Plasseraud L, Matranga V, Marin F. A minimal molecular toolkit for mineral deposition? Biochemistry and proteomics of the test matrix of adult specimens of the sea urchin Paracentrotus lividus. J Proteomics 2016; 136:133-44. [DOI: 10.1016/j.jprot.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/22/2015] [Accepted: 01/04/2016] [Indexed: 12/16/2022]
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The phylogeny, evolutionary developmental biology, and paleobiology of the Deuterostomia: 25 years of new techniques, new discoveries, and new ideas. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0270-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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45
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Holland ND. Nervous systems and scenarios for the invertebrate-to-vertebrate transition. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150047. [PMID: 26598728 PMCID: PMC4685584 DOI: 10.1098/rstb.2015.0047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2015] [Indexed: 01/09/2023] Open
Abstract
Older evolutionary scenarios for the origin of vertebrates often gave nervous systems top billing in accordance with the notion that a big-brained Homo sapiens crowned a tree of life shaped mainly by progressive evolution. Now, however, tree thinking positions all extant organisms equidistant from the tree's root, and molecular phylogenies indicate that regressive evolution is more common than previously suspected. Even so, contemporary theories of vertebrate origin still focus on the nervous system because of its functional importance, its richness in characters for comparative biology, and its central position in the two currently prominent scenarios for the invertebrate-to-vertebrate transition, which grew out of the markedly neurocentric annelid and enteropneust theories of the nineteenth century. Both these scenarios compare phyla with diverse overall body plans. This diversity, exacerbated by the scarcity of relevant fossil data, makes it challenging to establish plausible homologies between component parts (e.g. nervous system regions). In addition, our current understanding of the relation between genotype and phenotype is too preliminary to permit us to convert gene network data into structural features in any simple way. These issues are discussed here with special reference to the evolution of nervous systems during proposed transitions from invertebrates to vertebrates.
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Affiliation(s)
- Nicholas D Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093-0202, USA
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46
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Stach T, Anselmi C. High-precision morphology: bifocal 4D-microscopy enables the comparison of detailed cell lineages of two chordate species separated for more than 525 million years. BMC Biol 2015; 13:113. [PMID: 26700477 PMCID: PMC4690324 DOI: 10.1186/s12915-015-0218-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Understanding the evolution of divergent developmental trajectories requires detailed comparisons of embryologies at appropriate levels. Cell lineages, the accurate visualization of cleavage patterns, tissue fate restrictions, and morphogenetic movements that occur during the development of individual embryos are currently available for few disparate animal taxa, encumbering evolutionarily meaningful comparisons. Tunicates, considered to be close relatives of vertebrates, are marine invertebrates whose fossil record dates back to 525 million years ago. Life-history strategies across this subphylum are radically different, and include biphasic ascidians with free swimming larvae and a sessile adult stage, and the holoplanktonic larvaceans. Despite considerable progress, notably on the molecular level, the exact extent of evolutionary conservation and innovation during embryology remain obscure. RESULTS Here, using the innovative technique of bifocal 4D-microscopy, we demonstrate exactly which characteristics in the cell lineages of the ascidian Phallusia mammillata and the larvacean Oikopleura dioica were conserved and which were altered during evolution. Our accurate cell lineage trees in combination with detailed three-dimensional representations clearly identify conserved correspondence in relative cell position, cell identity, and fate restriction in several lines from all prospective larval tissues. At the same time, we precisely pinpoint differences observable at all levels of development. These differences comprise fate restrictions, tissue types, complex morphogenetic movement patterns, numerous cases of heterochronous acceleration in the larvacean embryo, and differences in bilateral symmetry. CONCLUSIONS Our results demonstrate in extraordinary detail the multitude of developmental levels amenable to evolutionary innovation, including subtle changes in the timing of fate restrictions as well as dramatic alterations in complex morphogenetic movements. We anticipate that the precise spatial and temporal cell lineage data will moreover serve as a high-precision guide to devise experimental investigations of other levels, such as molecular interactions between cells or changes in gene expression underlying the documented structural evolutionary changes. Finally, the quantitative amount of digital high-precision morphological data will enable and necessitate software-based similarity assessments as the basis of homology hypotheses.
