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Nucleic Acids Res. 2018 Jan 4;46(D1):D718-D725. doi: 10.1093/nar/gkx1108.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

Author information

1
CRBM, Université de Montpellier, CNRS, Montpellier, France.
2
Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France.
3
Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France.
4
Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France.
5
DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France.
6
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.
7
IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France.
8
Division of Biology, Kansas State University, Manhattan, Kansas.
9
ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.
10
AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France.
11
Université de Montpellier, Montpellier, France.
12
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.
13
Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.
14
Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
15
BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA.
16
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
17
Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan.
18
Population Health and Reproduction, UC Davis, Davis, CA 95616, USA.
19
New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA.
20
Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan.
21
Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
22
Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
23
Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA.

Abstract

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

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