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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 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.
Figure 1. Interactive gene Phylogenies. Screenshot from a part of the phylogenetic gene tree including genes Cirobu.g00002339 and Cirobu.g00002287. Species are color-coded and the tree can be compressed or extended lengthwise and zoomed in and out. Note the difference between the two groups of genes. In group I, the gene phylogeny follows the species phylogeny, and tunicate genes are considered orthologous to the vertebrate genes of the group. In group II by contrast, the gene phylogeny does not follow the species phylogeny, and we consider that the tunicate genes have no unequivocal vertebrate orthologs.
Figure 2. Genomicus and the study of global and local genome rearrangements. (A) Karyotype view showing the mapping of segments of Human Chromosome 1 onto Ciona robusta chromosomes. (B) Phyloview of the Phallusia mammillata gene Phmamm.g00004580 showing rapid loss of microsynteny within tunicates and complete loss with vertebrates.
Figure 3. Simultaneous visualization of candidate transcription factor binding sites in two known regulatory sequences. The WashU epigenome browser allows splitting the display to show two independent loci from the same genome. Here the display shows regulatory sequences of the Cirobu Otx (Cirobu.g00006940; left part of the window) and Nodal (Cirobu.g00010576; right part of the window) genes, and predicted local in silico binding affinity for transcription factors of the ETS and GATA families, known to regulate these enhancers.
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