Title | Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). |
Publication Type | Journal Article |
Year of Publication | 2012 |
Authors | vonHoldt, BM, Takuno, S, Gaut, BS |
Journal | Mol Biol Evol |
Volume | 29 |
Issue | 10 |
Pagination | 3193-203 |
Date Published | 2012 Oct |
ISSN | 1537-1719 |
Keywords | Cluster 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> |
DOI | 10.1093/molbev/mss129 |
Alternate Journal | Mol Biol Evol |
PubMed ID | 22593226 |