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 journalArticle

1 Citation (Scopus)

Abstract

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
Volume28
Issue number4
DOIs
StatePublished - Feb 1 2019

Fingerprint

Fungal DNA
DNA Copy Number Variations
Ribosomal DNA
lifestyle
ribosomal DNA
Life Style
genome
Genome
phylogenetics
DNA
phylogeny
Fungi
fungus
fungi
microorganism
microorganisms
Genome Size
Phylogeny
guild
Computer Simulation

Keywords

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

PubMed: MeSH publication types

  • Journal Article
  • Research Support, U.S. Gov't, Non-P.H.S.

Cite this

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles. / Lofgren, Lotus A.; Uehling, Jessie K.; Branco, Sara; Bruns, Thomas D.; Martin, Francis; Kennedy, Peter G.

In: Molecular ecology, Vol. 28, No. 4, 01.02.2019, p. 721-730.

Research output: Contribution to journalArticle

Lofgren, Lotus A. ; Uehling, Jessie K. ; Branco, Sara ; Bruns, Thomas D. ; Martin, Francis ; Kennedy, Peter G. / Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles. In: Molecular ecology. 2019 ; Vol. 28, No. 4. pp. 721-730.
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