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Series GSE79526 Query DataSets for GSE79526
Status Public on Sep 02, 2016
Title Widespread natural variation of DNA methylation within angiosperms
Organisms Cannabis sativa; Theobroma cacao; Cucumis sativus; Populus trichocarpa; Brassica rapa; Malus domestica; Prunus persica; Medicago truncatula; Manihot esculenta; Ricinus communis; Erythranthe guttata; Setaria viridis; Sorghum bicolor; Brachypodium distachyon; Vitis vinifera; Lotus japonicus; Panicum virgatum; Fragaria vesca; Eucalyptus grandis; Eutrema salsugineum; Citrus x clementina; Beta vulgaris; Panicum hallii
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing reduced CHG methylation levels and also reduced or loss of CG gene-body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species.
 
Overall design Bisulfite-seq of leaf tissue from plants representing diverse angiosperms. RNA-seq and small RNA-seq was performed on leaf tissue of a subset of the species.
 
Contributor(s) Niederhuth CE, Schmitz RJ
Citation(s) 27671052
Submission date Mar 23, 2016
Last update date May 15, 2019
Contact name Robert J Schmitz
E-mail(s) schmitz@uga.edu
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platforms (30)
GPL15671 Illumina HiSeq 2000 (Prunus persica)
GPL16310 Illumina HiSeq 2000 (Cucumis sativus)
GPL16761 Illumina HiSeq 2000 (Fragaria vesca)
Samples (34)
GSM2096945 B_distachyon
GSM2096947 B_vulgaris
GSM2096949 C_clementina
Relations
BioProject PRJNA316109
SRA SRP072226

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE79526_RAW.tar 13.4 Gb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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