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

被引：57

作者：

Brozovic, Matija ^{[1
]}

Martin, Cyril ^{[1
]}

Dantec, Christelle ^{[1
]}

Dauga, Delphine ^{[2
,3
]}

Mendez, Mickael ^{[1
]}

Simion, Paul ^{[4
]}

Percher, Madeline ^{[1
]}

Laporte, Baptiste ^{[2
]}

Scornavacca, Celine ^{[4
]}

Di Gregorio, Anna ^{[5
]}

Fujiwara, Shigeki ^{[6
]}

Gineste, Mathieu ^{[1
]}

Lowe, Elijah K. ^{[7
,8
]}

Piette, Jacques ^{[1
]}

Racioppi, Claudia ^{[9
]}

Ristoratore, Filomena ^{[7
]}

Sasakura, Yasunori ^{[10
]}

Takatori, Naohito ^{[11
,12
]}

Brown, Titus C. ^{[13
]}

Delsuc, Frederic ^{[4
]}

Douzery, Emmanuel ^{[4
]}

Gissi, Carmela ^{[14
]}

McDougall, Alex ^{[15
]}

Nishida, Hiroki ^{[12
]}

Sawada, Hitoshi ^{[16
]}

Swalla, Billie J. ^{[17
]}

Yasuo, Hitoyoshi ^{[15
]}

Lemaire, Patrick ^{[1
,2
]}

机构：

[1] Univ Montpellier, CNRS, UMR5237, CRBM, 1919 Route Mende, F-34090 Montpellier, France

[2] Aix Marseille Univ, CNRS, UMR7288, IBDM, F-13288 Marseille 9, France

[3] Bioself Commun, 28 Rue Bibliotheque, F-13001 Marseille, France

[4] Univ Montpellier, CNRS, UMR 5554, IRD,ISE M, F-34090 Montpellier, France

[5] NYU, Coll Dent, Dept Basic Sci & Craniofacial Biol, 345 E 24th St, New York, NY 10010 USA

[6] Kochi Univ, Dept Appl Sci, Kochi, Kochi 7808520, Japan

[7] Stn Zool Anton Dohrn, Dept Biol & Evolut Marine Organisms, I-80121 Naples, Italy

[8] Michigan State Univ, BEACON Ctr Study Evolut Act, E Lansing, MI 48824 USA

[9] NYU, Dept Biol, Ctr Dev Genet, New York, NY 10003 USA

[10] Univ Tsukuba, Shimoda Marine Res Ctr, Shimoda, Shizuoka 4150025, Japan

[11] Tokyo Metropolitan Univ, Sch Sci & Engn, Dept Biol Sci, Dev Biol Lab, 1-1 Minannioosawa, Tokyo 1920397, Japan

[12] Osaka Univ, Grad Sch Sci, Dept Biol Sci, 1-1 Machikaneyama Cho, Toyonaka, Osaka 5600043, Japan

[13] Univ Calif Davis, Populat Hlth & Reprod, Davis, CA 95616 USA

[14] Univ Milan, Dipartimento Biosci, Via Celoria 26, I-20133 Milan, Italy

[15] Univ Paris 06, Sorbonne Univ, CNRS, Lab Biol Dev Villefranche Sur Mer,Observ Oceanol, F-06230 Villefranche Sur Mer, France

[16] Nagoya Univ, Grad Sch Sci, Sugashima Marine Biol Lab, Toba, Aichi 5170004, Japan

[17] Friday Harbor Labs, 620 Univ Rd, Friday Harbor, WA 98250 USA

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

基金：

美国国家科学基金会;

关键词：

CENTRAL-NERVOUS-SYSTEM; CHORDATE CIONA-INTESTINALIS; TRANSCRIPTION FACTORS; REGULATORY NETWORKS; MATERNAL GATA; STEM-CELLS; GENOME; GENE; IDENTIFICATION; EVOLUTION;

D O I：

10.1093/nar/gkv966

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D808 / D818

页数：11

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