title: How to Isolate a Plant's Hypomethylome in One Shot.
abstract: Genome assembly remains a challenge for large and/or complex plant genomes due to their abundant repetitive regions resulting in studies focusing on gene space instead of the whole genome. Thus, DNA enrichment strategies facilitate the assembly by increasing the coverage and simultaneously reducing the complexity of the whole genome. In this paper we provide an easy, fast, and cost-effective variant of MRE-seq to obtain a plant's hypomethylome by an optimized methyl filtration protocol followed by next generation sequencing. The method is demonstrated on three plant species with knowingly large and/or complex (polyploid) genomes: Oryza sativa, Picea abies, and Crocus sativus. The identified hypomethylomes show clear enrichment for genes and their flanking regions and clear reduction of transposable elements. Additionally, genomic sequences around genes are captured including regulatory elements in introns and up- and downstream flanks. High similarity of the results obtained by a de novo assembly approach with a reference based mapping in rice supports the applicability for studying and understanding the genomes of nonmodel organisms. Hence we show the high potential of MRE-seq in a wide range of scenarios for the direct analysis of methylation differences, for example, between ecotypes, individuals, within or across species harbouring large, and complex genomes.
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenzstreet 24, 3430 Tulln, Austria.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Wischnitzki
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenzstreet 24, 3430 Tulln, Austria.
authors.forename: Eva Maria
authors.initials: EM
authors.lastname: Sehr
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenzstreet 24, 3430 Tulln, Austria.
authors.forename: Karin
authors.initials: K
authors.lastname: Hansel-Hohl
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenzstreet 24, 3430 Tulln, Austria.
authors.forename: Maria
authors.initials: M
authors.lastname: Berenyi
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenzstreet 24, 3430 Tulln, Austria.
authors.forename: Kornel
authors.initials: K
authors.lastname: Burg
authors.affiliation: AIT Austrian Institute of Technology GmbH, Konrad-Lorenzstreet 24, 3430 Tulln, Austria.
authors.forename: Silvia
authors.initials: S
authors.lastname: Fluch
mesh_terms: D003198:Computer Simulation; D027622:Crocus / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification*; D017343:Genes, Plant; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics; D028222:Picea / Q000235:genetics; D010944:Plants / Q000235:genetics*; D011123:Polyploidy; D012015:Reference Standards; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant