title: Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).
abstract: 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.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA. bvonhold@uci.edu
authors.forename: Bridgett M
authors.initials: BM
authors.lastname: Vonholdt
authors.forename: Shohei
authors.initials: S
authors.lastname: Takuno
authors.forename: Brandon S
authors.initials: BS
authors.lastname: Gaut
mesh_terms: D016000:Cluster Analysis; D019175:DNA Methylation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D058977:Molecular Sequence Annotation; D005810:Multigene Family / Q000235:genetics; D016254:Mutagenesis, Insertional / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D019655:Quantitative Trait, Heritable; D018626:Retroelements / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics; D013997:Time Factors
chemical_list: D018626:Retroelements