Extending the Integrated Ascidian Database to the Exploration And

Total Page:16

File Type:pdf, Size:1020Kb

Extending the Integrated Ascidian Database to the Exploration And ANISEED 2017: extending the integrated ascidian database to Title the exploration and evolutionary comparison of genome-scale datasets Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Author(s) Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Brown, C�Titus; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas; Lemaire, Patrick Citation Nucleic Acids Research (2018), 46: D718-D725 Issue Date 2018-01-04 URL http://hdl.handle.net/2433/229401 © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by- Right nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] Type Journal Article Textversion publisher Kyoto University D718–D725 Nucleic Acids Research, 2018, Vol. 46, Database issue Published online 15 November 2017 doi: 10.1093/nar/gkx1108 ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets Matija Brozovic1,†, Christelle Dantec1,†, Justine Dardaillon1,†, Delphine Dauga2,†, Emmanuel Faure3,4, Mathieu Gineste1, Alexandra Louis5, Magali Naville6, Kazuhiro R. Nitta7, Jacques Piette1, Wendy Reeves8,Celine´ Scornavacca9, Paul Simion9, Renaud Vincentelli10, Maelle Bellec11, Sameh Ben Aicha12, Marie Fagotto11, Marion Gueroult-Bellone´ 2, Maximilian Haeussler13, Edwin Jacox1, Elijah K. Lowe14,15, Mickael Mendez7, Alexis Roberge11, Alberto Stolfi16,RuiYokomori17,C.TitusBrown15,18, Christian Cambillau10, Lionel Christiaen19,Fred´ eric´ Delsuc9, Emmanuel Douzery9, Remi´ Dumollard12, Takehiro Kusakabe20, Kenta Nakai17, Hiroki Nishida21, Yutaka Satou22, Billie Swalla15,23, Michael Veeman8, Jean-Nicolas Volff6 and Patrick Lemaire1,3,* 1CRBM, Universite´ de Montpellier, CNRS, Montpellier, France, 2Bioself Communication; 28 rue de la Bibliotheque,` F-13001 Marseille, France, 3Institut de Biologie Computationnelle, Universite´ de Montpellier, Montpellier, France, 4Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France, 5DYOGEN, IBENS, Departement´ de Biologie, Ecole Normale Superieure,´ CNRS, Inserm, PSL Research University, F-75005, Paris, France, 6Institut de Genomique´ Fonctionnelle de Lyon, Universite´ de Lyon, Ecole Normale Superieure´ de Lyon, Universite´ Claude Bernard Lyon 1, CNRS; 46 allee´ d’Italie, F-69364 Lyon, France, 7IBDM, Aix-Marseille Universite,´ CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France, 8Division of Biology, Kansas State University, Manhattan, Kansas, 9ISEM, Universite´ de Montpellier, CNRS, IRD, EPHE, Montpellier, France, 10AFMB, Aix-Marseille Universite,´ CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France, 11Universite´ de Montpellier, Montpellier, France, 12Laboratoire de Biologie du Developpement´ de Villefranche-sur-mer (LBDV), Sorbonne Universites,´ Universite´ Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France, 13Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA, 14Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy, 15BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA, 16School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA, 17Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan, 18Population Health and Reproduction, UC Davis, Davis, CA 95616, USA, 19New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA, 20Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan, 21Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan, 22Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan and 23Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA Received September 18, 2017; Revised October 22, 2017; Editorial Decision October 23, 2017; Accepted November 09, 2017 ABSTRACT vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomi- ANISEED (www.aniseed.cnrs.fr) is the main model or- cal descriptions for nine ascidian species. It pro- ganism database for tunicates, the sister-group of *To whom correspondence should be addressed. Email: [email protected] †These authors contributed equally to this work as first authors. C The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] Downloaded from https://academic.oup.com/nar/article-abstract/46/D1/D718/4628129 by Library,Faculty of Agriculture/Graduate School of Agriculture,Kyoto University user on 23 February 2018 Nucleic Acids Research, 2018, Vol. 46, Database issue D719 vides increased integration with external molecular tion, initially relying on morpholino oligonucleotides, now and taxonomy databases, better support for epige- includes the use of TALENs (18)andCRISPR/cas9 strate- nomics datasets, in particular RNA-seq, ChIP-seq gies (19,20). and SELEX-seq, and features novel interactive in- ANISEED - Ascidian Network for In Situ Expression terfaces for existing and novel datatypes. In par- and Embryological Data––is