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4D Exploration of Genetic Data for an Extended Range of Tunicates Swarthmore College Works Biology Faculty Works Biology 11-4-2019 ANISEED 2019: 4D Exploration Of Genetic Data For An Extended Range Of Tunicates J. Dardaillon D. Dauga P. Simion E. Faure T. A. Onuma See next page for additional authors Follow this and additional works at: https://works.swarthmore.edu/fac-biology Part of the Biology Commons, and the Developmental Biology Commons Let us know how access to these works benefits ouy Recommended Citation J. Dardaillon; D. Dauga; P. Simion; E. Faure; T. A. Onuma; M. B. DeBiasse; A. Louis; K. R. Nitta; M. Naville; L. Besnardeau; W. Reeves; K. Wang; M. Fagotto; M. Guéroult-Bellone; S. Fujiwara; R. Dumollard; M. Veeman; J.-N. Volff; H. Roest Crollius; E. Douzery; J. F. Ryan; Bradley Justin Davidson , '91; H. Nishida; C. Dantec; and P. Lemaire. (2019). "ANISEED 2019: 4D Exploration Of Genetic Data For An Extended Range Of Tunicates". Nucleic Acids Research. DOI: 10.1093/nar/gkz955 https://works.swarthmore.edu/fac-biology/585 This work is licensed under a Creative Commons Attribution 4.0 License. This work is brought to you for free by Swarthmore College Libraries' Works. It has been accepted for inclusion in Biology Faculty Works by an authorized administrator of Works. For more information, please contact [email protected]. Authors J. Dardaillon; D. Dauga; P. Simion; E. Faure; T. A. Onuma; M. B. DeBiasse; A. Louis; K. R. Nitta; M. Naville; L. Besnardeau; W. Reeves; K. Wang; M. Fagotto; M. Guéroult-Bellone; S. Fujiwara; R. Dumollard; M. Veeman; J.-N. Volff; H. Roest Crollius; E. Douzery; J. F. Ryan; Bradley Justin Davidson , '91; H. Nishida; C. Dantec; and P. Lemaire This article is available at Works: https://works.swarthmore.edu/fac-biology/585 Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gkz955 ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates Justine Dardaillon1, Delphine Dauga 2, Paul Simion 3, Emmanuel Faure 4, Takeshi 5 6,7 8 9 A. Onuma , Melissa B. DeBiasse , Alexandra Louis , Kazuhiro R. Nitta , Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz955/5611675 by guest on 03 December 2019 Magali Naville 10, Lydia Besnardeau11, Wendy Reeves12, Kai Wang13, Marie Fagotto14, Marion Gueroult-Bellone´ 2, Shigeki Fujiwara 15,Remi´ Dumollard 11, Michael Veeman 12, Jean-Nicolas Volff 10, Hugues Roest Crollius 8, Emmanuel Douzery 3, Joseph F. Ryan 6,7, Bradley Davidson16, Hiroki Nishida 5, Christelle Dantec 1,*,† and Patrick Lemaire 1,*,† 1CRBM, Universite´ de Montpellier, CNRS, Montpellier, France, 2Bioself Communication; 28 rue de la Bibliotheque,` F-13001 Marseille, France, 3ISEM, Universite´ de Montpellier, CNRS, IRD, EPHE, Montpellier, France, 4Laboratoire d’Informatique de Robotique et de Microelectronique´ de Montpellier (LIRMM), Universite´ de Montpellier, CNRS, Montpellier, France, 5Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan, 6Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA, 7Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA, 8DYOGEN, IBENS, Departement´ de Biologie, Ecole Normale Superieure,´ CNRS, Inserm, PSL Research University, F-75005 Paris, France, 9IBDM, Universite´ Aix-Marseille, CNRS, Marseille, France, 10Institut 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, 11Laboratoire 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., 12Division of Biology, Kansas State University, Manhattan, KS 66506, USA, 13State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China, 14Universitede´ Montpellier, Montpellier, France, 15Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi-shi, Kochi, Japan and 16Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA Received September 16, 2019; Revised October 08, 2019; Editorial Decision October 09, 2019; Accepted October 11, 2019 ABSTRACT other genetic elements, including repeated elements and cis-regulatory modules. Gene expression pro- ANISEED (https://www.aniseed.cnrs.fr)isthemain files for several thousand genes are formalized in model organism database for the worldwide com- both wild-type and experimentally-manipulated con- munity of scientists working on tunicates, the ver- ditions, using formal anatomical ontologies. These tebrate sister-group. Information provided for each data can be explored