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Affiliation(s)
- Thomas Stach
- Institut für Biologie, Kompetenzzentrum Elektronenmikroskopie, Humboldt-Universität zu Berlin, Philippstrasse 13, Haus 14, 10115, Berlin, Germany.
| | - Chiara Anselmi
- Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.
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Hejnol A, Lowe CJ. Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution. Philos Trans R Soc Lond B Biol Sci 2015; 370:20150045. [PMID: 26554039 PMCID: PMC4650123 DOI: 10.1098/rstb.2015.0045] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2015] [Indexed: 12/14/2022] Open
Abstract
Molecular biology has provided a rich dataset to develop hypotheses of nervous system evolution. The startling patterning similarities between distantly related animals during the development of their central nervous system (CNS) have resulted in the hypothesis that a CNS with a single centralized medullary cord and a partitioned brain is homologous across bilaterians. However, the ability to precisely reconstruct ancestral neural architectures from molecular genetic information requires that these gene networks specifically map with particular neural anatomies. A growing body of literature representing the development of a wider range of metazoan neural architectures demonstrates that patterning gene network complexity is maintained in animals with more modest levels of neural complexity. Furthermore, a robust phylogenetic framework that provides the basis for testing the congruence of these homology hypotheses has been lacking since the advent of the field of 'evo-devo'. Recent progress in molecular phylogenetics is refining the necessary framework to test previous homology statements that span large evolutionary distances. In this review, we describe recent advances in animal phylogeny and exemplify for two neural characters-the partitioned brain of arthropods and the ventral centralized nerve cords of annelids-a test for congruence using this framework. The sequential sister taxa at the base of Ecdysozoa and Spiralia comprise small, interstitial groups. This topology is not consistent with the hypothesis of homology of tripartitioned brain of arthropods and vertebrates as well as the ventral arthropod and rope-like ladder nervous system of annelids. There can be exquisite conservation of gene regulatory networks between distantly related groups with contrasting levels of nervous system centralization and complexity. Consequently, the utility of molecular characters to reconstruct ancestral neural organization in deep time is limited.
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Affiliation(s)
- Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen 5008, Norway
| | - Christopher J Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, USA
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48
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Silvia M, Paolo T, Nobile M, Denise F, Cinta P, Michela S. Unraveling estradiol metabolism and involvement in the reproductive cycle of non-vertebrate animals: The sea urchin model. Steroids 2015; 104:25-36. [PMID: 26277857 DOI: 10.1016/j.steroids.2015.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 08/05/2015] [Accepted: 08/10/2015] [Indexed: 01/08/2023]
Abstract
Estradiol (E2) is a well-known hormone in vertebrates whereas in invertebrates its unambiguous presence was verified only in some species. Weather this presence is also associated to similarly conserved roles in animal phylogeny is similarly uncertain. Due to their phylogenetic position, echinoderms represent ideal experimental models to provide evolutionary insights into estrogen appearance and function. Therefore, in this research, we investigated if E2 is truly present and has a role in the reproductive biology of the sea urchin Paracentrotus lividus. Presence of 17β estradiol in body fluids was confirmed by liquid chromatography-mass spectrometry. By immunological methods (RIA) we evaluated the physiological circulating E2 levels of adult specimens and, on the basis of these, we directly administered E2 to study its metabolism and its putative effects on gonad development at physiological doses. Although different E2 tested concentrations, a correspondent dose-dependent increase of hormone levels was not found in both body fluids and gonads, suggesting the presence of potent homeostatic/detoxification mechanisms. These latter do not involve enzymes such as aromatase-like, sulfotransferase-like and acyltransferase-like, whose activities were not affected by E2 administration. Despite the increase of endogenous E2, the treatment did not induce significant variations in none of the considered reproductive parameters. Overall, this research (1) provides definitive evidence of E2 presence in sea urchin tissues and (2) demonstrate that, differently from vertebrates and starfish, E2 does not play a key role in sea urchins reproductive processes. Intra-phylum differences suggest the existence of class-specific hormonal mechanisms and highlight the risk of Phylum generalization.
