Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives

Menzel, Gerhard; Krebs, Carmen; Díez, Mercedes; Holtgräwe, Daniela; Weißhaar, Bernd; Minoche, André E.; Dohm, Juliane C.; Himmelbauer, Heinz; Schmidt, Thomas

doi:10.1007/s11103-011-9872-z

Cited by 14 publications

(10 citation statements)

References 53 publications

(72 reference statements)

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“…which harbors 16 SINE copies . Therefore, we propose that DNA transposons and SINEs in sugar beet also influence gene expression in euchromatic generich regions (Menzel et al, 2006(Menzel et al, , 2012Schwichtenberg et al, 2016), because they might be targets for siRNAdirected CHH methylation. Accordingly, increased CHH methylation levels of small dispersed satellite DNA arrays (in the presence of corresponding 24-nucleotide siRNAs) in euchromatic regions hint at a functional role for small satellite arrays in gene silencing via CHH methylation .…”

Section: Asymmetric Chh Methylation Is Very Different Between Callus mentioning

confidence: 99%

“…Because repeats are fragmentarily included in the sugar beet reference genome, this bottleneck has recently been overcome by chromatin immunoprecipitation sequencing with antibodies against the sugar beet-specific centromeric variant of histone H3 and the dimethylation of lysine 9 of histone H3 (H3K9me2), uncovering the proportion of repetitive sequences in centromeric chromatin and non-centromeric heterochromatin (Kowar et al, 2016). Both regions are predominantly enriched with satellite DNA, long terminal repeat (LTR) retrotransposons and DNA transposons of different families and, thus far, a large number of these repeats have been described in detail (Schmidt and Heslop-Harrison, 1998;Weber and Schmidt, 2009;Wenke et al, 2009;Weber et al, 2010Weber et al, , 2013Zakrzewski et al, 2010Zakrzewski et al, , 2011Zakrzewski et al, , 2013Zakrzewski et al, , 2014Menzel et al, 2012;Wollrab et al, 2012;Heitkam et al, 2014;Schwichtenberg et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

et al. 2017

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The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H = A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves.

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Section: Asymmetric Chh Methylation Is Very Different Between Callus mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

et al. 2017

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“…Transposable element contributes in plant gene regulation ( 53 ). Such transposable elements are present in sugarbeet also ( 54 ). It is probable that short sequence repeats in those locations are also involved in the regulation of gene expression ( 55 ).…”

Section: Utility Of the Databasementioning

confidence: 99%

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

et al. 2015

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DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world’s first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of ‘mono’ repeat (76.82%) over ‘di’ repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change.Database URL: http://webapp.cabgrid.res.in/sbmdb/

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“…The subtelomeric heterochromatic regions are characterized by the presence of the satellite family pAV [ 40 ]. Small dispersed heterochromatic spots consist of a variety of different repetitive elements including satellite DNAs, DNA transposons and LTR and Non-LTR retrotransposons [ 41 – 44 ]. In interphase nuclei it has been shown that sugar beet heterochromatin is characterized by the presence of H3K9me2.…”

Section: Introductionmentioning

confidence: 99%

Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris)

et al. 2016

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BackgroundSugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the recently published genome sequence, due to the fact that regions with high repetitive DNA contents (e.g. satellite DNAs) are only partially included. Therefore, to fill these gaps and to gain information about the repeat composition of centromeres and heterochromatic regions, we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using antibodies against the centromere-specific histone H3 variant of sugar beet (CenH3) and the heterochromatic mark of dimethylated lysine 9 of histone H3 (H3K9me2).ResultsChIP-Seq analysis revealed that active centromeres containing CenH3 consist of the satellite pBV and the Ty3-gypsy retrotransposon Beetle7, while heterochromatin marked by H3K9me2 exhibits heterogeneity in repeat composition. H3K9me2 was mainly associated with the satellite family pEV, the Ty1-copia retrotransposon family Cotzilla and the DNA transposon superfamily of the En/Spm type. In members of the section Beta within the genus Beta, immunostaining using the CenH3 antibody was successful, indicating that orthologous CenH3 proteins are present in closely related species within this section.ConclusionsThe identification of repetitive genome portions by ChIP-Seq experiments complemented the sugar beet reference sequence by providing insights into the repeat composition of poorly characterized CenH3-chromatin and H3K9me2-heterochromatin. Therefore, our work provides the basis for future research and application concerning the sugar beet centromere and repeat-rich heterochromatic regions characterized by the presence of H3K9me2.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0805-5) contains supplementary material, which is available to authorized users.

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Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives

Cited by 14 publications

References 53 publications

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris)

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