Falk Zakrzewski
Dresden University of Technology
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Featured researches published by Falk Zakrzewski.
Nature | 2014
Juliane C. Dohm; André E. Minoche; Daniela Holtgräwe; Salvador Capella-Gutiérrez; Falk Zakrzewski; Hakim Tafer; Oliver Rupp; Thomas Rosleff Sörensen; Ralf Stracke; Richard Reinhardt; Alexander Goesmann; Thomas Kraft; Britta Schulz; Peter F. Stadler; T. Schmidt; Toni Gabaldón; Hans Lehrach; Bernd Weisshaar; Heinz Himmelbauer
Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world’s annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714–758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant’s potential in energy biotechnology.
BMC Plant Biology | 2010
Falk Zakrzewski; Torsten Wenke; Daniela Holtgräwe; Bernd Weisshaar; T. Schmidt
BackgroundRepetitive DNA is a major fraction of eukaryotic genomes and occurs particularly often in plants. Currently, the sequencing of the sugar beet (Beta vulgaris) genome is under way and knowledge of repetitive DNA sequences is critical for the genome annotation. We generated a c0t-1 library, representing highly to moderately repetitive sequences, for the characterization of the major B. vulgaris repeat families. While highly abundant satellites are well-described, minisatellites are only poorly investigated in plants. Therefore, we focused on the identification and characterization of these tandemly repeated sequences.ResultsAnalysis of 1763 c0t-1 DNA fragments, providing 442 kb sequence data, shows that the satellites pBV and pEV are the most abundant repeat families in the B. vulgaris genome while other previously described repeats show lower copy numbers. We isolated 517 novel repetitive sequences and used this fraction for the identification of minisatellite and novel satellite families. Bioinformatic analysis and Southern hybridization revealed that minisatellites are moderately to highly amplified in B. vulgaris. FISH showed a dispersed localization along most chromosomes clustering in arrays of variable size and number with exclusion and depletion in distinct regions.ConclusionThe c0t-1 library represents major repeat families of the B. vulgaris genome, and analysis of the c0t-1 DNA was proven to be an efficient method for identification of minisatellites. We established, so far, the broadest analysis of minisatellites in plants and observed their chromosomal localization providing a background for the annotation of the sugar beet genome and for the understanding of the evolution of minisatellites in plant genomes.
Chromosoma | 2011
Falk Zakrzewski; Bernd Weisshaar; Jörg Fuchs; Ekaterina Bannack; André E. Minoche; Juliane C. Dohm; Heinz Himmelbauer; T. Schmidt
Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.
Annals of Botany | 2013
Rabeya Begum; Falk Zakrzewski; Gerhard Menzel; Beatrice Weber; Sheikh Shamimul Alam; T. Schmidt
BACKGROUND AND AIMS The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. METHODS A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. KEY RESULTS Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. CONCLUSIONS The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.
Plant Journal | 2014
Falk Zakrzewski; Veit Schubert; Andr e E. Minoche; Juliane C. Dohm; Heinz Himmelbauer; Bernd Weisshaar; T. Schmidt
Methylation of DNA is important for the epigenetic silencing of repetitive DNA in plant genomes. Knowledge about the cytosine methylation status of satellite DNAs, a major class of repetitive DNA, is scarce. One reason for this is that arrays of tandemly arranged sequences are usually collapsed in next-generation sequencing assemblies. We applied strategies to overcome this limitation and quantified the level of cytosine methylation and its pattern in three satellite families of sugar beet (Beta vulgaris) which differ in their abundance, chromosomal localization and monomer size. We visualized methylation levels along pachytene chromosomes with respect to small satellite loci at maximum resolution using chromosome-wide fluorescent in situ hybridization complemented with immunostaining and super-resolution microscopy. Only reduced methylation of many satellite arrays was obtained. To investigate methylation at the nucleotide level we performed bisulfite sequencing of 1569 satellite sequences. We found that the level of methylation of cytosine strongly depends on the sequence context: cytosines in the CHH motif show lower methylation (44-52%), while CG and CHG motifs are more strongly methylated. This affects the overall methylation of satellite sequences because CHH occurs frequently while CG and CHG are rare or even absent in the satellite arrays investigated. Evidently, CHH is the major target for modulation of the cytosine methylation level of adjacent monomers within individual arrays and contributes to their epigenetic function. This strongly indicates that asymmetric cytosine methylation plays a role in the epigenetic modification of satellite repeats in plant genomes.
Cytogenetic and Genome Research | 2014
Martin Schmidt; Sarah Hense; André E. Minoche; Juliane C. Dohm; Heinz Himmelbauer; T. Schmidt; Falk Zakrzewski
DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet Beta procumbens. The pEV satellite is widespread in species-specific pEV subfamilies in the genus Beta and most likely originated before the radiation of the Betoideae and Chenopodioideae. In B. procumbens, the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation.
Archive | 2017
Falk Zakrzewski; T. Schmidt
Satellite DNA is a major and abundant component of plant genomes and comprises important genomic regions such as heterochromatic knobs and centromeric chromatin. However, technical barriers of assembling first- and second-generation sequencing data hampered the complete arrangement of satellite DNAs in current plant genome sequences. Consequently, heterochromatic and centromeric regions possessing satellite DNA lack detailed characterization and assignment, which limits knowledge about their epigenetic status. We applied methods to overcome these limitations and to gain insight into the epigenetic modifications of satellite DNA-rich heterochromatic and centromeric regions of the sugar beet (Beta vulgaris) genome. Sugar beet is an important crop of temperate climate zones, which provides nearly 30% of the world’s annual sugar needs. Due to the 11% of the genome consisting of satellite DNAs, sugar beet is a suitable research object for comparative investigation and epigenetic characterization of this repeat class. We analyzed the epigenetic modifications of satellite DNA by using bisulfite sequencing, chromatin immunoprecipitation followed by sequencing (ChiP-Seq) using antibodies against histone CenH3 and dimethylated H3K9me2, and small RNA-seq data. Immunostaining of methylated cytosines and histone modifications combined with fluorescent in situ hybridization (FISH) coupled with super-resolution fluorescence microscopy complemented the epigenetic analysis. As a result, we uncovered individual epigenetic characteristics of plant satellite DNAs at high resolution and hypothesized a model for satellite DNA-directed heterochromatization.
Plant Journal | 2017
Falk Zakrzewski; Martin Schmidt; Mieke Van Lijsebettens; T. Schmidt
Plant Journal | 2016
Katrin Schwichtenberg; Torsten Wenke; Falk Zakrzewski; Kathrin M. Seibt; André E. Minoche; Juliane C. Dohm; Bernd Weisshaar; Heinz Himmelbauer; T. Schmidt
Genome | 2009
K. Anamthawat‐Jónsson; Torsten Wenke; Æ. T. Thórsson; S. Sveinsson; Falk Zakrzewski; T. Schmidt