Publications

Covers

Preprints and accepted articles

Publications

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

2025

• S. Taniguchi, S. Ishiguro, N. Schmidt, M. Jost, S. Wanke, T. Heitkam, N. Ohmido (2025): "Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication", Annals of Botany; doi: 10.1093/aob/mcae184.
  --> bioRxiv preprint, doi: 10.1101/2024.06.05.597687

• A. El-nagish, S. Liedtke, S. Breitenbach and T. Heitkam (2025): "Preparing high-quality chromosome spreads from Crocus species for karyotyping and FISH", Molecular Cytogenetics, doi: 10.1186/s13039-025-00706-7
  --> bioRxiv preprint, doi: 10.1101/2024.11.18.624136.

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.

• N.-A. Ankrah, A. El-nagish, S. Breitenbach, A. Tetteh and T. Heitkam (2024):  “Comparative cytogenetics of kenaf (Hibiscus cannabinus L.) breeding lines reveals chromosomal instability and variability”, Genetic Resources and Crop Evolution; doi: 10.1007/s10722-024-02176-z
  --> bioRxiv preprint, doi: 10.1101/2023.11.18.567672.
  --> Please also visit the site from our partners in Ghana.

• S. Garcia, A. Kovarik, S. Maiwald, L. Mann, N. Schmidt, J. P. Pascual-Diaz, D. Vitales, B. Weber, T. Heitkam (2024): "The Dynamic Interplay between Ribosomal DNA and Transposable Elements: A Perspective from Genomics and Cytogenetics", Molecular Biology and Evolution 41(3), msae025; doi: 10.1093/molbev/msae025. 

• S. Maiwald, L. Mann, S. Garcia, T. Heitkam (2024): "Evolving together: Cassandra retrotransposons gradually mirror promoter mutations of the 5S rRNA genes", Molecular Biology and Evolution, 41(2), msae10; doi: 10.1093/molbev/msae010.
  --> bioRxiv preprint, doi:  10.1101/2023.07.14.548913
  --> Twitter thread explaining the paper

• 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

• L. Mann and T. Heitkam: "Die Rückkehr der Ringe: Sequenzierung extra-chromosomaler zirkulärer DNA", Biospektrum 29, 475–478 (2023); doi: 10.1007/s12268-023-1981-0. 

• T. Heitkam and S. Garcia (eds.) (2023): “Plant Cytogenetics and Cytogenomics”, volume 2672 of the “Methods in Molecular Biology” series, J. Walker (series ed.), Humana New York, US, ISBN: 978-1-0716-3225-3; doi: 10.1007/978-1-0716-3226-0.

• 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.

• N. Hartig, K. M. Seibt and T. Heitkam (2023): “How to start a LINE: 5’ switching rejuvenates LINE retrotransposons in tobacco and related Nicotiana species”, The Plant Journal doi: 10.1111/tpj.16208.
  --> bioRxiv preprint, doi: 10.1101/2022.11.04.512097.
  --> Twitter thread explaining the paper

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. 

• L. Schulte, S. Meucci, K. Stoof-Leichsenring, T. Heitkam, N. Schmidt, B. von Hippel, B. Diekmann, B. K. Biskaborn, B. Wagner, M. Melles, L. A. Pestryakova, K. V. Krutovsky and U. Herzschuh (2022): “Dynamics of larch species ranges in Siberia since the Last Glacial captured from sedimentary ancient DNA”, Communications Biology 5 (570), doi: 10.1038/s42003-022-03455-0. 

• S.-S. Kazemi-Shahandashti, L. Mann, A. El-nagish, D. Harpke, Z. Nemati, B. Usadel and T. Heitkam (2022): “Ancient artworks and crocus genetics both support saffron’s origin in early Greece”, Frontiers in Plant Science, doi: 10.3389/fpls.2022.834416.
  --> the journal featured this art/genetics review, which resulted in wide press coverage (see Altmetric).

• 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.

• N. Sultana, G. Menzel, K. M. Seibt, S. Garcia, B. Weber, S. Serçe and T. Heitkam (2022): „Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon“, Journal of Berry Research, doi: 10.3233/jbr-211515.
  --> bioRxiv preprint, doi: 10.1101/2021.07.15.452536.

2021

• T. Heitkam and S. Garcia (2021): “Can we have it all? Repurposing target-capture for repeat genomics. A commentary on: Aiming off the target: recycling target-capture sequencing reads for investigating repetitive DNA”, invited commentary for Annals of Botany, doi: 10.1093/aob/mcab080.

• The TE Hub Consortium, T. Elliott, T. Heitkam, R. Hubley, H. Quesneville, A. Suh and T. Wheeler (2021): “TE Hub: a community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation”, Mobile DNA 12(16), doi: 10.1186/s13100-021-00244-0.    

