Beet Publications

Beet Preprints

Beet Publications

Please also see the updated lists via ORCID, ResearchGate and Google Scholar.

2026

• Wulfhorst M, Sielemann K, Schmidt N, Viehöver P, Kolbecher A, Johannes F, Vilperte V, Schulz B, Heitkam T, Holtgräwe D. (2026): "Towards epigenetics in sugar beet – the ONT based reference 5mC methylome of Beta vulgaris ssp. vulgaris", Current Plant Biology, 45: 100583, doi: 10.1016/j.cpb.2026.100583.

2024

• N. Schmidt, S. Maiwald, L. Mann, B. Weber, K. M. Seibt, S. Breitenbach, S. Liedtke, G. Menzel, B. Weisshaar, D. Holtgräwe, T. Heitkam (2024): “BeetRepeats: reference sequences for genome and polymorphism annotation in sugar beet and wild relatives”, in press at BMC Research Notes; doi: 10.1186/s13104-024-06993-4
  --> The database of beet repeat sequences can be already accessed via Zenodo: 10.5281/zenodo.8255813.

• L. Mann, K. Balasch, N. Schmidt and T. Heitkam (2024): "High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly", BMC Genomics, 25(109); doi: 10.1186/s12864-023-09948-4.
  --> bioRxiv preprint, doi: 10.1101/2023.10.26.564123).
  --> Twitter thread explaining the paper & shortie on BlueSky

• N. Schmidt, K. Sielemann, S. Breitenbach, J. Fuchs, B. Pucker, B. Weisshaar, D. Holtgräwe, T. Heitkam (2024): "Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets", The Plant Journal, 118, 117-190; doi: 10.1111/tpj.16599.
  --> bioRxiv preprint, doi: 10.1101/2023.09.01.555723
  --> Twitter thread explaining the paper

2023

• N. Schmidt, B. Weber, J. Klekar, S. Liedtke, S. Breitenbach and T. Heitkam (2023): “Preparation of mitotic chromosomes using the dropping technique”, chapter in Methods in Molecular Biology 2672: Plant Cytogenetics and Cytogenomics, T. Heitkam and S. Garcia (eds.); J. Walker (series ed.), Humana New York, US; doi: 10.1007/978-1-0716-3226-0_8.

• L. Mann and S. Maiwald (2023): “Visualization of Oligonucleotide-Based Probes Along Pseudochromosomes Using RIdeogram, KaryoploteR, and Circlize (Circos)”, chapter in Methods in Molecular Biology 2672: Plant Cytogenetics and Cytogenomics, T. Heitkam and S. Garcia (eds.); J. Walker (series ed.), Humana New York, US; doi: 10.1007/978-1-0716-3226-0_26.

2022

• S. Liedtke, S. Breitenbach and T. Heitkam (2022): “FISH – in plant chromosomes”, chapter in Cytogenetics and Molecular Cytogenetics, T. Liehr (ed.), Taylor and Francis, doi: 10.1201/9781003223658-28. 

• K. Sielemann, B. Pucker, N. Schmidt, P. Viehöver, B. Weisshaar, T. Heitkam and D. Holtgräwe (2022): “Pan-plastome of Betoideae species reveals phylogenetic relationships of closely related beets” BMC Genomics, doi: 10.1186/s12864-022-08336-8.
  --> bioRxiv preprint, doi: 10.1101/2021.10.08.463637.

• L. Mann, K. M. Seibt, B. Weber and T. Heitkam (2022): “ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data”, BMC Bioinformatics 23(40), doi: 10.1186/s12859-021-04545-2.
  --> bioRxiv preprint, doi: 10.1101/2021.06.08.447410.
  --> Twitter thread explaining the paper.

2021

• N. Schmidt,  K. M. Seibt, B. Weber, T. Schwarzacher, T. Schmidt and T. Heitkam (2021): Broken, silent, and in hiding: Tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). Annals of Botany, doi: 10.1093/aob/mcab042, free access link.
  --> bioRxiv preprint, doi: 10.1101/2020.12.02.407783.
  --> Twitter thread explaining the paper.

• S. Maiwald, B. Weber, K. M. Seibt, T. Schmidt and T. Heitkam (2021): “The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and the Amaranthaceae: Recombination and re-shuffling lead to a high structural variability”, Annals of Botany 127(1), 91-109, doi: 10.1093/aob/mcaa176, free access link.
  --> Twitter thread explaining the paper.

