Lost in translation: Population genomics and long-read sequencing reveals relaxation of concerted evolution of the ribosomal DNA cistron

[Display omitted] •The mechanisms of concerted evolution may insufficiently homogenize the rDNA array.•Alleles persist in the ITS regions at low frequencies, and may be undetectable by Sanger Sequencing.•ITS gene relatedness and gene flow in Boletus edulis does not correlate with genomic relatedness...

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Bibliographic Details
Published in:Molecular phylogenetics and evolution 2020-07, Vol.148, p.106804-106804, Article 106804
Main Authors: Tremble, Keaton, Suz, Laura M., Dentinger, Bryn T.M.
Format: Article
Language:English
Subjects:
Boletus edulis
Concerted evolution
Fungi
Internal transcribed spacers
Phylogeny
Population genomics
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Summary:[Display omitted] •The mechanisms of concerted evolution may insufficiently homogenize the rDNA array.•Alleles persist in the ITS regions at low frequencies, and may be undetectable by Sanger Sequencing.•ITS gene relatedness and gene flow in Boletus edulis does not correlate with genomic relatedness.•Significant inbreeding may allow fixation of novel ITS alleles, creating false signals of gene flow.•ITS barcoding for identification of population boundaries and complex species resolution is suspect. Concerted evolution of the ribosomal DNA array has been studied in numerous eukaryotic taxa, yet is still poorly understood. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome (Eickbush and Eickbush, 2007) and it is believed that these arrays are homogenized through concerted evolution (Zimmer et al., 1980; Dover, 1993) preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific variation in the rDNA array (Ganley and Kobayashi, 2011; Naidoo et al., 2013; Hughes and Petersen, 2001; Lindner and Banik, 2011; Li et al., 2013; Lindner et al., 2013; Hughes et al., 2018), contradicting our current understanding of concerted evolution. The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi (Schoch et al., 2012), and rely on concerted evolution to homogenize the rDNA array leading to a “barcode gap” (Puillandre et al., 2012). Here we show that in Boletus edulis Bull., ITS intragenomic variation persists at low allele frequencies throughout the rDNA array, this variation does not correlate with genomic relatedness between populations, and rDNA genes may not evolve in a strictly concerted fashion despite the presence of unequal recombination and gene conversion. Under normal assumptions, heterozygous positions found in ITS sequences represent hybridization between populations, yet through allelic mapping of the rDNA array we found numerous heterozygous alleles to be stochastically introgressed throughout, presenting a dishonest signal of gene flow. Moreover, despite the signal of gene flow in ITS, our organisms were highly inbred, indicating a disconnect between true gene flow and barcoding signals. In addition, we show that while the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, they are not fully homogenizing the ITS array. Concerted evolution of the rDNA a
ISSN:1055-7903
1095-9513
DOI:10.1016/j.ympev.2020.106804