the major database system in ticular, the cross-species navigation and compari- the Tunicate community, hosting and giving access to ge- nomic, genetic and anatomical data on ascidian develop- son is enhanced through a novel taxonomy section ment. First published in 2010 (21), the database hosts and describing each represented species and through gives access to genomic, genetic and anatomical data on tu- the implementation of interactive phylogenetic gene nicates. Its refactoring using the Chado schema philosophy trees for 60% of tunicate genes. The gene expres- and its extension to 11 ascidian species was completed in sion section displays the results of RNA-seq exper- 2015 (22). Since then, tunicate laboratories have rapidly em- iments for the three major model species of soli- braced genomics, including ChIP-seq (23,24), RNA-seq of tary ascidians. Gene expression is controlled by the whole embryos (24) or FACS-sorted single cells (25), bisul- binding of transcription factors to cis-regulatory se- phite sequencing (26), SELEX-seq and TSS-seq (27). The quences. A high-resolution description of the DNA- aim of the ANISEED 2017 update is to accompany the en- binding specificity for 131 Ciona robusta (formerly C. try of tunicate biology into the genome-scale era through / intestinalis type A) transcription factors by SELEX- three types of improvements: extension refactoring of min- ing and display tools, extension of pre-existing datasets and seq is provided and used to map candidate binding development of modules to host and give access to novel sites across the Ciona robusta and Phallusia mam- types of genomics data. millata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Ge- NEW DATA MINING/DISPLAY TOOLS nomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Taxonomy pages Amphioxus, echinoderms and hemichordates. A taxonomy page accessible from the home page was intro- duced in ANISEED 2017 to place the covered species into INTRODUCTION their phylogenetic context and facilitate the interpretation of comparative studies. The page shows a cladogram of the The tunicate clade of marine invertebrate deuterostomes in- twelve species currently described at the anatomical or ge- cludes the sessile ascidians and the pelagic appendicularians netic level in the database. Each node gives access to a page and thaliaceans (1,2). A major interest of the scientific com- describing the corresponding species. Following the novel munity for tunicates stems from the phylogenetic position of taxonomy (28) and a community decision at the 2017 in- this chordate group, now considered to be the long-diverged ternational Tunicate Meeting, Ciona intestinalis type A has sister group of vertebrates (3). Solitary ascidians and all ap- been renamed Ciona robusta
Recommended publications
  • Marine Biology
    Marine Biology Spatial and temporal dynamics of ascidian invasions in the continental United States and Alaska. --Manuscript Draft-- Manuscript Number: MABI-D-16-00297 Full Title: Spatial and temporal dynamics of ascidian invasions in the continental United States and Alaska. Article Type: S.I. : Invasive Species Keywords: ascidians, biofouling, biogeography, marine invasions, nonindigenous, non-native species, North America Corresponding Author: Christina Simkanin, Phd Smithsonian Environmental Research Center Edgewater, MD UNITED STATES Corresponding Author Secondary Information: Corresponding Author's Institution: Smithsonian Environmental Research Center Corresponding Author's Secondary Institution: First Author: Christina Simkanin, Phd First Author Secondary Information: Order of Authors: Christina Simkanin, Phd Paul W. Fofonoff Kristen Larson Gretchen Lambert Jennifer Dijkstra Gregory M. Ruiz Order of Authors Secondary Information: Funding Information: California Department of Fish and Wildlife Dr. Gregory M. Ruiz National Sea Grant Program Dr. Gregory M. Ruiz Prince William Sound Regional Citizens' Dr. Gregory M. Ruiz Advisory Council Smithsonian Institution Dr. Gregory M. Ruiz United States Coast Guard Dr. Gregory M. Ruiz United States Department of Defense Dr. Gregory M. Ruiz Legacy Program Abstract: SSpecies introductions have increased dramatically in number, rate, and magnitude of impact in recent decades. In marine systems, invertebrates are the largest and most diverse component of coastal invasions throughout the world. Ascidians are conspicuous and well-studied members of this group, however, much of what is known about their invasion history is limited to particular species or locations. Here, we provide a large-scale assessment of invasions, using an extensive literature review and standardized field surveys, to characterize the invasion dynamics of non-native ascidians in the continental United States and Alaska.
