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

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...

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Published in:Nucleic acids research Vol. 46; no. D1; pp. D718 - D725
Main Authors: Brozovic, Matija, Dantec, Christelle, Dardaillon, Justine, Dauga, Delphine, Faure, Emmanuel, Gineste, Mathieu, Louis, Alexandra, Naville, Magali, Nitta, Kazuhiro R, Piette, Jacques, Reeves, Wendy, Scornavacca, Céline, Simion, Paul, Vincentelli, Renaud, Bellec, Maelle, Aicha, Sameh Ben, Fagotto, Marie, Guéroult-Bellone, Marion, Haeussler, Maximilian, Jacox, Edwin, Lowe, Elijah K, Mendez, Mickael, Roberge, Alexis, Stolfi, Alberto, Yokomori, Rui, Brown, C Titus, Cambillau, Christian, Christiaen, Lionel, Delsuc, Frédéric, Douzery, Emmanuel, Dumollard, Rémi, Kusakabe, Takehiro, Nakai, Kenta, Nishida, Hiroki, Satou, Yutaka, Swalla, Billie, Veeman, Michael, Volff, Jean-Nicolas, Lemaire, Patrick
Format: Journal Article
Language:English
Published: England Oxford University Press 04.01.2018
Subjects:
Animals
Biological Evolution
Ciona intestinalis - genetics
Computer Science
Data Mining
Database Issue
Databases, Genetic
Datasets as Topic
DNA - metabolism
Evolution, Molecular
Gene Expression
Gene Ontology
Genome
Internet
Modeling and Simulation
Molecular Sequence Annotation
Phylogeny
Protein Binding
Species Specificity
Transcription Factors - metabolism
Transcription, Genetic
Urochordata - genetics
Vertebrates - genetics
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ISSN:0305-1048, 1362-4962, 1362-4962
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Summary: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.
Bibliography:ObjectType-Article-2
SourceType-Scholarly Journals-1
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PMCID: PMC5753386
These authors contributed equally to this work as first authors.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkx1108