Genomicus-tunicates

Genomicus-tunicates enables multi-dimensional exploration and comparative analysis of tunicate genomes leveraging ANISEED resources to support studies of gene function, regulation, and evolution.

Key Features:

• Multi-Dimensional Navigation: Genome exploration is provided linearly along chromosomes, transversely across species, and chronologically through evolutionary time.
• Orthology Relationships: Functionally annotated gene and transcript models include orthology relationships within tunicates and with echinoderms, cephalochordates, and vertebrates.
• Genetic Elements Description: Annotation of repeated sequences and cis-regulatory modules complements gene models.
• Gene Expression Profiles: Expression data are available for thousands of genes under wild-type and experimentally manipulated conditions using formal anatomical ontologies.
• Complementary Browsers: Includes a developmental browser (gene- or territory-centric), advanced genomic browsers for gene-centered feature integration, and a Genomicus synteny browser for local gene order conservation across deuterostomes.
• Extended Taxonomic Range: The release covers 14 species, including the appendicularian Oikopleura dioica, enabling broader comparative studies.
• Enhanced Functional Annotations: Functional annotation improvements arise from manual curation of gene models and refined orthology-detection pipelines.
• 4D Morphogenetic Exploration: Integration with the Morphonet morphogenetic browser enables exploration of gene expression profiles and anatomical territories in four dimensions.
• Integration with External Databases: Data integration includes external molecular and taxonomy databases for cross-referencing.
• Epigenomics Support: Support for epigenomics datasets includes RNA-seq, ChIP-seq, and SELEX-seq data.
• Phylogenetic Gene Trees: Phylogenetic gene trees are provided for a significant portion of tunicate genes.
• DNA-Binding Specificity: High-resolution DNA-binding specificity descriptions for transcription factors in Ciona robusta facilitate mapping of candidate binding sites across genomes.
• Microsynteny Exploration: A Genomicus server is used to explore microsynteny relationships within tunicates and between tunicates and other deuterostomes.

Scientific Applications:

• Comparative Genomics: Analysis of gene order conservation and microsynteny across deuterostomes and among tunicate species.
• Evo-Devo Research: Investigation of developmental gene expression patterns and anatomical territory dynamics using Morphonet and anatomical ontologies.
• Evolutionary Biology: Study of orthology relationships and phylogenetic gene trees to infer gene family evolution and vertebrate ancestry.
• Gene Regulation and Epigenomics: Integration of RNA-seq, ChIP-seq, and SELEX-seq data to analyze regulatory elements and transcription factor binding specificity, particularly in Ciona robusta.
• Functional Annotation Improvement: Use of manual curation and orthology-detection pipelines to refine gene and transcript model annotations.

Methodology:

Manual curation of gene models; orthology-detection pipelines and generation of phylogenetic gene trees; integration of RNA-seq, ChIP-seq, and SELEX-seq datasets; use of a Genomicus server for microsynteny analysis; and use of the Morphonet morphogenetic browser for 4D expression and anatomical territory exploration.