2020

• T. Heitkam, B. Weber, I. Walter, S. Liedtke, C. Ost and T. Schmidt (2020): “Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes”, The Plant Journal 103(1), 32-52, doi: 10.1111/tpj.14705.
  --> bioRxiv preprint, doi: 10.1101/774828.
  --> Twitter thread explaining the paper.

before 2020

• T. Heitkam, D. Holtgräwe, J. C. Dohm, A. E. Minoche, H. Himmelbauer, B. Weisshaar and T. Schmidt (2014): “Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades”, The Plant Journal 79 (3), 385-397, doi: 10.1111/tpj.12565. 

• B. Weber, T. Heitkam, D. Holtgräwe, B. Weisshaar, A. E. Minoche, J. C. Dohm, H. Himmelbauer and T. Schmidt (2013): “Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration patterns”, Mobile DNA 4, 8, doi: 10.1186/1759-8753-4-8. 

• C. Wollrab, T. Heitkam, D. Holtgräwe, B. Weisshaar, A. E. Minoche, J. C. Dohm, H. Himmelbauer and T.  Schmidt (2012): “Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome.” The Plant Journal 72 (4), 636-251, doi: 10.1111/j.1365-313x.2012.05107.x. 

• B. Weber, T. Wenke, U. Frömmel, T. Schmidt and T. Heitkam (2010): “The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution and age.” Chromosome Research 18 (2), 247-263, doi: 10.1007/s10577-009-9104-4. 

• T. Heitkam and T. Schmidt (2009): BNR – a LINE family from Beta vulgaris – contains a RRM domain in open reading frame 1 and defines a L1 sub-clade present in diverse plant genomes. The Plant Journal 59:872-882, doi: 10.1111/j.1365-313X.2009.03923.x. 

Beet Publications of Thomas Schmidt (1961-2019)

2021

Schmidt N., Seibt K. M., Weber B., Schwarzacher T., Schmidt T., and Heitkam T. (2021): Broken, silent, and in hiding: Tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). Annals of Botany, doi: 10.1093/aob/mcab042.   read article (free access link)
Read the corresponding preprint: bioRxiv, doi: 10.1101/2020.12.02.407783

Maiwald S., Weber B., Seibt K. M., Schmidt T., and Heitkam T. (2021): The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and the Amaranthaceae: Recombination and re-shuffling lead to a high structural variability. Annals of Botany 127(1): 91-109, doi: 10.1093/aob/mcaa176.   read article (free access link)

2020

Heitkam T., Weber B., Walter I., Liedtke S., Ost C. and Schmidt T. (2020): Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes. The Plant Journal 103(1): 32-52.   read article
Read the corresponding preprint (open access): bioRxiv, doi: 10.1101/774828

2019

Rodríguez del Río Á., Minoche A., Zwickl N., Friedrich A., Liedtke S., Schmidt T., Himmelbauer H. and Dohm J. (2019): Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima. The Plant Journal 99: 1242-1253   read article

2017

Zakrzewski F. and Schmidt, T. (2017): Epigenetic Characterization of Satellite DNA in Sugar Beet (Beta vulgaris). In: Rajewsky N., Jurga S., Barciszewski J. (eds) Plant Epigenetics. RNA Technologies. SpringerBook  read article

Zakrzewski F., Schmidt M., Van Lijsebettens M. and Schmidt T. (2017): DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.). The Plant Journal 92: 676-695   read article

2016

Dechyeva, D. and Schmidt, T. (2016): Fluorescent in situ hybridization on extended chromatin fibers for high-resolution analysis of plant chromosomes. Methods in Molecular Biology, Plant Cytogenetics 1429: 23-33  read article

Kowar, T., Zakrzewski, F., Macas, J., Koblizkova, A., Viehöver, P., Weisshaar, B. and Schmidt, T. (2016): Repeat composition of CenH3- chromatin and H3K9me2-marked heterochromatin in sugar beet (Beta vulgaris). BMC Plant Biology 16: 120   read article

Schwichtenberg K., Wenke T., Zakrzewski F., Seibt K. M., Minoche A. E., Dohm J. C., Weisshaar B., Himmelbauer H. and Schmidt T. (2016): Diversification, evolution and methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species. The Plant Journal 85: 229-244 read article

