In the acellular slime mold Physarum polycephalum, the several hundred genes coding for rRNA are located on linear extrachromosomal DNA molecules of a discrete size, 60 kilobases. Each molecule contains two genes that are arranged in a palindromic fashion and separated by a central spacer region. We investigated how rDNA is inherited after meiosis. Two Physarum amoebal strains, each with an rDNA recognizable by its restriction endonuclease cleavage pattern, were mated, the resulting diploid plasmodium was induced to sporulate, and haploid progeny clones were isolated from the germinated spores. The type of rDNA in each was analyzed by blotting hybridization, with cloned rDNA sequences used as probes. This analysis showed that rDNA was inherited in an all-or-nothing fashion; that is, progeny clones contained one or the other parental rDNA type, but not both. However, the rDNA did not segregate in a simple Mendelian way; one rDNA type was inherited more frequently than the other. The same rDNA type was also in excess in the diploid plasmodium before meiosis, and the relative proportions of the two rDNAs changed after continued plasmodial growth. The proportion of the two rDNA types in the population of progeny clones reflected the proportion in the parent plasmodium before meoisis. The rDNAs in many of the progeny clones contained specific deletions of some of the inverted repeat sequences at the central palindromic symmetry axis. To explain the pattern of inheritance of Physarum rDNA, we postulate that a single copy of rDNA is inserted into each spore or is selectively replicated after meiosis.In some lower eucaryotic organisms, the multiple genes coding for rRNA are located on extrachromosomal DNA molecules. In the best studied of these systems, Tetrahymena species (ciliates) and Physarum polycephalum (an acellular slime mold), the extrachromosomal rDNAs are of a discrete size (about 20 and 60 kilobases [kb], respectively) and have a similar structure. The molecules are linear and are organized as palindromes, with two transcription units arranged in opposite orientations near the ends of the DNA, separated by a spacer region with a rotational symmetry axis in the middle (13, 21). In P. polycephalum rDNA this spacer is 20 kb in size and contains a complex series of directly repeated, inversely repeated, and unique sequences (8). Replication of P. polycephalum rDNA molecules (22) commences at one of four potential origins in the central spacer region and proceeds bidirectionally towards the ends of the linear molecules. In contrast to chromosomal DNA replication, rDNA replication takes place during most of the mitotic cycle, notjust in the S phase, and is unscheduled. That is, some rDNA molecules replicate once, some more than once, and some not at all, with the end result being that the total number of molecules after each mitosis is unchanged. The ends of the linear P. polycephalum rDNA molecules are heterogeneous in size, and near each end are located onenucleotide gaps on one strand at specific nucleotide seq...