• T. Heitkam, L. Schulte, B. Weber, S. Liedtke, S. Breitenbach, A. Kögler, K. Morgenstern, M. Brückner, U. Tröber, H. Wolf, D. Krabel and T. Schmidt (2021): “Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only one fast-evolving satellite DNA”, Frontiers in Genetics 12, 1049, doi: 10.3389/fgene.2021.683668.
  --> bioRxiv preprint, doi: 10.1101/2021.03.21.436054.
  --> Twitter thread explaining the paper.

• B. Reiche, A. Kögler, K. Morgenstern, M. Brückner, B. Weber, T. Heitkam, K. M. Seibt, U. Tröber, M. Meyer, H. Wolf, T. Schmidt and D. Krabel (2021): “Application of retrotransposon-based Inter-SINE Amplified Polymorphism (ISAP) markers for the differentiation of common poplar genotypes”, Canadian Journal of Forest Research, doi: 10.1139/cjfr-2020-0209. 

• 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

• N. Sultana, G. Menzel, T. Heitkam, K. K. Kojima, W. Bao, and S. Serçe (2020): “Bioinformatic and molecular analysis of satellite repeat diversity in Vaccinium genomes”, Genes 11(5), 527, doi: 10.3390/genes11050527. 

• B. Reiche, A. Kögler, K. Morgenstern, M. Brückner, B. Weber, T. Heitkam, K. M. Seibt, U. Tröber, M. Meyer, H. Wolf, T. Schmidt and D. Krabel (2020): “Anwendung des SINE-basierten Markersystems ISAP zur Identifizierung von Pappelklonen” Chapter in Thünen Report 76: Forstpflanzenzüchtung für die Praxis, M. Liesebach (ed.), 144-154, doi: 10.3220/rep1584625360000. 

• A. Kögler, K. M. Seibt, T. Heitkam, K. Morgenstern, B. Reiche, M. Brückner, H. Wolf, D. Krabel, and T. Schmidt (2020): “Divergence of 3’ ends as driver of Short Interspersed Nuclear Element (SINE) evolution in the Salicaceae”, The Plant Journal 103(1), 443-458, doi: 10.1111/tpj.14721. 

• 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.

• K. M. Seibt, T. Schmidt, and T. Heitkam (2020): “The conserved 3’ Angio-domain defines a superfamily of short interspersed nuclear elements (SINEs) in higher plants”, The Plant Journal 101(3), 681-699, doi: 10.1111/tpj.14567.
  --> Twitter thread explaining the paper.

before 2020

• T. Heitkam (2019): Balancing retrospection and visions: The Cytogenetics group of the Society of Plant Breeding (GPZ) came together in Dresden. Cytogenetic and Genome Research 159:163-168, doi: 10.1159/000505280.

• T. Schmidt, T. Heitkam, S. Liedtke, V. Schubert and G. Menzel (2019): “Adding color to a century-old enigma: Multi-color chromosome identification unravels the autotriploid nature of saffron (Crocus sativus) as a hybrid of wild Crocus cartwrightianus cytotypes”, New Phytologist 22(4), 1965-1980, doi: 10.1111/nph.15715.
  --> Twitter thread explaining the paper.
  --> Press release & Altmetric.

• K. M. Seibt, T. Schmidt and T. Heitkam (2018): “FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses”, Bioinformatics 34 (20), 3575–3577, doi: 10.1093/bioinformatics/bty395, free access link,
  --> FlexiDot github.
  --> nice Twitter-example of FlexiDot to resolve TE regions.

• N. Sultana, S. Serçe, G. Menzel, T. Heitkam and T. Schmidt (2017): “Comparative analysis of repetitive sequences reveals genome differences between two common cultivated Vaccinium species (V. corymbosum and V. macrocarpon)”, Journal of Molecular Biology and Biotechnology 1(2), 07-15. read

• T. Heitkam, S. Petrasch, F. Zakrzewski, A. Kögler, T. Wenke, S. Wanke and T. Schmidt (2015): “Next generation sequencing reveals differentially amplified tandem repeats as major genome component of Northern Europe’s oldest Camellia japonica”, Chromosome Research 23(4):791-806, doi: 10.1007/s10577-015-9500-x. 

• G. Menzel, T. Heitkam, K. M. Seibt, F. Nouroz, M. Müller-Stoermer, J. S. Heslop-Harrison and T. Schmidt (2014): “The diversification and activity of a hAT transposon family in Musa genomes”, Chromosome Research 22 (4), 559-571, doi: 10.1007/s10577-014-9445-5. 

• A. Gilly, M. Etcheverry, M.-A. Madoui, J. Guy, L. Quadrana, A. Alberti, A. Martin, T. Heitkam, S. Engelen, K. Labadie, J. Le Pen, P. Wincker, V. Colot and J.-M. Aury (2014): “TE-Tracker: systematic identification of transposition events through whole-genome resequencing”, BMC Bioinformatics 15 (1), 377, doi: 10.1186/s12859-014-0377-z. 

• 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. 

• A. Just, F. Butter, M. Trenkmann, T. Heitkam, M. Mörl and H. Betat (2008): “A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme.” Nucleic Acids Research 36 (16), 5212-5220, doi: 10.1093/nar/gkn494.