2014

Schmidt M., Hense S., Minoche, A.E., Dohm, J.C., Himmelbauer, H., Schmidt T. and Zakrzewski F. (2014): Cytosine methylation of an ancient satellite family in the wild beet Beta procumbens. Cytogenetic and Genome Research 143: 157-167  read article

Heitkam T, Holtgräwe D, Dohm JC, Minoche AE, Himmelbauer H, Weisshaar B and Schmidt T (2014): Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades. The Plant Journal, 79: 385-397   read article

Zakrzewski, F., Schubert, V., Viehöver, P., Minoche, A.E., Dohm, J.C., Himmelbauer, H., Weisshaar, B. and Schmidt, T. (2014): The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation. The Plant Journal 78: 937-950   read article

Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H. (2014) : The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).  Nature 505: 546–549   read article

2013

Weber B., Heitkam T., Holtgräwe D., Weishaar B., Minoche A.E., Himmelbauer H., Dohm J.C., Schmidt T. (2013): Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration. Mobile DNA 4: 8   read article

Zakrzewski F, Weber B, Schmidt T. (2013): A molecular cytogenetic analysis of the structure, evolution and epigenetic modifications of major DNA sequences in centromeres of Beta species. In: Jiang J, Bircher JA, editors. Plant centromere biology. Chichester, UK: Wiley-Blackwell; 2013. p. 39-56 read book chapter

2012

Wollrab C., Heitkam T., Holtgräwe D., Weisshaar B., Minoche A.E., Dohm J.C., Himmelbauer H.,  Schmidt T. (2012): Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. Plant Journal 72: 636-651 read article

Paesold S., Borchardt D., Schmidt T., Dechyeva D. (2012): A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome arm identification, integration of genetic linkage groups and analysis of major repeat family distribution. Plant Journal 72: 600-611 read article

Menzel G., Krebs C., Mercedes D., Holtgräwe D., Weisshaar B., Minoche A. E., Dohm J. C., Himmelbauer H. and Schmidt T. (2012): Survey of sugar beet (Beta vulgaris) hAT transposons and MITE-like hATpin derivatives. Plant Mol. Biol. 78: 393-405 read article

2011

Zakrzewski, F., Weisshaar B., Fuchs J., Bannack E., Minoche A. E., Dohm J. C., Himmelbauer H. and Schmidt, T. (2011): Epigenetic profiling of heterochromatic satellite DNA. Chromosoma 120: 409-422  read article

2010

Zakrzewski, F., Wenke, T., Holtgrawe, D., Weisshaar, B. and Schmidt, T. (2010): Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biol. 10: 8. read article

Weber, B., Wenke, T., Frommel, U., Schmidt, T. and Heitkam, T. (2010): The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age. Chromosome Res. 18: 247-263. read article

2009

Wenke, T., Holtgrawe, D., Horn, A.V., Weisshaar, B. and Schmidt, T. (2009): An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris. Plant Mol. Biol. 71: 585-597. read article

Dechyeva, D. and Schmidt, T. (2009): Molecular cytogenetic mapping of chromosomal fragments and immunostaining of kinetochore proteins in Beta. Int J Plant Genomics 721091. read article

Heitkam, T., T.Schmidt (2009): BNR – a LINE family from Beta vulgaris – contains a RRM domain in open reading frame 1 and defines a L1 sub-clade present in diverse plant genomes. Plant Journal 59: 872-882 read article

Weber, B. and Schmidt, T. (2009): Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain. Chromosome Research, 17: 379-396 read article

Jacobs, G., D. Dechyeva, T. Wenke, B. Weber, T.Schmidt (2009): A BAC library of Beta vulgaris L. for the targeted isolation of centromeric DNA and molecular cytogenetics of Beta species. Genetica, 135: 157-167 read article

Schmidt, T., D. Dechyeva, C. Fiege, T. Heitkam, G. Menzel, B. Weber, T. Wenke, F. Zakrzewski (2009): Comparative physical mapping of rearranged and normal plant chromosomes by high-resolution FISH and megabase DNA techniques. TecDoc of the IAEA/FAO Coordinated Research Programm “Physical mapping technologies for the identification and characterization of mutated genes contributing to crop quality”

1990 - 2008

Menzel G, Dechyeva D, Wenke T, Holtgräwe D, Weisshaar B, Schmidt T (2008): Diversity of a complex centromeric satellite and molecular characterization of dispersed sequence families in sugar beet (Beta vulgaris). Annals of Botany 102: 521-530.

