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

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.

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

“…While this could be due to a bias of the ITS1 primers for this family at the exclusion of others, it could also be that metagenome sequences from this family are more often erroneously assigned to other, sequence related families, deflating counts of Helotiaceae. Another source of noise between the datasets could come from the fact that fungal genomes vary more widely than bacteria in size, and the fact that rDNA copies are not well correlated with fungal genome size [45] . This can introduce biases because organisms with larger genomes would appear to have higher abundances in metagenomes due to more mapped reads.…”

Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast

“…A) The number of rDNA repeats varies in different strains in a way that depends on ploidy, except for cell size haploid mutants (see Figure S3). B) In a cln3 mutant, the copy number is small, similar to its parental wt haploid (n: BY4741) when it is a recent transformant, but increases along with the number of generations for four independent clones (#9, 13,20,24). The dashed horizontal lines mark the repeat copy number for the Euroscarf ∆cln3 (BQS2006) and wt (BY4741) strains.…”

“…This is a slow form of TR regulation because the change in the rDNA copy number can be done only during genome replication using an unequal homologous recombination between sister chromatids [6,8,9]. rDNA loci are very dynamic genome regions whose copy number varies considerably in a single species between individuals, and even between cells in a single individual [5,[10][11][12][13]. Apart from regulating the rDNA copy number, it is also possible to regulate rRNA synthesis by acting on RNA pol I transcription initiation [14] or elongation (see [15] for a recent review), and by controlling the proportion of active rDNA repeats.…”

Host genotype and colonist arrival order jointly govern plant microbiome composition and function

“…We then used Sanger sequencing and Primer 3 (Untergasser et al, 2012) to design custom qPCR primers to quantify the concentrations of our pure culture extracts. We targeted the TEF1-α gene for qPCR quantification because it is a single-copy gene, unlike the ITS region, which can vary in copy number among fungi over several orders of magnitude (Lofgren et al, 2019), likely representing a large source of bias in fungal ITS metabarcoding.…”