Journal
NUCLEIC ACIDS RESEARCH
Volume 46, Issue D1, Pages D718-D725Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkx1108
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Funding
- Agence Nationale de la Recherche (ANR) [Equipex Morphoscope2 ANR-11-EQPX-0029, Chor-Reg-Net NT05-2_42083, Chor-Evo-Net ANR-08-BLAN-0067-01, ANR-11-BINF-0002, ANR-11-INBS-0013, ANR-13-BSV2-0011-01, ANR-10-BINF-01-03, ANR-10-LABX-54 MEMO-LIFE, ANR-10-IDEX-0001-02 PSL*, ANR-16-CE92-0019]
- Dopaminet European project
- National Institutes of Health (NIGMS) [R01 GM096032]
- Japan Society for the Promotion of Science (JSPS) KAKENHI [16H04724]
- ANR
- CNRS
- ANR TED project
- Marie Curie IIF cis-reg-logic
- National Institutes of Health [R00 HD084814]
- National Institutes of Health (NHGRI) [5U41HG002371-15]
- Institut de Biologie Computationnelle, Montpellier, France
- Direct For Biological Sciences [1456555] Funding Source: National Science Foundation
- Grants-in-Aid for Scientific Research [17KT0023] Funding Source: KAKEN
- EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT [R01HD085909, R00HD084814] Funding Source: NIH RePORTER
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [U41HG002371] Funding Source: NIH RePORTER
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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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