Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).

TitleRecent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).
Publication TypeJournal Article
Year of Publication2012
AuthorsvonHoldt, BM, Takuno, S, Gaut, BS
JournalMol Biol Evol
Volume29
Issue10
Pagination3193-203
Date Published2012 Oct
ISSN1537-1719
KeywordsCluster Analysis, DNA Methylation, Genome, Plant, Molecular Sequence Annotation, Multigene Family, Mutagenesis, Insertional, Oryza, Phylogeny, Quantitative Trait, Heritable, Retroelements, Terminal Repeat Sequences, Time Factors
Abstract

<p>In plants, the genome of the host responds to the amplification of transposable elements (TEs) with DNA methylation. However, neither the factors involved in TE methylation nor the dynamics of the host-TE interaction are well resolved. Here, we identify 5,522 long terminal repeat retrotransposons (LTR-RT) in the genome of Oryza sativa ssp. japonica and then assess methylation for individual elements. Our analyses uncover three strong trends: long LTR-RTs are more highly methylated, the insertion times of LTR-RTs are negatively correlated with methylation, and young LTR-RTs tend to be closer to genes than older insertions. Additionally, a phylogenetic examination of the gypsy-like LTR-RT superfamily revealed that methylation is phylogenetically correlated. Given these observations, we present a model suggesting that the phylogenetic correlation among related LTR-RTs is a primary mechanism driving methylation. In this model, bursts of transposition produce new elements with high sequence similarity. The host machinery identifies proliferating elements as well as closely related LTR-RTs through cross-homology. In addition, our data are consistent with previous hypotheses that methylated LTR-RT elements are removed preferentially from regions near genes, explaining some of the observed age distribution.</p>

DOI10.1093/molbev/mss129
Alternate JournalMol. Biol. Evol.
PubMed ID22593226