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How to Isolate a Plant's Hypomethylome in One Shot

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...

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Autores principales: Wischnitzki, Elisabeth, Sehr, Eva Maria, Hansel-Hohl, Karin, Berenyi, Maria, Burg, Kornel, Fluch, Silvia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573423/
https://www.ncbi.nlm.nih.gov/pubmed/26421293
http://dx.doi.org/10.1155/2015/570568
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author Wischnitzki, Elisabeth
Sehr, Eva Maria
Hansel-Hohl, Karin
Berenyi, Maria
Burg, Kornel
Fluch, Silvia
author_facet Wischnitzki, Elisabeth
Sehr, Eva Maria
Hansel-Hohl, Karin
Berenyi, Maria
Burg, Kornel
Fluch, Silvia
author_sort Wischnitzki, Elisabeth
collection PubMed
description 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.
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spelling pubmed-45734232015-09-29 How to Isolate a Plant's Hypomethylome in One Shot Wischnitzki, Elisabeth Sehr, Eva Maria Hansel-Hohl, Karin Berenyi, Maria Burg, Kornel Fluch, Silvia Biomed Res Int Research Article 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. Hindawi Publishing Corporation 2015 2015-09-03 /pmc/articles/PMC4573423/ /pubmed/26421293 http://dx.doi.org/10.1155/2015/570568 Text en Copyright © 2015 Elisabeth Wischnitzki et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Wischnitzki, Elisabeth
Sehr, Eva Maria
Hansel-Hohl, Karin
Berenyi, Maria
Burg, Kornel
Fluch, Silvia
How to Isolate a Plant's Hypomethylome in One Shot
title How to Isolate a Plant's Hypomethylome in One Shot
title_full How to Isolate a Plant's Hypomethylome in One Shot
title_fullStr How to Isolate a Plant's Hypomethylome in One Shot
title_full_unstemmed How to Isolate a Plant's Hypomethylome in One Shot
title_short How to Isolate a Plant's Hypomethylome in One Shot
title_sort how to isolate a plant's hypomethylome in one shot
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573423/
https://www.ncbi.nlm.nih.gov/pubmed/26421293
http://dx.doi.org/10.1155/2015/570568
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