through three complementary species includes functionally-annotated gene and types of browsers, each offering a different view- transcript models with orthology relationships within point. A developmental browser summarizes the in- tunicates, and with echinoderms, cephalochordates formation in a gene- or territory-centric manner. and vertebrates. Beyond genes the system describes Advanced genomic browsers integrate the genetic *To whom correspondence should be addressed. Tel: +33 4 34 35 94 00; Email: [email protected] Correspondence may also be addressed to Christelle Dantec. Tel: +33 4 34 35 94 00; Email: [email protected] †The authors wish it to be known that, in their opinion, the last two authors should be regarded as Joint Last Authors. Present addresses: Paul Simion, Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Namur, Belgium. Kazuhiro R. Nitta, Juntendo University, Graduate School of Medicine, Diagnostics and Therapeutics of Intractable Diseases Intractable Disease Research Center, Tokyo, Japan. C The Author(s) 2019. 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/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Nucleic Acids Research, 2019 features surrounding genes or gene sets within a phylogenies as a comparative framework to study the devel- species. A Genomicus synteny browser explores the opmental programs of different species; (iii) a multispecies conservation of local gene order across deuteros- genomic browser to visualize the position of genetic features tome. This new release covers an extended taxo- along chromosomes; (iv) a Genomicus synteny browser (25) nomic range of 14 species, including for the first time to analyse the evolution of gene order across tunicate and other chordate genomes. Care was taken during the devel- a non-ascidian species, the appendicularian Oiko- opment of ANISEED that the tool remains generic and pleura dioica. Functional annotations, provided for adaptable with minimal effort to any developmental model Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz955/5611675 by guest on 03 December 2019 each species, were enhanced through a combination organism. of manual curation of gene models and the develop- During the preparation of ANISEED 2019, we added ment of an improved orthology detection pipeline. Fi- three additional solitary or colonial ascidian species with nally, gene expression profiles and anatomical terri- recently sequenced genome: Molgula occulta, Corella in- tories can be explored in 4D online through the newly flata and Botryllus leachii and extended for the first time developed Morphonet morphogenetic browser. the system to a non-ascidian species, the appendicularian Oikopleura dioica. We significantly improved the functional annotation of genes, through the manual curation of gene INTRODUCTION model sets in some species and the refinement of our orthol- Tunicates are marine invertebrates with a key phylogenetic ogy assignment procedure, which now detects vertebrate or- position as the sister group of the vertebrates (1,2). Three thologs for a majority of genes from all ascidians species, major groups of tunicates have been classically described. including the main ascidian model species, Ciona robusta The sessile ascidians form the largest group with several (formerly referred to as Ciona intestinalis type A). We en- thousand species listed. Two additional groups of tuni- riched the genomics datasets related to the control of gene cates have a pelagic life-style and rapid molecular evolu- expression in existing and new species. Finally, we inter- tion rates, the thaliaceans and the appendicularians. Their faced the developmental browser of ANISEED 2019 to the phylogenetic position with respect to ascidians has long re- MORPHONET morphogenetic browser, allowing 4D ex- mained debated. Molecular phylogenies suggest that the ploration of gene expression profiles. fast-evolving appendicularians are the sister group of all other tunicates, and that thaliaceans form a monophyletic Extension of the taxonomic range covered group nested within ascidians (3,4) Tunicates studies have led to important discoveries in a In addition to the ten ANISEED 2017 species, three new variety of scientific fields. They illuminated the origin of ascidian
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