ANISEED

ANISEED integrates curated genomic, gene expression, phenotypic, anatomical and phylogenetic data for tunicates to support comparative developmental biology and evolutionary genomics.

Key Features:

• Integrated knowledge base: Functionally annotated gene and transcript models with orthology relationships among tunicates and other deuterostomes (echinoderms, cephalochordates, vertebrates) are centralized for comparative analyses.
• Data diversity: Inclusion of repeated elements, cis-regulatory modules, phenotyping data and formal anatomical ontologies describing gene expression in wild-type and experimentally manipulated conditions.
• 3D and 4D visualization: A 3D Virtual Embryo module provides quantitative geometrical descriptions of developing cells from reconstructed three-dimensional embryos up to gastrula stages, and Morphonet-based morphogenetic 4D visualization maps gene expression and anatomical territories in time.
• Data integration and analysis: Heterogeneous datasets are integrated at multiple scales to enable automatic inference of gene regulatory interactions, identification of inducing signals, and discovery of novel asymmetric cell divisions.
• Genomicus synteny comparisons: Local gene order conservation across deuterostomes is analyzed using Genomicus synteny data.
• Expanded taxonomic coverage: The resource covers 14 tunicate species, including the appendicularian Oikopleura dioica, for broader comparative studies.
• Enhanced functional annotations: Manual curation of gene models combined with an improved orthology detection pipeline provides higher-quality annotations.

Scientific Applications:

• Developmental systems biology: Linking genomic information to phenotypic outcomes at cellular, tissue and embryo scales to study developmental programs.
• Embryonic dynamics: Quantitative analysis of cell geometry and spatiotemporal gene expression during embryogenesis up to gastrulation.
• Gene regulatory network reconstruction: Integration of expression data and cis-regulatory modules to infer regulatory interactions and inducing signals.
• Evolutionary genomics: Comparative analyses of orthology, synteny and anatomical ontologies across deuterostomes to study evolutionary relationships.
• Functional genomics: Correlating annotated gene models, regulatory elements and phenotypes to investigate organ encoding and functional outcomes.

Methodology:

Integration of functional, gene expression, phenotyping, anatomical and phylogenetic datasets; generation and manual curation of functionally annotated gene and transcript models; improved orthology detection pipeline and orthology relationships; inclusion of repeated elements and cis-regulatory modules; formal anatomical ontologies; reconstruction of three-dimensional embryos and quantitative geometrical descriptions up to gastrula stages; Morphonet-based 4D morphogenetic visualization; Genomicus synteny comparisons; and automated inference of gene regulatory interactions, inducing signals and novel asymmetric divisions across 14 species including Oikopleura dioica.