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

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 Celine
• Simion Paul
• Vincentelli Renaud
• Bellec Maëlle
• Aicha Sameh Ben
• Fagotto Marie
• Gueroult-Bellone Marion
• Haeussler Maximilian
• Jacox Edwin
• Lowe Elijah K.
• Mendez Mickaël
• Roberge Alexis
• Stolfi Alberto
• Yokomori Rui
• Brown C. Titus
• Cambillau Christian
• Christiaen Lionel
• Delsuc Frédéric
• Douzery Emmanuel J.P.
• Dumollard Rémi
• Kusakabe Takehiro
• Nakai Kenta
• Nishida Hiroki
• Satou Yutaka
• Swalla Billie
• Veeman Michael
• Volff Jean-Nicolas
• Lemaire Patrick

document type

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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