    [Show full text]
  • And Description of a New Species, Ciona Interme
    An integrative taxonomic framework for the study of the genus Ciona (Ascidiacea) and description of a new species, Ciona intermedia Francesco Mastrototaro, Federica Montesanto, Marika Salonna, Frédérique Viard, Giovanni Chimienti, Egidio Trainito, Carmela Gissi To cite this version: Francesco Mastrototaro, Federica Montesanto, Marika Salonna, Frédérique Viard, Giovanni Chimi- enti, et al.. An integrative taxonomic framework for the study of the genus Ciona (Ascidiacea) and description of a new species, Ciona intermedia. Zoological Journal of the Linnean Society, Linnean Society of London, 2020, 10.1093/zoolinnean/zlaa042. hal-02861027 HAL Id: hal-02861027 https://hal.archives-ouvertes.fr/hal-02861027 Submitted on 8 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Doi: 10.1093/zoolinnean/zlaa042 An integrative taxonomy framework for the study of the genus Ciona (Ascidiacea) and the description of the new species Ciona intermedia Francesco Mastrototaro1, Federica Montesanto1*, Marika Salonna2, Frédérique Viard3, Giovanni Chimienti1, Egidio Trainito4, Carmela Gissi2,5,* 1 Department of Biology and CoNISMa LRU, University of Bari “Aldo Moro” Via Orabona, 4 - 70125 Bari, Italy 2 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona, 4 - 70125 Bari, Italy 3 Sorbonne Université, CNRS, Lab.
    [Show full text]
  • The Role of Metalloproteases in Fertilisation in the Ascidian Ciona
    www.nature.com/scientificreports OPEN The role of metalloproteases in fertilisation in the ascidian Ciona robusta Received: 8 August 2018 Shiori Nakazawa 1,2, Maki Shirae-Kurabayashi1 & Hitoshi Sawada1 Accepted: 12 December 2018 In the ascidian Ciona robusta (formerly C. intestinalis type A), the mechanism underlying sperm Published: xx xx xxxx penetration through the egg investment remains unknown. We previously reported that proteins containing both an astacin metalloprotease domain and thrombospondin type 1 repeats are abundant in the sperm surface protein-enriched fraction of C. robusta. Here we investigated the involvement of those proteins in fertilisation. We refned the sequences of astacin metalloproteases, confrmed that fve of them are present in the sperm, and labelled them as tunicate astacin and thrombospondin type 1 repeat-containing (Tast) proteins. Fertilisation of C. robusta eggs was potently inhibited by a metalloprotease inhibitor GM6001. The eggs cleaved normally when they were vitelline coat-free or the inhibitor was added after insemination. Furthermore, vitelline coat proteins were degraded after incubation with intact sperm. These results suggest that sperm metalloproteases are indispensable for fertilisation, probably owing to direct or indirect mediation of vitelline-coat digestion during sperm penetration. TALEN-mediated knockout of Tast genes and the presence of GM6001 impaired larval development at the metamorphic stage, suggesting that Tast gene products play a key role in late development. Egg fertilisation is key to achieving genetic diversity in the next generation. In most animals, the eggs are covered with an acellular investment called the egg coat, also called the vitelline coat (VC) in some marine invertebrates, including ascidians and zona pellucida in mammals.
    [Show full text]
  • Using Linkage Logic Theory to Control Dynamics of a Gene Regulatory
    www.nature.com/scientificreports OPEN Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo Kenji Kobayashi1, Kazuki Maeda2, Miki Tokuoka1, Atsushi Mochizuki3* & Yutaka Satou1* Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are collectively called a feedback vertex set (FVS). Because many biological functions emerge from dynamics of biological networks, this theory provides a promising tool for controlling biological functions. By manipulating the activity of FVS molecules identifed in a gene regulatory network (GRN) for fate specifcation of seven tissues in ascidian embryos, we previously succeeded in reproducing six of the seven cell types. Simultaneously, we discovered that the experimentally reconstituted GRN lacked information sufcient to reproduce muscle cells. Here, we utilized linkage logic theory as a tool to fnd missing edges in the GRN. Then, we identifed a FVS from an updated version of the GRN and confrmed that manipulating the activity of this FVS was sufcient to induce all seven cell types, even in a multi-cellular environment. Thus, linkage logic theory provides tools to fnd missing edges in experimentally reconstituted networks, to determine whether reconstituted networks contain sufcient information to fulfl expected functions, and to reprogram cell fate. Animal embryos diferentiate a variety of cell types, each of which expresses a specifc set of genes. Such specifc gene expression patterns emerge from dynamics of gene regulatory networks (GRNs)1. In GRNs, nodes represent genes, and edges represent regulatory interactions between nodes. Regulatory genes that encode transcription factors and signaling molecules regulate one another, and constitute the core of GRNs.
