Abstract
During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.
Highlights
The nuclear ribosomal internal transcribed spacer (ITS) region is part of the ribosomal DNA cistron
The Signal Recognition Particle (SRP) RNAs found in the internal transcribed spacer 1 (ITS1) region most probably are fully functional, but there may be another copy in the genome that constitutes the major transcript
The surprising lack of mutations, as compared to other identified basidiomycete Signal Recognition Particle RNA (SRP RNA) (Suppl. material 4), could be explained by the insertion being a recent event, and by the need to preserve the secondary structure of the SRP RNA region and the remaining parts of ITS1
Summary
The nuclear ribosomal internal transcribed spacer (ITS) region is part of the ribosomal DNA cistron. The ITS region is transcribed together with the 18S, 5.8S, and 28S genes but removed in the post-transcriptional processing of the rRNA. The ITS region varies significantly in length among fungal species (Taylor and McCormick 2008, Tedersoo et al 2015), and both of ITS1 and ITS2 form secondary structures with stems, bulges, and loops (Freire et al 2012, Rampersad 2014). The secondary structure is important for correct processing of the rRNA; the ITS1 and ITS2 regions are not expressed in the ribosome, there are constraints on the evolution of the ITS region, and it has both fast evolving and more conserved regions (Nazar 2004, Mullineaux and Hausner 2009). The fast evolving regions of ITS has made it a cornerstone in species/genuslevel phylogenetic inference in fungi and other organisms for more than 20 years, and it is the formal fungal barcode used for molecular species identification (Álvarez and Wendel 2003, Schoch et al 2012)
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