ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

Matija Brozovic 1 Cyril Martin 1 Christelle Dantec 1 Delphine Dauga 2, 3 Mickäel Mendez 1 Paul Simion 4 Madeline Percher 1 Baptiste Laporte 2 Celine Scornavacca 4 Anna Di Gregorio 5 Shigeki Fujiwara 6 Mathieu Gineste 1 Elijah K. Lowe 7, 8 Jacques Piette 1 Claudia Racioppi 9 Filomena Ristoratore 7 Yasunori Sasakura 10 Naohito Takatori 11, 12 Titus C. Brown 13 Fréderic Delsuc 4 Emmanuel Douzery 4 Carmela Gissi 14 Alex Mcdougall 15 Hiroki Nishida 11 Hitoshi Sawada 16 Billie J. Swalla 17 Hitoyoshi Yasuo 15 Patrick Lemaire 1, 2
1 CRBM - Centre de recherche en Biologie Cellulaire
2 IBDM - Institut de Biologie du Développement de Marseille
3 Bioself Communication [Marseille]
4 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
5 New York University College of Dentistry
6 Kochi University
7 Stazione Zoologica Napoli
8 Michigan State University [East Lansing]
9 NYU - New York University [New York]
10 Shimoda Marine Research Center
11 Osaka University [Osaka]
12 Tokyo Metropolitan University [Tokyo]
13 UC Davis - University of California [Davis]
14 Università degli studi di Milano [Milano]
15 LBDV - Laboratoire de Biologie du Développement de Villefranche sur mer
16 NAGOYA - Nagoya
17 Friday Harbor Laboratories
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.
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UPMC | ISEM | LBDV | IRD | AGROPOLIS | UNIV-AMU | BS | B3ESTE | UNIV-MONTPELLIER | SORBONNE-UNIVERSITE | SU-SCIENCES | INSU | UMS-829 | PSL | EPHE | CIRAD | IBPS

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Matija Brozovic, Cyril Martin, Christelle Dantec, Delphine Dauga, Mickäel Mendez, et al.. ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Research, Oxford University Press, 2016, 44 (D1), pp.D808-D818. ⟨10.1093/nar/gkv966⟩. ⟨hal-01295171⟩

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