    [Show full text]
  • Asymmetric Fitness of Second-Generation Interspecific
    G3: Genes|Genomes|Genetics Early Online, published on June 9, 2020 as doi:10.1534/g3.120.401427 1 Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and 2 Ciona intestinalis 3 4 Naoyuki Ohta*, Nicole Kaplan, James Tyler Ng, Basile Jules Gravez, Lionel Christiaen* 5 6 Center for Developmental Genetics, Department of Biology 7 New York University, New York, NY, USA 8 9 * Authors for correspondence: [email protected] (NO) , [email protected] (LC) 10 11 12 13 Abstract 14 Reproductive isolation is central to speciation, but interspecific crosses between two closely related species 15 can produce viable and fertile hybrids. Two different species of tunicates in the same ascidian genus, Ciona 16 robusta and Ciona intestinalis, can produce hybrids. However, wild sympatric populations display limited gene 17 flow, suggesting the existence of obstacles to interspecific reproduction that remain unknown. Here, we took 18 advantage of a closed culture system to cross C. robusta with C. intestinalis and established F1 and F2 hybrids. We 19 monitored post-embryonic development, survival, and sexual maturation to characterize the genetic basis of 20 simple traits, and further probe the physiological mechanisms underlying reproductive isolation. Partial viability 21 of first and second generation hybrids suggested that both pre- and postzygotic mechanisms contributed to 22 genomic incompatibilities in hybrids. We observed asymmetric fitness, whereby the C. intestinalis maternal lines 23 fared more poorly in our system, pointing to maternal origins of species-specific sensitivity. We discuss the 24 possibility that asymmetrical second generation inviability and infertility emerge from interspecific 25 incompatibilities between the nuclear and mitochondrial genomes, or other maternal effect genes.
    [Show full text]
  • A Nearly Complete Genome of Ciona Intestinalis Type a (C
    GBE A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona Yutaka Satou 1,*, Ryohei Nakamura2,DeliYu1, Reiko Yoshida1, Mayuko Hamada3, Manabu Fujie4, Kanako Hisata5, Hiroyuki Takeda2, and Noriyuki Satoh5 1Department of Zoology, Graduate School of Science, Kyoto University, Japan 2Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan 3Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Japan 4DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan 5Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan *Corresponding author: E-mail: [email protected]. Accepted: October 15, 2019 Data deposition: This project has been deposited at the DDBJ BioProject database under the accessions PRJDB8078 (whole genome) and PRJDB8620 (Hi-C data). Accession numbers for genome sequence data are BJTB01000001–BJTB01000067; accession numbers for raw sequenc- ing data are DRA008508 (genomic sequencing data for two wild-caught animals) and DRA008742 (Hi-C data). Abstract Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence infor- mation in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data.
    [Show full text]
  • Ascidian News #76 December 2015
    ASCIDIAN NEWS* Gretchen Lambert 12001 11th Ave. NW, Seattle, WA 98177 206-365-3734 [email protected] home page: http://depts.washington.edu/ascidian/ Number 76 December 2015 I greatly enjoyed participating in teaching a two week ascidian course at Nagoya University’s Sugashima Marine Lab from the end of June to July 10, and then attended the Intl. Tunicata meeting in Aomori, Japan from July 13-17. This issue is the second for my 40th year of compiling Ascidian News. I would greatly appreciate hearing from you whether you still find it useful and interesting. There are 93 New Publications listed at the end of this issue. *Ascidian News is not part of the scientific literature and should not be cited as such. NEWS AND VIEWS 1. Ciona intestinalis now shown to be 2 separate species. Because so many researchers work on Ciona intestinalis, and so many papers are published on this species, I draw your attention to 2 new publications showing at last that Ciona intestinalis A and B are different species and designating the correct names to be used in all future publications: Brunetti, R., Gissi, C., Pennati, R., Caicci, F., Gasparini, F. and Manni, L. 2015. Morphological evidence indicates that Ciona intestinalis (Tunicata, Ascidiacea) type A and type B are different species. Journal of Zool. Systematics & Evolutionary Research 53 (3): 186–193. [Type A is now designated C. robusta; type B retains the name C. intestinalis.] The second new publication describes larval differences between the two species: Pennati, R., Ficetola, G. F., Brunetti, R., Caicci, F., Gasparini, F., Griggio, F., Sato, A., Stach, T., Kaul-Strehlow, S., Gissi, C.
