ncOrtho

ncOrtho identifies microRNA (miRNA) orthologs across unannotated genomes using a synteny-informed approach to enable evolutionary and comparative analyses of miRNAs.

Key Features:

• Synteny-Informed Approach: Leverages synteny information to enhance the precision of miRNA ortholog detection through targeted searches.
• Scalability and Precision: Scales to analyze hundreds of species simultaneously while matching miRNA annotations derived from multi-tissue transcriptomes with high precision.
• Comprehensive Ortholog Detection: Identifies orthologs across a wide range of vertebrate species and has been applied to 266 human miRNA families across 402 vertebrate species.

Scientific Applications:

• Evolutionary Analysis: Detects temporal patterns of miRNA acquisition, including four distinct bursts across vertebrate evolution with the most recent in the last common ancestor of higher primates.
• Phylogenomic Marker: Uses miRNA family presence as low-diversity markers for phylogenomic analyses to help resolve clades affected by incomplete lineage sorting.
• Genome Duplication Insights: Infers lineage-specific whole genome duplications from presence–absence patterns of miRNA orthologs.
• Comparative Genomics: Enables routine incorporation of miRNAs into evolutionary studies traditionally focused on protein-coding genes.

Methodology:

ncOrtho employs a synteny-informed pipeline that integrates multi-tissue transcriptome-derived miRNA annotations to identify miRNA orthologs across unannotated genomes.