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

Abstract

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 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 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.

Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error

“…Other estimates are approximately 316 000 rDNA copies in Vorticella sp. (CI: Oligohymenophorea) [23] and 59 000 to 80 000 in Chilodonella uncinata (CI: Phyllopharyngea) [24].…”

Insights into transgenerational epigenetics from studies of ciliates

“…For example, each chromosome in Paramecium tetraurelia is amplified to ~800 copies (Duret et al, 2008). In contrast, copy numbers in Oxytricha and Chilodonella range from a couple hundred up to a million for each of 15,000–20,000 different nanochromosomes (Huang and Katz, 2014; Jonsson et al, 2009). …”

Evolutionary origins and impacts of genome architecture in ciliates

“…The efficiency of phenotypic assortment through amitosis (and the efficacy of selection) is strongly tied to the structure of the somatic genome. For instance, in Chilodonella and Oxytricha , the somatic nuclei harbor thousands of unique gene‐sized chromosomes, with each chromosome at independent copy numbers ranging from several hundred to nearly a million copies . The fate of every gene in these genomes is independent of the others.…”

“…For instance, in Chilodonella and Oxytricha, the somatic nuclei harbor thousands of unique gene-sized chromosomes, with each chromosome at independent copy numbers ranging from several hundred to nearly a million copies. [66][67][68][69] The fate of every gene in these genomes is independent of the others. Selection can favor those nuclei harboring fewer deleterious mutations/arrangements, which could be lost over time without impacting other genes/chromosomes.…”