    [Show full text]
  • Asymmetric Fitness of Second-Generation Interspecific
    INVESTIGATION Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis Naoyuki Ohta,1 Nicole Kaplan, James Tyler Ng, Basile Jules Gravez, and Lionel Christiaen1 Center for Developmental Genetics, Department of Biology, New York University, NY ORCID IDs: 0000-0001-7495-7655 (N.O.); 0000-0001-5930-5667 (L.C.) ABSTRACT Reproductive isolation is central to speciation, but interspecific crosses between two closely KEYWORDS related species can produce viable and fertile hybrids. Two different species of tunicates in the same ascidian Tunicate genus, Ciona robusta and Ciona intestinalis, can produce hybrids. However, wild sympatric populations Ascidian display limited gene flow, suggesting the existence of obstacles to interspecific reproduction that remain hybrids unknown. Here, we took advantage of a closed culture system to cross C. robusta with C. intestinalis and reproductive established F1 and F2 hybrids. We monitored post-embryonic development, survival, and sexual maturation isolation to characterize the genetic basis of simple traits, and further probe the physiological mechanisms underlying speciation reproductive isolation. Partial viability of first and second generation hybrids suggested that both pre- and evolution postzygotic mechanisms contributed to genomic incompatibilities in hybrids. We observed asymmetric fitness, whereby the C. intestinalis maternal lines fared more poorly in our system, pointing to maternal origins of species-specific sensitivity. We discuss the possibility that asymmetrical second generation inviability and infertility emerge from interspecific incompatibilities between the nuclear and mitochondrial genomes, or other maternal effect genes. This work paves the way to quantitative genetic approaches to study the mechanisms underlying genomic incompatibilities and other complex traits in the genome-enabled Ciona model.
    [Show full text]
  • Contrasting Patterns of Native and Introduced Ascidians in Subantarctic and Temperate Chile
    Management of Biological Invasions (2016) Volume 7, Issue 1: 77–86 DOI: http://dx.doi.org/10.3391/mbi.2016.7.1.10 Open Access © 2016 The Author(s). Journal compilation © 2016 REABIC Proceedings of the 5th International Invasive Sea Squirt Conference (October 29–31, 2014, Woods Hole, USA) Research Article Too cold for invasions? Contrasting patterns of native and introduced ascidians in subantarctic and temperate Chile 1 2 3,4 5 6 Xavier Turon *, Juan I. Cañete , Javier Sellanes , Rosana M. Rocha and Susanna López-Legentil 1Center for Advanced Studies of Blanes (CEAB-CSIC), Accés Cala S. Francesc 14, 17300 Blanes, Girona, Spain 2Facultad de Ciencias, Universidad de Magallanes, Chile 3Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile 4Millenium Nucleus for Ecology and Sustainable Management of Oceanic Islands (ESMOI), Chile 5Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil 6Dep. of Biology and Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28409, USA *Corresponding author E-mail: [email protected] Received: 6 May 2015 / Accepted: 30 September 2015 / Published online: 26 November 2015 Handling editor: Mary Carman Abstract We analysed the biodiversity of ascidians in two areas located in southern and northern Chile: Punta Arenas in the Strait of Magellan (53º latitude, subantarctic) and Coquimbo (29º latitude, temperate). The oceanographic features of the two zones are markedly different, with influence of the Humboldt Current in the north, and the Cape Horn Current System, together with freshwater influxes, in the Magellanic zone. Both regions were surveyed twice during 2013 by SCUBA diving and pulling ropes and aquaculture cages.
