The ecological importance of rDNA CNV has been well characterized among prokaryotes, with rDNA copy number being linked to ecosystem stoichiometry, growth rate and competitive ability, as well as bias in estimates of organismal abundance in high throughput amplicon sequencing. How rDNA CNV varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. To address this knowledge gap, we examined rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes. We assessed copy number conservation across phylogenetic scales, ecological lifestyles, and genome size. Further, we explored the contribution of rDNA CNV to estimates of fungal relative abundance in high-throughput amplicon sequencing datasets.
Results/Conclusions
We found that rDNA copy number varied considerably across fungi, ranging from an estimated 14 to 1,442 copies (mean = 113, median = 82), and copy number similarity was inversely correlated with phylogenetic distance. No correlations were found between rDNA CNV and fungal trophic mode or ecological guild. Although rDNA copy number has been reported to be significantly positively correlated with genome size in other eukaryotes, we found no such correlation in fungi. Mock community analysis of fungi with known rDNA copy number revealed factors other than rDNA CNV are likely most important in determining sequence read counts, most notably stochasticity linked to PCR amplification. Taken together, these results show that like other microorganisms, fungi exhibit substantial variation in rDNA copy number, which is linked to their phylogeny in a scale-dependent manner. The ecological role of rDNA CNV in terms of guild associations or high-throughput sequencing read counts, however, appears to be less consistent than observed in other microorganisms.