Dardaillon J et al. (2020), ANISEED 2019: 4D exploration of genetic data fo...

ECB-ART-49893

Nucleic Acids Res 2020 Jan 08;48D1:D668-D675. doi: 10.1093/nar/gkz955.

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ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates.

Dardaillon J , Dauga D , Simion P , Faure E , Onuma TA , DeBiasse MB , Louis A , Nitta KR , Naville M , Besnardeau L , Reeves W , Wang K , Fagotto M , Guéroult-Bellone M , Fujiwara S , Dumollard R , Veeman M , Volff JN , Roest Crollius H , Douzery E , Ryan JF , Davidson B , Nishida H , Dantec C , Lemaire P .

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ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.

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	Figure 1. Evolution of the species covered by successive ANISEED releases. A blue cross indicates a species covered by the ANISEED genome browser only, without dedicated section in the developmental browser. A black cross indicates a species fully covered by the system.
	Figure 2. Comparison of the one-to-one, one-to-many and many-to-many orthology relationships detected across the whole genome in the ANISEED 2017 and 2019 releases. Each half of the bar graphs present the analysis in 2017 (left half) and 2019 (right half) of the percentage (and number) of orthology relationships linking one Ciona robusta (Cirobu) gene to one gene in the second species indicated (Phmamm: Phallusia mammillata; Harore: Halocynthia roretzi; Moocul; Molgula oculata; Hasp: Homo sapiens). Four scenarios are distinguished, as illustrated on the right side of the figure. Same orthology relationships 2017–2019: orthology relationships found with both the 2017 and 2019 orthology pipelines. Different orthology relationships 2017–2019: the Cirobu gene has orthologs in the second species according to both pipelines, but these orthologs differ. New orthology relationships in 2019: 2019 orthology relationships linking a Cirobu gene, without 2017 ortholog in the second species, to one or more orthologs in this species. A minority of these cases (e.g. 35 in Cirobu/Hsap one-to-one) correspond to orthology relationships for Cirobu NCBI gene models that were added to complement the KH gene model set. Deleted orthology relationships in 2019: 2017 orthology relationships linking a Cirobu gene, without 2019 ortholog in the second species, to one or more orthologs in this species.
	Figure 3. Visualization of in silico predicted transcription Factor binding sites based on SELEX-seq data at the Otx (KH.C4.84) locus in Ciona robusta. The top panel provides a global view of the organization of the locus, including exon positions, chormatin accessible regions, and TF-binding predictions. The bottom panel is an enlarged view of the Otx a-element (REG00000010), a short enhancer activated by ETS and GATA4/5/6 factors (35) through two ETS sites (blue boxes) and three GATA sites (green boxes). ‘Score’ indicated a continuous scoring of predicted affinity. ‘Summits’ associate the highest score of each peak to its summit base.
	Figure 4. 4D exploration of in situ hybridization expression patterns using the Morphonet browser. Left: Developmental browser display of the expression pattern of the Ciona robusta Nodal gene (KH.L106.16) at the early gastrula stage (Stage 10). Center and right: two views of the same experiment in the Morphonet browser.

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