    [Show full text]
  • The Comprehensive Ontology of the Anatomy and Development of the Solitary Ascidian Ciona: the Swimming Larva and Its Metamorphosis
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.09.140640; this version posted June 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: The comprehensive ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis. Authors: Kohji Hotta1*, Delphine Dauga2 & Lucia Manni3* 1 Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kouhoku-ku, Yokohama 223-8522, Japan, [email protected] 2 Bioself Communication, 28 rue de la bibliotheque, 13001 Marseille, France, contact@bioself- communication.com 3 Department of Biology, University of Padova, Padova, Italy, [email protected] -------------------------------------------------------- *Author for correspondence: Kohji Hotta, Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kouhoku-ku, Yokohama 223-8522, Japan E-mail: [email protected] and Lucia Manni, Department of Biology, University of Padova Via Ugo Bassi 58/B, 35121, Padova, Italy. E-mail: [email protected] -------------------------------------------------------- Running title: Ontology of anatomy and development of a solitary ascidian -------------------------------------------------------- 29 pages of manuscript including references and figure legends 6 figures and 1 table Additional files: 16 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.09.140640; this version posted June 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Ascidiacea Ascidiacea
    ASCIDIACEA ASCIDIACEA The Ascidiacea, the largest class of the Tunicata, are fixed, filter feeding organisms found in most marine habitats from intertidal to hadal depths. The class contains two orders, the Enterogona in which the atrial cavity (atrium) develops from paired dorsal invaginations, and the Pleurogona in which it develops from a single median invagination. These ordinal characters are not present in adult organisms. Accordingly, the subordinal groupings, Aplousobranchia and Phlebobranchia (Enterogona) and Stolidobranchia (Pleurogona), are of more practical use at the higher taxon level. In the earliest classification (Savigny 1816; Milne-Edwards 1841) ascidians-including the known salps, doliolids and later (Huxley 1851), appendicularians-were subdivided according to their social organisation, namely, solitary and colonial forms, the latter with zooids either embedded (compound) or joined by basal stolons (social). Recognising the anomalies this classification created, Lahille (1886) used the branchial sacs to divide the group (now known as Tunicata) into three orders: Aplousobranchia (pharynx lacking both internal longitudinal vessels and folds), Phlebobranchia (pharynx with internal longitudinal vessels but lacking folds), and Stolidobranchia (pharynx with both internal longitudinal vessels and folds). Subsequently, with thaliaceans and appendicularians in their own separate classes, Lahille's suborders came to refer only to the Class Ascidiacea, and his definitions were amplified by consideration of the position of the gut and gonads relative to the branchial sac (Harant 1929). Kott (1969) recognised that the position of the gut and gonads are linked with the condition and function of the epicardium. These are significant characters and are informative of phylogenetic relationships. However, although generally conforming with Lahille's orders, the new phylogeny cannot be reconciled with a too rigid adherence to his definitions based solely on the branchial sac.
    [Show full text]
  • Rimbp, a New Marker for the Nervous System of the Tunicate Ciona Robusta
    G C A T T A C G G C A T genes Article Rimbp, a New Marker for the Nervous System of the Tunicate Ciona robusta 1,2, , 1, 1 2 Ugo Coppola y z , Paola Olivo y, Enrico D’Aniello , Christopher J. Johnson , Alberto Stolfi 2,* and Filomena Ristoratore 1,* 1 Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; [email protected] (U.C.); [email protected] (P.O.); [email protected] (E.D.) 2 School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; [email protected] * Correspondence: alberto.stolfi@biosci.gatech.edu (A.S.); fi[email protected] (F.R.) These authors contributed equally to the work. y Current Address: The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati z Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. Received: 21 July 2020; Accepted: 25 August 2020; Published: 27 August 2020 Abstract: Establishment of presynaptic mechanisms by proteins that regulate neurotransmitter release in the presynaptic active zone is considered a fundamental step in animal evolution. Rab3 interacting molecule-binding proteins (Rimbps) are crucial components of the presynaptic active zone and key players in calcium homeostasis. Although Rimbp involvement in these dynamics has been described in distantly related models such as fly and human, the role of this family in most invertebrates remains obscure. To fill this gap, we defined the evolutionary history of Rimbp family in animals, from sponges to mammals. We report, for the first time, the expression of the two isoforms of the unique Rimbp family member in Ciona robusta in distinct domains of the larval nervous system.
    [Show full text]