Nanochromosome Copy Number Does not Correlate with RNA Levels Though Patterns are Conserved between Strains of the Ciliate Morphospecies Chilodonella uncinata

In some ciliates, extensive genome fragmentation leads to a macronucleus (i.e. somatic nucleus) containing gene-sized chromosomes that vary in copy number. Yet the relationship between copy number and expression level is not well understood as previous work has shown a variety of patterns. For example, nanochromosome copy numbers are positively correlated to mRNA levels in spirotrichous ciliates, while one study of Chilodonella uncinata suggested that they were inversely correlated. To study further copy number and expression levels in C. uncinata, we analyzed 11 members in five gene families (SSU-rDNA, actin, alpha-tubulin, histidine acid phosphatase family protein and a protein kinase domain containing protein) from one strain. We find that macronuclear copy numbers of these genes range from hundreds to thousands per cell, and that copy number does not correlate with expression level as measured by steady-state RNA in predominantly-vegetative cultures. We also compared six of these genes to their orthologs in a second genetically-isolated strain of C. uncinata to reveal that patterns of nanochromosome and transcript copy numbers are conserved between strains. Our data suggest that nanochromosome copy number may be related to a feature like nuclear architecture.