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Lost in Translation: population genomics of porcini (Boletus edulis) challenges use of ITS for DNA barcoding in Fungi

View ORCID ProfileKeaton Tremble, View ORCID ProfileLaura M. Suz, View ORCID ProfileBryn T.M. Dentinger
doi: https://doi.org/10.1101/811216
Keaton Tremble
aSchool of Biological Sciences,University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA
bNatural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108, USA
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  • For correspondence: keaton.tremble@utah.edu
Laura M. Suz
cComparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Richmond, Surrey, TW9 3DS, UK
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Bryn T.M. Dentinger
aSchool of Biological Sciences,University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA
bNatural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108, USA
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Abstract

The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi [1]. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome [2] and it is believed that these arrays are homogenized through concerted evolution [3, 4] preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific ITS variation [5–11], contradicting our current understanding of concerted evolution. 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 showed that the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, yet are not homogenizing the ITS array. Concerted evolution of the rDNA array may insufficiently homogenize the ITS gene, allowing for misleading signals of gene flow to persist, vastly complicating the use of the ITS locus for DNA barcoding in Fungi.

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Posted October 21, 2019.
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Lost in Translation: population genomics of porcini (Boletus edulis) challenges use of ITS for DNA barcoding in Fungi
Keaton Tremble, Laura M. Suz, Bryn T.M. Dentinger
bioRxiv 811216; doi: https://doi.org/10.1101/811216
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Lost in Translation: population genomics of porcini (Boletus edulis) challenges use of ITS for DNA barcoding in Fungi
Keaton Tremble, Laura M. Suz, Bryn T.M. Dentinger
bioRxiv 811216; doi: https://doi.org/10.1101/811216

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