Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

Lotus A. Lofgren, Jessie K. Uehling, Sara Branco, Thomas D. Bruns, Francis Martin, Peter G. Kennedy

Research output: Contribution to journalArticlepeer-review

127 Scopus citations


Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. 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, ecological guild or genome size. 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.

Original languageEnglish (US)
Pages (from-to)721-730
Number of pages10
JournalMolecular ecology
Issue number4
StatePublished - Feb 1 2019

Bibliographical note

Funding Information:
#1441604 to J. Uehling, and NSF grant #1554375 to P.G. Kennedy.

Funding Information:
We thank R. Vilgalys for sharing cultures and access to the unpub‐ lished genomic data of four fungal species, A. Gryganskyi for use of unpublished genomic data for three species of early diverging fungi, R. de Vries, M. Mäkelä and K. Hildén for use of unpublished genomic data for the D. squalens sequencing projects, I. Grigoriev and the JGI MycoCosm team for assistance accessing fungal ge‐ nomes, F. Keck for assistance with using Phylosignal and 3 anony‐ mous reviewers for helpful comments and feedback. Support for this study was provided by a National Science Foundation

Publisher Copyright:
© 2019 John Wiley & Sons Ltd


  • copy number variation
  • fungi
  • lifestyle
  • phylogenetic signal
  • rDNA
  • read depth


Dive into the research topics of 'Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles'. Together they form a unique fingerprint.

Cite this