Review Diversification of uniparental inheritance mechanisms — Orchestrating the fine balance of cytoplasmic genome populations

Chloroplasts and mitochondria harbor their own genomes, collectively referred to as chloroplast (cp) and mitochondrial (mt) DNA or cytoplasmic DNA. These genomes encode essential gene sets required for the maintenance of chloroplast and mitochondrial functions, including components of the photosynthetic and respiratory electron transport chains as well as ribosomal machinery. The faithful transmission of cytoplasmic DNA to the next generation is therefore critical for eukaryotic life. Across diverse eukaryotic taxa—including fungi, algae, animals, and land plants—cytoplasmic genomes are transmitted predominantly through the maternal lineage. The molecular mechanisms underlying maternal inheritance have been actively investigated in a wide range of organisms, and multiple, not mutually exclusive models have been proposed, including selective autophagy, nuclease-mediated degradation, ubiquitin–proteasome–dependent pathways, and regulation of organelle protein import and stability. A distinctive feature of cytoplasmic DNA inheritance is their high copy number per cell, which renders their transmission dynamics fundamentally different from those of nuclear genes and not readily explained by classical Mendelian genetics. This review summarizes current understanding of the cellular, molecular, and evolutionary mechanisms underlying the maternal inheritance of chloroplast and mitochondrial DNA across eukaryotes, with particular emphasis on intracellular population genetics, nucleoid organization, and copy-number dynamics.