CORD

CORD annotates olfactory receptor genes across chordate genomes to provide a comprehensive resource for comparative and evolutionary analyses of olfactory receptor repertoires.

Key Features:

• Genome annotation (nhmmer/Genome2OR): Processes and annotates olfactory receptors from 1,695 sequenced chordate genomes from the NCBI Assembly database (January 2021) using the nhmmer-based tool Genome2OR, yielding 765,248 olfactory receptor genes (404,426 functional and 360,822 pseudogenes).
• Protein sequence similarity network: Constructs a large protein sequence similarity network encompassing all annotated receptors.
• Community clustering: Clusters the sequence similarity network into 20 communities.
• Community classification by taxa: Classifies the 20 communities into three categories based on presence or absence in ray-finned fish and lobe-finned fish.
• Structural models and sequence profiles: Provides structural models and sequence profiles for annotated receptors.
• Cross-references and species metadata: Includes cross-references to public databases and species images linked to annotated entries.
• Mechanistic sequence/structure analysis: Analyzes sequences and structural models to provide insights into olfactory receptor activation and desensitization mechanisms.

Scientific Applications:

• Comparative genomics: Comparative and evolutionary analyses of olfactory receptor repertoires across 1,695 chordate genomes.
• Evolutionary pattern analysis: Investigation of evolutionary patterns and functional diversification using community classification and sequence similarity networks.
• Structure–function studies: Structural and sequence-based studies of olfactory receptor activation and desensitization mechanisms.

Methodology:

Annotation was performed with the nhmmer-based Genome2OR on 1,695 chordate genomes from NCBI Assembly (January 2021); a protein sequence similarity network was constructed and clustered into 20 communities, with communities classified by presence/absence in ray-finned versus lobe-finned fish; structural models and sequence profiles were generated and analyzed alongside sequences to investigate activation and desensitization features.