Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

BMC Genomics
Joëlle AmselemHadi Quesneville

Abstract

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. 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. We identified fung...Continue Reading

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Citations

Sep 16, 2016·Current Genetics·Eugene Gladyshev, Nancy Kleckner
Feb 26, 2016·Molecular Plant Pathology·Jan A L Van KanGabriel Scalliet
Jan 12, 2017·Applied Microbiology and Biotechnology·Raúl CastaneraLucía Ramírez
Jun 28, 2018·Journal of Experimental Botany·Björn Sabelleck, Ralph Panstruga
Dec 4, 2016·G3 : Genes - Genomes - Genetics·Christina A CuomoJohn P Fellers
Nov 14, 2018·Nature Ecology & Evolution·Claude MuratFrancis M Martin
Feb 6, 2019·Mobile DNA·Joëlle AmselemHadi Quesneville
Oct 22, 2018·Fungal Biology·Stefan KuschRalph Panstruga
Apr 2, 2021·G3 : Genes - Genomes - Genetics·Peri A TobiasRobert F Park
Jul 20, 2017·Microbiology Spectrum·Eugene Gladyshev
May 30, 2021·Genome Biology and Evolution·Markus HiltunenHanna Johannesson
Nov 15, 2019·Journal of Molecular Biology·Alexey K MazurEugene Gladyshev

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Methods Mentioned

BETA
RIP
deamination

Software Mentioned

signalp
hmmpir
Gblocks
Tmel
hmmtigr
blastprodom
REPET
gene3d
Phylogeny
TEdenovo

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