Data from: Intragenomic nuclear RNA variation in a cryptic Amanita taxon

Amanita cf. lavendula collections in eastern North America, Mexico, and Costa Rica were found to consist of four cryptic taxa, one of which exhibited consistently unreadable nuclear rDNA ITS1-5.8S-ITS2 (fungal barcode) sequences after ITS1 base 130. This taxon is designated here as Amanita cf. lavendula taxon 1. ITS sequences from dikaryotic basidiomata were cloned, but sequences recovered from cloning did not segregate into distinct haplotypes. Rather, there was a mix of haplotypes that varied among themselves predominantly at 28 ITS positions. Analysis of each of these 28 variable bases showed predominantly two alternate bases at each position. Based on these findings and additional sequence data from the nuclear rDNA 28S, RNA polymerase II subunit 2 (RPB2) and mitochondrial rDNA small subunit (SSU) and 23S genes, we speculate that taxon 1 represents an initial hybridization event between two divergent taxa followed by failure of the ribosomal repeat to homogenize. Homogenization failure may be a result of repeated hybridization between divergent internal transcribed spacer (ITS) types with inadequate time for concerted evolution of the ribosomal repeat or, alternately, a complete failure of the ribosomal homogenization process. To our knowledge, this finding represents the first report of a geographically widespread taxon (Canada, eastern USA, Costa Rica) with apparent homogenization failure across all collections. Findings such as these have implications for fungal barcoding efforts and the application of fungal barcodes in identifying environmental sequences.Amanita afn lavendula taxon 1 cloned ITS sequencesCloned Amanita afn lavendula taxon 1 ITS1-5.8S-ITS2 sequencesAmanita afn_lavendua Taxon 1 ITS consensus sequenceAmanita afn lavendula taxon 1 ITS consensus sequenceAmanita afn_lavendual Taxon 1 ITS consensus sequence.txtML tree of Amanita afn lavendula taxon 1 ML1-2Nexus file. PhyML tree based on Mitochondrial rRNA large subunit sequences amplified with primers ML1 and ML2ML tree of Amanita afn lavendula taxon 1 ML5-6Nexus file: PhyML analyses of mitochondrial rRNA large subunit sequences amplified with primers ML5 and ML6ML tree of Amanita afn lavendula taxon 1 MS1-2Nexus file: PhyML analysis of mitochondrial rRNA 16S sequences amplified with primers MS1 and MS2ML tree of Amanita afn lavendula taxon 1 nrLSUNexus file: PhyML analysis of nuclear ribosomal LSU sequences of Amanita afn lavendula taxon 1ML tree of Amanita afn lavendula taxon 1 RPB2_trimmedNexus File: PhyML analysis of RPB2 (RNA polymerase 2nd largest subunit) amplified with primers bRPB2-6F and fRPB2-7cR (Matheny, PB 2005).Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: NSF DEB 114497