homoplasmy

Homoplasmy refers to the condition in which all copies of a given genome in an organism’s cells are identical. Most notably, mitochondrial DNA (mtDNA) and plastid DNA (cpDNA) in plants carry multiple, separate copies per cell, and homoplasmy describes when these copies share an identical sequence.

In contrast, heteroplasmy is the coexistence of more than one mtDNA or plastid genome variant within a cell or organism. Causes include de novo mutations in some copies, paternal leakage in rare cases, and, in long-lived tissues, the accumulation of mutations over time; recombination is rare in animal mtDNA.

Mechanisms that lead to homoplasmy involve bottlenecks during oogenesis that drastically reduce mtDNA copy number and permit random genetic drift to fix a haplotype, followed by clonal expansion. In plants, sorting of plastids during development can similarly drive the genome toward a single haplotype.

Clinically, heteroplasmy levels influence disease expression: many mitochondrial disorders show variable penetrance depending on the proportion of mutant genomes. Some pathogenic mtDNA mutations are associated with disease even when present in all copies (homoplasmy), while others require a threshold of mutant genomes to manifest; tissue energy demands affect sensitivity. Detection relies on sequencing technologies, with variant load reported as a percentage.

In summary, homoplasmy describes uniform organellar genomes within a cell, reflecting clonal expansion and selection that remove variation; it contrasts with heteroplasmy, which captures intra-cellular genomic diversity. Understanding the balance between homoplasmy and heteroplasmy is central to explaining mitochondrial genetics, inheritance, and disease.