Schulz B., B. Weisshaar, D. Holtgräwe, T. Rosleff Sörensen, G. Koch, H. Himmelbauer, C. Lange, J. Dohm, T. Schmidt, K. Schneider (2007): GABI Beet Physical Map: A physical map of the sugar beet genome to integrate genetics and genomics. GenomXpress, Special Issue 2007

Dechyeva, D., T. Schmidt (2006): Molecular organization of terminal repetitive DNA in Beta species. Chromosome Res. 14: 881-897

Menzel, G.,  D. Dechyeva, H. Keller, C. Lange, H. Himmelbauer, T. Schmidt (2006): Mobilization and evolutionary history of minitiature-inverted-repeat transposable elements (MITEs) in Beta vulgaris L.. Chromosome Res. 14: 831-844

Jacobs, G., D. Dechyeva, G. Menzel, C. Dombrowski, T. Schmidt (2004): Molecular characterization of Vulmar1, a complete mariner transposon of sugar beet and diversity of mariner- and En/Spm-like sequences in the genus Beta. Genome 47: 1192-1201

Schmidt, T.,  C. Desel , D. Dechyeva, B. Fleischer, F. Gindullis, A. Schmidt, J.S. Heslop-Harrison, R.L. Doudrick (2004): FISHing repeated DNA sequences in Beta genomes. In: Chromosomes Today 14 (eds. M. Schmid, I. Nanda), Chapter 5.1 pp. 249-266, Kluwer Academic Publishers

Dechyeva, D., F. Gindullis, T. Schmidt (2003): Divergence of satellite DNA and interspersion of dispersed repeats in the genome of the wild beet Beta procumbens. Chromosome Res. 11:3-21

Desel, D., R. Jansen, G. Dedong, T. Schmidt (2002): Painting of parental chromatin in Beta hybrids by multi-colour fluorescent in situ hybridization. Annals of Botany 89:171-181

Staginnus, C., B. Huettel, C. Desel, T. Schmidt, G. Kahl (2001): A PCR-based assay to detect En/Spm-like transposon sequences in plants. Chromosome Res. 9:591-605

Gindullis, F., D. Dechyeva, T. Schmidt (2001): Construction and characterization of a BAC library for the molecular dissection of a single wild beet centromere and sugar beet (Beta vulgaris) genome analysis. Genome 44:846-855

Gindullis, F., C. Desel, I. Galasso, T. Schmidt (2001): The large-scale organization of centromeric DNA in Beta species. Genome Res. 11:253-265

Desel, C., C. Jung, D. Cai, M. Kleine, T. Schmidt (2001): High resolution mapping of YACs and single-copy gene Hs1pro-1 on Beta vulgaris chromosomes by multi-colour fluorescence in situ hybridization. Plant Mol. Biol. 45:113-122

Gao, D., T. Schmidt, C. Jung (2000): Molecular characterization and chromosomal distribution of species-specific repetitive DNA sequences from Beta corolliflora, a wild relative of sugar beet. Genome 43:1073-1080

Schmidt, T., S. Kubis, A. Katsiotis, C. Jung, J.S. Heslop-Harrison (1998): Molecular and chromosomal organization of two repetitive DNA sequences with intercalary locations in sugar beet and other Beta species. Theor. Appl. Genet. 97:696-704

Kubis, S., J.S. Heslop-Harrison, C. Desel, T. Schmidt (1998): The genomic organization of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms. Plant Mol. Biol. 36:821-831

Schmidt, T., S. Kubis, C. Desel, C. Jung, J.S. Heslop-Harrison (1997): Molekulare Zytogenetik von Wild- und Kulturrüben der Gattung Beta. Vorträge für Pflanzenzüchtung 37:125-143

Schmidt, T., C. Desel, F. Gindullis, S. Kubis, I. Galasso, J.S. Heslop-Harrison (1997): The structural model of Beta vulgaris chromosomes. In: 100 Years of Genetics for Plant Breeding – Mendel, Meiosis and Marker. Mendel Cenetary Congress, Vorträge für Pflanzenzüchtung 48:196-204

