title: ANISEED 2015: a digital framework for the comparative developmental biology of ascidians.
abstract: Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France.
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authors.lastname: Brozovic
authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France.
authors.forename: Cyril
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authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France.
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authors.affiliation: Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France Bioself Communication, 28 rue de la Bibliothèque, F-13001 Marseille, France.
authors.forename: Delphine
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authors.lastname: Dauga
authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France.
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authors.affiliation: Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France.
authors.forename: Paul
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authors.lastname: Simion
authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France.
authors.forename: Madeline
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authors.lastname: Percher
authors.affiliation: Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France.
authors.forename: Baptiste
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authors.lastname: Laporte
authors.affiliation: Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France.
authors.forename: Céline
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authors.affiliation: Department of Applied Science, Kochi University, Kochi-shi, Kochi 780-8520, Japan.
authors.forename: Shigeki
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authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France.
authors.forename: Mathieu
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authors.affiliation: Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA.
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authors.initials: EK
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authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France.
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authors.affiliation: Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
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authors.affiliation: Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan.
authors.forename: Yasunori
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authors.affiliation: Developmental Biology Laboratory, Department of Biological Sciences, School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiooji, Tokyo 192-0397, Japan Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
authors.forename: Naohito
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authors.affiliation: Population Health and Reproduction, UC Davis, Davis, CA 95616, USA.
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authors.initials: TC
authors.lastname: Brown
authors.affiliation: Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France.
authors.forename: Frédéric
authors.initials: F
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authors.affiliation: Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Douzery
authors.affiliation: Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy.
authors.forename: Carmela
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authors.affiliation: Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.
authors.forename: Alex
authors.initials: A
authors.lastname: McDougall
authors.affiliation: Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
authors.forename: Hiroki
authors.initials: H
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authors.affiliation: Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba 517-0004, Japan.
authors.forename: Hitoshi
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authors.forename: Billie J
authors.initials: BJ
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authors.affiliation: Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.
authors.forename: Hitoyoshi
authors.initials: H
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authors.affiliation: Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France patrick.lemaire@crbm.cnrs.fr.
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mesh_terms: D000818:Animals; D002938:Ciona intestinalis / Q000196:embryology* / Q000235:genetics*; D030541:Databases, Genetic; D047108:Embryonic Development / Q000235:genetics; D023281:Genomics; D014561:Urochordata / Q000033:anatomy & histology / Q000196:embryology* / Q000235:genetics*