RGD v2.0

RGD v2.0 provides an integrated ruminant genomics resource that aggregates 78 ruminant genome assemblies, multi-omics datasets including 1,936 RNA-seq and 1,053 epigenomic datasets, conserved and cis-regulatory elements, 21,012 orthologous gene clusters with Gene Ontology and pathway annotations, and analysis tools such as UCSC Genome Browser, BLAT, BLAST, Table Browser, and LiftOver to support comparative genomics, functional annotation, and trait association in cattle, sheep, goats, and wild ungulates.

Key Features:

• Extensive Genomic Data: Contains 78 ruminant genomes spanning major livestock species (cattle, sheep, goats) and wild ungulates.
• Synteny Alignments and Orthologous Gene Clusters: Includes 110-species synteny alignments and 21,012 orthologous gene clusters annotated with Gene Ontology and pathway information.
• Conserved and Regulatory Elements: Catalogues approximately 8.6 million conserved elements and around 1 million cis-regulatory elements derived from 1,053 epigenomic datasets.
• Expanded Transcriptome Data: Integrates 1,936 RNA-seq datasets for expression analyses across tissues and conditions.
• Phenotypic Data Integration: Links roughly 155,174 phenotypic datasets to genomic data for trait association studies.
• Visualization and Analysis Tools: Provides UCSC Genome Browser, BLAT, BLAST, and Table Browser for six ruminant livestock species and LiftOver for coordinate conversion between assemblies.
• Tissue Specificity Index (Tau): Implements a Tau metric for batch screening of tissue-specific gene expression.

Scientific Applications:

• Comparative Genomics: Enables cross-species synteny and orthology analyses to study genome conservation and divergence among ruminants.
• Genome Evolution: Supports identification of conserved elements and orthologous clusters to investigate evolutionary patterns.
• Regulatory and Functional Annotation: Facilitates discovery of cis-regulatory elements and functional annotation using Gene Ontology and pathway mappings.
• Expression and Tissue-Specificity Studies: Allows expression profiling and tissue-specific gene screening using 1,936 RNA-seq datasets and the Tau index.
• Trait Association and Breeding Research: Integrates phenotypic datasets to link genomic variation with observable traits for livestock improvement and biomedical investigations.

Methodology:

Synteny alignments across 110 species; identification of 21,012 orthologous gene clusters with Gene Ontology and pathway annotation; detection of ~8.6 million conserved elements and ~1 million cis-regulatory elements from 1,053 epigenomic datasets; processing of 1,936 RNA-seq datasets; and use of BLAT, BLAST, UCSC Genome Browser, Table Browser, and LiftOver for analysis and coordinate conversion.