Heslop-Harrison, J.S., A. Brandes, S. Taketa, T. Schmidt, A.V. Vershinin, E.G. Alkhimova, A. Kamm, A. Katsiotis, R.L. Doudrick, T. Schwarzacher, S. Kubis, A. Kumar, S.R. Pearce, A.J. Flavell, G.E. Harrison (1997): The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution. Genetica 100:197-204

Schmidt, T., C. Jung, J.S. Heslop-Harrison, M. Kleine (1997): Detection of alien chromatin conferring resistance to the beet cyst nematode (Heterodera schachtii Schm.) in cultivated beet (Beta vulgaris L.) using in situ hybridization. Chromosome Res. 5:186-193

Schondelmaier, J., T. Schmidt, J.S. Heslop-Harrison, C. Jung (1997): Genetic and chromosomal localization of the 5S rDNA locus in sugar beet (Beta vulgaris L.). Genome 40:171-175

Kubis, S., J.S. Heslop-Harrison, T. Schmidt (1997): A family of differentially amplified repetitive DNA sequences in the genus Beta reveals genetic variation in Beta vulgaris subspecies and cultivars. J. Mol. Evol. 44:310-320

Schmidt, T., J.S. Heslop-Harrison (1996): The physical and genomic organization of microsatellites in sugar beet (Beta vulgaris). Proc. Natl. Acad. Sci. USA 93:8761-8765

Schmidt, T., J.S. Heslop-Harrison (1996): High-resolution mapping of repetitive DNA by in situ hybridization: molecular and chromosomal features of prominent dispersed and discretely localized DNA families from the wild beet species Beta procumbens. Plant Mol. Biol. 30:1099-1119

Schmidt, T., S. Kubis, J.S. Heslop-Harrison (1995): Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements as major components of the genome. Chromosome Res. 3:335-345

Galasso, I., T. Schmidt, D. Pignone, J.S. Heslop-Harrison (1995): The molecular cytogenetics of Vigna unguiculata (L.) Walp: the physical organization and characterization of 18S-5.8S-25S rRNA genes, 5S rRNA, telomere-like sequences, and a family of centromeric repetitive DNA sequences. Theor. Appl. Genet. 91:928-935

Schmidt, T., J.S. Heslop-Harrison (1994): Variability and evolution of highly repeated DNA sequences in the genus Beta. Genome 36:1074-1079

Schmidt, T., T. Schwarzacher, J.S. Heslop-Harrison (1994): Physical mapping of rRNA genes by fluorescent in situ hybridization and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Beta vulgaris). Theor. Appl. Genet. 88:629-636

Schmidt, T., K. Boblenz, M. Metzlaff, D. Kaemmer, K. Weising, G. Kahl (1993): DNA-fin­gerprinting in sugar beet (Beta vulgaris) - identification of double-haploid breeding lines. Theor. Appl. Genet. 85:653-657

Schmidt, T., K. Boblenz, M. Metzlaff (1992): Satellite polymorphisms and genome diagnosis in the genus Beta. In: BioTechForum - Advances in molecular genetics (Kahl, G., H. Appelhans, J. Kämpf, A.J Driesel, eds), Vol.10: DNA-Polymor­phisms in Eukaryotic Genomes. 197-208, Hüthig, Heidelberg

Schmidt, T., K. Boblenz, K. Weising (1992): Use of highly repeated DNA polymorphisms for genome diagnosis and evolutionary studies in the genus Beta. In: DNA Fingerprinting - State of the Science (Pena, S.D.J., R. Chakraborty, J.T. Epplen, A.J. Jeffreys, eds.), 453 – 459, Birkhäuser, Basel

Schmidt, T., C. Jung, M. Metzlaff (1991): Distribution and evolution of two satellite DNAs in the genus Beta. Theor. Appl. Genet. 82:793-799

Schmidt, T., M. Metzlaff (1991): Cloning and characterization of a Beta vulgaris satellite DNA family. Gene 101:247-250

Schmidt, T., H. Junghans, M. Metzlaff (1990): Construction of B. procumbens-specific DNA probes and their application for the screening of B.vulgaris x B.procumbens (2n = 19) addi­tion lines. Theor. Appl. Genet. 79:177-181