ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

  • Justine Dardaillon
    CRBM, Université de Montpellier, CNRS, Montpellier, France
  • Delphine Dauga
    Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
  • Paul Simion
    ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
  • Emmanuel Faure
    Laboratoire d’Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, Montpellier, France
  • Takeshi A Onuma
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
  • Melissa B DeBiasse
    Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
  • Alexandra Louis
    DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
  • Kazuhiro R Nitta
    IBDM, Université Aix-Marseille, CNRS, Marseille, France
  • Magali Naville
    Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
  • Lydia Besnardeau
    Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
  • Wendy Reeves
    Division of Biology, Kansas State University, Manhattan, KS 66506, USA
  • Kai Wang
    State 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
  • Marie Fagotto
    Université de Montpellier, Montpellier, France
  • Marion Guéroult-Bellone
    Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
  • Shigeki Fujiwara
    Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi-shi, Kochi, Japan
  • Rémi Dumollard
    Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
  • Michael Veeman
    Division of Biology, Kansas State University, Manhattan, KS 66506, USA
  • Jean-Nicolas Volff
    Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
  • Hugues Roest Crollius
    DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
  • Emmanuel Douzery
    ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
  • Joseph F Ryan
    Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
  • Bradley Davidson
    Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
  • Hiroki Nishida
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
  • Christelle Dantec
    CRBM, Université de Montpellier, CNRS, Montpellier, France
  • Patrick Lemaire
    CRBM, Université de Montpellier, CNRS, Montpellier, France

抄録

<jats:title>Abstract</jats:title><jats:p>ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.</jats:p>

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