Dataset Information

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

ABSTRACT: Sugar 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).ChIP-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.The 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.

SUBMITTER: Kowar T

PROVIDER: S-EPMC4881148 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Publications

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

Kowar Teresa T Zakrzewski Falk F Macas Jiří J Kobližková Andrea A Viehoever Prisca P Weisshaar Bernd B Schmidt Thomas T

BMC plant biology 20160526 1

<h4>Background</h4>Sugar 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 ...[more]

PMID: 27230558

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Project description:Cover crops are supposed to decrease the soil mineral N content (Nmin) during winter and increase the N supply to subsequent main crops due to mineralization of N previously prevented from leaching. However, data on N supply from cover crops grown before sugar beet have rarely been reported for Central European conditions. Therefore, our study aimed to provide information for cover crops differing in frost resistance and biomass quantity applicable for N fertilizer dressing in the subsequent main crop. In 2018/19 and 2019/20, field trials were conducted on two Luvisol sites in Germany typical for sugar beet cultivation, comprising a sequence of autumn sown cover crops grown after field pea followed by unfertilized sugar beet main crops sown in next spring. Apparent net N mineralization and the N effect of cover crops on sugar beet were calculated according to a mass balance approach including Nmin and sugar beet N uptake. Winter rye and oil radish revealed the greatest potential for scavenging nitrate from the soil profile while reductions caused by frost-sensitive saia oat and spring vetch were more variable. The amount of N in the cover crop biomass was negatively correlated with Nmin in autumn and also in spring. Thus, for environmentally effective cover cropping in Central Europe, species with a sufficiently high frost tolerance should be chosen. Despite cover crop N uptake up to 170 kg N ha-1 and C:N ratios < 20, a positive N effect on sugar beet was only found between March and July of the beet growing season and was 50 kg N ha-1 at maximum, while between August and September, net immobilization was predominant with up to 100 kg N ha-1. Differences among crop species were not consistent across the site/years investigated. Sugar yield was lowest after rye at 3 sites/years and correlated positively with Nmin in spring. Correlation between yield and cover crop N effect was mostly low and inconsistent and could not be improved by a multiple regression approach. Thus, factors other than in-season N supply from cover crops apparently impacted sugar beet yield formation to a larger extent.

Project description:Third generation sequencing methods, like SMRT (Single Molecule, Real-Time) sequencing developed by Pacific Biosciences, offer much longer read length in comparison to Next Generation Sequencing (NGS) methods. Hence, they are well suited for de novo- or re-sequencing projects. Sequences generated for these purposes will not only contain reads originating from the nuclear genome, but also a significant amount of reads originating from the organelles of the target organism. These reads are usually discarded but they can also be used for an assembly of organellar replicons. The long read length supports resolution of repetitive regions and repeats within the organelles genome which might be problematic when just using short read data. Additionally, SMRT sequencing is less influenced by GC rich areas and by long stretches of the same base.We describe a workflow for a de novo assembly of the sugar beet (Beta vulgaris ssp. vulgaris) chloroplast genome sequence only based on data originating from a SMRT sequencing dataset targeted on its nuclear genome. We show that the data obtained from such an experiment are sufficient to create a high quality assembly with a higher reliability than assemblies derived from e.g. Illumina reads only. The chloroplast genome is especially challenging for de novo assembling as it contains two large inverted repeat (IR) regions. We also describe some limitations that still apply even though long reads are used for the assembly.SMRT sequencing reads extracted from a dataset created for nuclear genome (re)sequencing can be used to obtain a high quality de novo assembly of the chloroplast of the sequenced organism. Even with a relatively small overall coverage for the nuclear genome it is possible to collect more than enough reads to generate a high quality assembly that outperforms short read based assemblies. However, even with long reads it is not always possible to clarify the order of elements of a chloroplast genome sequence reliantly which we could demonstrate with Fosmid End Sequences (FES) generated with Sanger technology. Nevertheless, this limitation also applies to short read sequencing data but is reached in this case at a much earlier stage during finishing.

Dataset Information

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

Publications

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

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