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

Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Magali Naville, Kazuhiro R. Nitta, Jacques Piette, Wendy Reeves, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin JacoxElijah K. Lowe, Mickael Mendez, Alexis Roberge, Alberto Stolfi, Rui Yokomori, Charles Brown, Christian Cambillau, Lionel Christiaen, Frédéric Delsuc, Emmanuel Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie Swalla, Michael Veeman, Jean Nicolas Volff, Patrick Lemaire

Research output: Contribution to journalArticle

22 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)D718-D725
JournalNucleic Acids Research
Volume46
Issue numberD1
DOIs
StatePublished - Jan 1 2018

Fingerprint

Urochordata
Genome
Databases
Gene Expression
Vertebrates
Transcription Factors
Lancelets
Chemical Databases
RNA
Epigenomics
Genes
Binding Sites
Datasets
DNA

ASJC Scopus subject areas

  • Genetics

Cite this

Brozovic, M., Dantec, C., Dardaillon, J., Dauga, D., Faure, E., Gineste, M., ... Lemaire, P. (2018). ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Research, 46(D1), D718-D725. https://doi.org/10.1093/nar/gkx1108

ANISEED 2017 : Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. / 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, Charles; 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.

In: Nucleic Acids Research, Vol. 46, No. D1, 01.01.2018, p. D718-D725.

Research output: Contribution to journalArticle

Brozovic, M, Dantec, C, Dardaillon, J, Dauga, D, Faure, E, Gineste, M, Louis, A, Naville, M, Nitta, KR, Piette, J, Reeves, W, Scornavacca, C, Simion, P, Vincentelli, R, Bellec, M, Aicha, SB, Fagotto, M, Guéroult-Bellone, M, Haeussler, M, Jacox, E, Lowe, EK, Mendez, M, Roberge, A, Stolfi, A, Yokomori, R, Brown, C, Cambillau, C, Christiaen, L, Delsuc, F, Douzery, E, Dumollard, R, Kusakabe, T, Nakai, K, Nishida, H, Satou, Y, Swalla, B, Veeman, M, Volff, JN & Lemaire, P 2018, 'ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets', Nucleic Acids Research, vol. 46, no. D1, pp. D718-D725. https://doi.org/10.1093/nar/gkx1108
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, Charles ; 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. / ANISEED 2017 : Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. In: Nucleic Acids Research. 2018 ; Vol. 46, No. D1. pp. D718-D725.
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AU - Dauga, Delphine

AU - Faure, Emmanuel

AU - Gineste, Mathieu

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