The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth
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The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth. / Malinowska, Marta; Nagy, Istvan; Wagemaker, Cornelis A. M.; Ruud, Anja K.; Svane, Simon F.; Thorup-Kristensen, Kristian; Jensen, Christian S.; Eriksen, Birger; Krusell, Lene; Jahoor, Ahmed; Jensen, Jens; Eriksen, Lars Bonde; Asp, Torben.
In: The Plant Genome, Vol. 13, No. 3, 20049, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth
AU - Malinowska, Marta
AU - Nagy, Istvan
AU - Wagemaker, Cornelis A. M.
AU - Ruud, Anja K.
AU - Svane, Simon F.
AU - Thorup-Kristensen, Kristian
AU - Jensen, Christian S.
AU - Eriksen, Birger
AU - Krusell, Lene
AU - Jahoor, Ahmed
AU - Jensen, Jens
AU - Eriksen, Lars Bonde
AU - Asp, Torben
PY - 2020
Y1 - 2020
N2 - Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgareL.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those inArabidopsis thaliana(L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposonsGypsyandCopia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.
AB - Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgareL.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those inArabidopsis thaliana(L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposonsGypsyandCopia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.
KW - DNA-METHYLATION
KW - EPIGENETIC MUTATION
KW - GENOME
KW - PLANTS
KW - LIBRARIES
KW - MODEL
KW - SUITE
KW - RNA
U2 - 10.1002/tpg2.20049
DO - 10.1002/tpg2.20049
M3 - Journal article
C2 - 33217208
VL - 13
JO - The Plant Genome
JF - The Plant Genome
SN - 1940-3372
IS - 3
M1 - 20049
ER -
ID: 249767851