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

Matija Brozovic 1 Christelle Dantec 1 Justine Dardaillon 1 Delphine Dauga 2 Emmanuel Faure 3, 4 Mathieu Gineste 1 Alexandra Louis 5 Magali Naville 6 Kazuhiro R. Nitta 7 Jacques Piette 1 Wendy Reeves 8 Celine Scornavacca 9 Paul Simion 9 Renaud Vincentelli 10 Maëlle Bellec 11 Sameh Ben Aicha 12 Marie Fagotto 11 Marion Gueroult-Bellone 2 Maximilian Haeussler 13 Edwin Jacox 1 Elijah K. Lowe 14 Mickaël Mendez 7 Alexis Roberge 11 Alberto Stolfi 15 Rui Yokomori 16 C. Titus Brown 14 Christian Cambillau 10 Lionel Christiaen 17 Frédéric Delsuc 9 Emmanuel Douzery 9 Rémi Dumollard 12 Takehiro Kusakabe 18 Kenta Nakai 16 Hiroki Nishida 19 Yutaka Satou 20 Billie Swalla 14 Michael Veeman 8 Jean-Nicolas Volff 21 Patrick Lemaire 1, 3
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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Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, et al.. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Research, Oxford University Press, 2018, 46 (D1), pp.D718-D725. ⟨10.1093/nar/gkx1108⟩. ⟨hal-01636650⟩

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