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Affiliation(s)
- Mercurio Silvia
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Tremolada Paolo
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Maria Nobile
- Department of Veterinary Sciences and Public Health, University of Milan, Via Celoria 10, 20133 Milan, Italy
| | - Fernandes Denise
- FCT, CIMA, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Porte Cinta
- Department of Environmental Chemistry, IDAEA-CSIC, calle Jordi Girona 18, 08034 Barcelona, Spain
| | - Sugni Michela
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy.
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49
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Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su YH, Putnam NH, Schmutz J, Fujiyama A, Yu JK, Tagawa K, Worley KC, Gibbs RA, Kirschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J. Hemichordate genomes and deuterostome origins. Nature 2015; 527:459-65. [PMID: 26580012 PMCID: PMC4729200 DOI: 10.1038/nature16150] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/13/2015] [Indexed: 12/12/2022]
Abstract
Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.
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Affiliation(s)
- Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.,Department of Molecular Evolution, Centre for Organismal Studies, University of Heidelberg, 69115 Heidelberg, Germany
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | | | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jessen Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Fuki Gyoja
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jia-Xing Yue
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Robert M Freeman
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Akane Sasaki
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | - Tomoe Hikosaka-Katayama
- Natural Science Center for Basic Research and Development, Gene Science Division, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Atsuko Sato
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kenneth W Baughman
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Judith Levine
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Paul Gonzalez
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Christopher Cameron
- Départment de sciences biologiques, University of Montreal, Quebec H3C 3J7, Canada
| | - Jens H Fritzenwanker
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Ariel M Pani
- University of North Caroline at Chapel Hill, North Carolina 27599, USA
| | - Hiroki Goto
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Shinichi Yamasaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Andrew Cree
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Yan Ding
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Lora R Lewis
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Donna Morton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Lynne V Nazareth
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Wu
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Tom Humphreys
- Institute for Biogenesis Research, University of Hawaii, Hawaii 96822, USA
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Nicholas H Putnam
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Kunifumi Tagawa
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher J Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.,Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - John Gerhart
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
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Matassi G, Imai JH, Di Gregorio A. Molecular phylogeny of four homeobox genes from the purple sea star Pisaster ochraceus. Dev Genes Evol 2015; 225:359-65. [PMID: 26432455 DOI: 10.1007/s00427-015-0516-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
Abstract
Homeobox genes cloned from the purple sea star Pisaster ochraceus (Phylum Echinodermata/Class Asteroidea) were used along with related sequences available from members of other representative animal phyla to generate molecular phylogenies for Distal-less/Dlx, Hox5, Hox7, and Hox9/10 homeobox genes. Phylogenetic relationships were inferred based on the predicted 60 amino acid homeodomain, using amino acid (AA) and nucleotide (NT) models as well as the recently developed codon substitution models of sequence evolution. The resulting phylogenetic trees were mostly congruent with the consensus species-tree, grouping these newly identified genes with those isolated from other Asteroidea. This analysis also allowed a preliminary comparison of the performance of codon models with that of NT and AA evolutionary models in the inference of homeobox phylogeny. We found that, overall, the NT models displayed low reliability in recovering major clades at the Superphylum/Phylum level, and that codon models were slightly more dependable than AA models. Remarkably, in the majority of cases, codon substitution models seemed to outperform both AA and NT models at both the Class level and homeobox paralogy-group level of classification.
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Affiliation(s)
- Giorgio Matassi
- Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Janice Hitomi Imai
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Anna Di Gregorio
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA. .,Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY, 10010, USA.
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