All ciliates have both a micronucleus, which is mostly inactive during vegetative growth, and a macronucleus, which is enlarged (owing to DNA amplification) and transcriptionally active. In Oxytricha trifallax, 96% of the micronuclear genome is eliminated during formation of the macronucleus. The macronuclear genome in Oxytricha is composed of tens of thousands of tiny chromosomes. Laura Landweber and colleagues now report the first Oxytricha macronuclear genome (PLoS Biol. 11, e1001473, 2013). The authors found very high levels of nucleotide diversity, with mean SNP heterozygosity of 4.0%. The authors estimated that the haploid number of nanochromosomes was ∼15,600, with a mean length of ∼3.2 kb. Extensive alternative fragmentation, in which there are multiple versions of nanochromosomes that have overlapping genic regions, was observed in up to 40% of surveyed nanochromosomes. Nanochromosome copy number was also highly variable, as was nanochromosome length. The authors note that the most remarkable aspect of this macronuclear genome is the number of telomeres, which are present on every nanochromosome. Not surprisingly, this organism has acquired multiple new telomere-binding proteins.