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