Physical evidence indicates that the chloroplast DNA of Chlamydomonas reinhardtii is composed of approximately 75 copies of a small unique sequence. Genetic analysis of zygotes biparental for chloroplast genes shows rapid vegetative segregation of parental chloroplast alleles. Zygote clones composed entirely of homoplasmic progeny cells predominate within 10-20 post-mating generations. A model is proposed here which reconciles the high multiplicity of chloroplast genes with their rapid vegetative segregation rates. Clustering of genomes into a small number of discrete areas (nucleoids) within the chloroplast reduces the effective number of segregating units. A non-random distribution of nucleoids to daughter cells, dictated solely by the spatial arrangement of parental nucleoids with respect to the plane of chloroplast division, further increases the rate of segregation from heteroplasmic cells. Recombination between parental chloroplast genomes is viewed as an indication of nucleoid fusion, and can account for differences in the patterns and rates of segregation at different gene loci. Within such fused nucleoids, clustering of parental genomes and a non-random distribution, again based solely on physical positioning of the genomes, to daughter nucleoids, could act to promote rapid genetic purification of heteroplasmic nucleoids. The effects of biased parental nucleoid ratios, and of potentially unequal nucleoid distributions to daughter chloroplasts are also discussed with respect to observed rates and patterns of chloroplast gene segregation.
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