Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on 5 factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.indica reference japonica query genome alignment result in BED formatBED format genome alignment results where indica 93-11 was used as reference and japonica nipponbare genome was used as query genome. Indica chromosome was named as SAI.chromosome_number and japonica chromosome named as SAJ.chromosome_number.Osat_indica_9311_REF-Osat_japonica_NPB_QUERY.sorted.bedjaponica reference indica query genome alignment result in BED formatBED format genome alignment results where japonica nipponbare was used as reference and indica 93-11 was used as query genome. Indica chromosome was named as SAI.chromosome_number and japonica chromosome named as SAJ.chromosome_number.Osat_japonica_NPB_REF-Osat_indica_9311_QUERY.sorted.bedjaponica genome LTR-RT and nearby host gene and the host genes' expression valuesjaponica_transcript.txtindica genome LTR-RT and nearby host gene and the host genes' expression valuesindica_transcript.txtjaponica genome LTR-RT methylation levelsjaponica_methyl.txtindica genome LTR-RT methylation levelsindica_methyl.txtjaponica genome LTR-RT up and downstream region methylation levelsjaponica_methyl_updown.txtindica genome LTR-RT up and downstream region methylation levelsindica_methyl_updown.txtMethylation level for LTR-RT and its up or downstream region in japonica genome and its orthologous region in indicajaponica_methyl_updown_ortholog.txtMethylation level for LTR-RT and its up or downstream region in indica genome and its orthologous region in japonicaindica_methyl_updown_ortholog.txtFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: IOS-154621