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ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
Brozovic, M.; Dantec, C.; Dardaillon, J.; Dauga, D.; Faure, E.; Gineste, M.; Louis, A.; Naville, M.; Nitta, K.R.; Piette, J.; Reeves, w.; Scornavacca, C.; Simon, P.; Vincentelli, R.; Bellec, M.; Aicha, S.B.; Fagotto, M.; Guéroult-Bellone, M.; Haeussler, M.; Jacox, E.; Lowe, E.K.; Mendez, M.; Roberge, A.; Stolfi, A.; Yokomori, R.; Brown, C.T.; Cambillau, C.; Christiaen, L.; Delsuc, F.; Douzery, E.; Dumollard, R.; Kusakabe, T.G.; Nakai, K.; Nishida, H.; Satou, Y.; Swalla, B.; Veeman, M.; Volff, J.-N.; Lemaire, P. (2018). ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res. 46(D1): D718-D725. https://dx.doi.org/10.1093/nar/gkx1108
In: Nucleic Acids Research. Information Retrieval: London. ISSN 0305-1048; e-ISSN 1362-4962
Peer reviewed article  
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  • Brozovic, M.
  • Dantec, C.
  • Dardaillon, J.
  • Dauga, D.
  • Faure, E.
  • Gineste, M.
  • Louis, A.
  • Naville, M.
  • Nitta, K.R.
  • Piette, J.
  • Reeves, w.
  • Scornavacca, C.
  • Simon, P.
  • Vincentelli, R.
  • Bellec, M.
  • Aicha, S.B.
  • Fagotto, M.
  • Guéroult-Bellone, M.
  • Haeussler, M.
  • Jacox, E.
  • Lowe, E.K.
  • Mendez, M.
  • Roberge, A.
  • Stolfi, A.
  • Yokomori, R.
  • Brown, C.T.
  • Cambillau, C.
  • Christiaen, L.
  • Delsuc, F.
  • Douzery, E.
  • Dumollard, R.
  • Kusakabe, T.G.
  • Nakai, K.
  • Nishida, H.
  • Satou, Y.
  • Swalla, B.
  • Veeman, M.
  • Volff, J.-N.
  • Lemaire, P.
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 DNAbinding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEXseq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mam-millata genomes. Finally, use of aWashU 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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