title: Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes.
abstract: BACKGROUND
  Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP (Methylation Induced Premeiotically) and Quelling (RNA interference). RIP inactivates repeated sequences by promoting Cytosine to Thymine mutations, whereas MIP only methylates TEs at C residues. Both mechanisms require specific cytosine DNA Methyltransferases (RID1/Masc1) of the Dnmt1 superfamily.
  
  
  RESULTS
  We annotated TE sequences from 10 fungal genomes with different TE content (1-70%). We then used these TE sequences to carry out a genome-wide analysis of C to T mutations biases. Genomes from either Ascomycota or Basidiomycota that were massively invaded by TEs (Blumeria, Melampsora, Puccinia) were characterized by a low frequency of C to T mutation bias (10-20%), whereas other genomes displayed intermediate to high frequencies (25-75%). We identified several dinucleotide signatures at these C to T mutation sites (CpA, CpT, and CpG). Phylogenomic analysis of fungal Dnmt1 MTases revealed a previously unreported association between these dinucleotide signatures and the presence/absence of sub-classes of Dnmt1.
  
  
  CONCLUSIONS
  We identified fungal genomes containing large numbers of TEs with many C to T mutations associated with species-specific dinucleotide signatures. This bias suggests that a basic defense mechanism against TE invasion similar to RIP is widespread in fungi, although the efficiency and specificity of this mechanism differs between species. Our analysis revealed that dinucleotide signatures are associated with the presence/absence of specific Dnmt1 subfamilies. In particular, an RID1-dependent RIP mechanism was found only in Ascomycota.
authors.affiliation: INRA, UR1164 URGI Research Unit in Genomics-Info, F-78026, Versailles, France. joelle.amselem@versailles.inra.fr.|INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, F-78850, Thiverval-Grignon, France. joelle.amselem@versailles.inra.fr.
authors.forename: Joëlle
authors.initials: J
authors.lastname: Amselem
authors.affiliation: INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, F-78850, Thiverval-Grignon, France. marc-henri.lebrun@versailles.inra.fr.
authors.forename: Marc-Henri
authors.initials: MH
authors.lastname: Lebrun
authors.affiliation: INRA, UR1164 URGI Research Unit in Genomics-Info, F-78026, Versailles, France. hadi.quesneville@versailles.inra.fr.
authors.forename: Hadi
authors.initials: H
authors.lastname: Quesneville
mesh_terms: D001203:Ascomycota / Q000235:genetics; D001487:Basidiomycota / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D016681:Genome, Fungal; D058977:Molecular Sequence Annotation; D009154:Mutation / Q000235:genetics*; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements