singlecopy

Singlecopy, often written as single-copy, is a term used in genetics and genomics to describe genes or loci that occur in exactly one copy within a genome. In practice, a single-copy gene is a gene that does not have a recent paralog within the same genome, making it a useful reference for comparative analyses. The concept contrasts with multi-copy genes, which exist in several copies due to duplication events, or with assembly fragmentation that can obscure true copy number.

In comparative genomics and phylogenomics, single-copy genes are sought as orthologous markers because they reduce complications from paralogy when reconstructing species trees or performing multi-species alignments. Researchers compile libraries of single-copy orthologs across taxa to improve phylogenetic resolution and to estimate divergence times. Databases and software pipelines, such as OrthoFinder, BUSCO, and others, identify candidate single-copy genes across genomes by clustering gene families and checking copy number and completeness.

Identification criteria include consistent single copy across the majority of studied species, presence in coding regions, and absence of recent lineage-specific duplications. Data quality, genome completeness, and assembly fragmentation influence accuracy; incomplete or misannotated genomes can misclassify copy number. Pseudogenes and assembly artifacts must be filtered out.

Applications include phylogenetics, molecular dating, and as reference genes for normalization in expression studies, though suitability depends on lineage-specific evolution and functional constraints. Caution is advised when using single-copy genes from highly duplicated lineages or when data coverage is uneven.