title: Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA.
abstract: BACKGROUND
  Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of fungal group I introns including 9 putatively ancient group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri.
  
  
  RESULTS
  Our analyses reveal a complex evolutionary history of the fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then group I intron loss was widespread in fungal rDNA evolution.
  
  
  CONCLUSIONS
  On the basis of these results, we suggest that the extensive distribution of fungal group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.
authors.affiliation: Department of Biological Sciences, Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242-1324, USA. debashi-bhattacharya@uiowa.edu
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
authors.forename: Valérie
authors.initials: V
authors.lastname: Reeb
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Simon
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
mesh_terms: D017398:Alternative Splicing; D001203:Ascomycota / Q000235:genetics*; D004247:DNA / Q000378:metabolism; D004271:DNA, Fungal / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D007438:Introns; D008957:Models, Genetic; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017433:Protein Structure, Secondary; D012313:RNA / Q000378:metabolism; D012326:RNA Splicing; D012335:RNA, Ribosomal; D011995:Recombination, Genetic
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal; D012335:RNA, Ribosomal; D012313:RNA; D004247:DNA