Abstract
The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high degree of sequence diversity in the D1/D2 domains of two pulcherrimin-producing Metschnikowia (Saccharomycotina) species which appeared to evolve by reticulation. The major goals of this study were the examination of the diversity of the ITS segments and their evolution. We show that the ITS sequences of these species are not homogenized either, differ from each other by up to 38 substitutions and indels which have dramatic effects on the predicted secondary structures of the transcripts. The high intragenomic diversity makes the D1/D2 domains and the ITS spacers unsuitable for barcoding of these species and therefore the taxonomic position of strains previously assigned to them needs revision. By analyzing the genome sequence of the M. fructicola type strain, we also show that the rDNA of this species is fragmented, contains pseudogenes and thus evolves by the birth-and-death mechanism rather than by homogenisation, which is unusual in yeasts. The results of the network analysis of the sequences further indicate that the ITS regions are also involved in reticulation. M. andauensis and M. fructicola can form interspecies hybrids and their hybrids segregate, providing thus possibilities for reticulation of the rDNA repeats.
Highlights
The internal transcribed spacers ITS1 and ITS2 of the ribosomal DNA cistrons separate genes coding for ribosomal RNAs which are essential components of ribosomes
When the DNA amplified with the ITS1 and ITS4 primers from the type strains was directly sequenced with the ITS1 primer, the chromatograms were not readable in the segments corresponding to the ITS1 spacers, and the sequences of the 5.8S and ITS2 parts contained about 20% ambiguous nucleotides
In a previous study we found that the type strains of M. andauensis and M fructicola had highly heterogeneous large subunit (LSU) (26S) rRNA gene paralogs that formed a continuous pool leaving no barcode gap suitable for differentiation of these two species by D1/D2 sequencing (Sipiczki et al, 2013)
Summary
The internal transcribed spacers ITS1 and ITS2 of the ribosomal DNA (rDNA) cistrons separate genes coding for ribosomal RNAs which are essential components of ribosomes. The rDNA cistrons are repeated many times in the genome accross the tree of life, so that enough rRNA can be produced when demand for ribosomes is high. Metschnikowia ITS Diversity as tandem head-to-tail repeats (rDNA repeats) in continuous arrays (for a review see Torres-Machorro et al, 2010). In spite of the large number of repeats, nucleotide polymorphism within the rDNA array is usually very low (e.g., Ganley and Kobayashi, 2007). By a process called “concerted evolution” (Zimmer et al, 1980; Elder and Turner, 1995), the repeats within the arrays are maintained essentially identical (homogenized) even over evolutionarily significant timescales. It ensures that a mutation that arises in one repeat is either eliminated or spreads by intercopy interactions through the array until fixation
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