Publications

Covers

Cover of our article that unravels the genetic origin of saffron crocus.

Cover of our article on Cassandra retrotransposons: These are transposons that have caught and use the 5S rDNA promoters.

Cover of our protocol book "Plant Cytogenetics and Cytogenomics" in the "Methods in Molecular Biology" series.

Preprints

insights into the chromosomal variability of kenaf breeding lines from Ghana...

N.-A. Ankrah, A. El-nagish, S. Breitenbach, A. Tetteh and T. Heitkam (2023): “Comparative cytogenetics of kenaf (Hibiscus cannabinus L.) breeding lines reveals chromosomal instability and variability”, bioRxiv, doi: 10.1101/2023.11.18.567672.

Please also visit the site from our partners in Ghana.

the quest for consensus...

L. Mann, K. Balasch, N. Schmidt and T. Heitkam (2023): "High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly", bioRxiv, doi: 10.1101/2023.10.26.564123. read preprint

Twitter thread explaining the paper & shortie on BlueSky

chromosomal causes of barriers between beet gene pools...

N. Schmidt, K. Sielemann, S. Breitenbach, J. Fuchs, B. Pucker, B. Weisshaar, D. Holtgräwe and T. Heitkam (2023): "Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets", bioRxiv, doi: 10.1101/2023.09.01.555723. read preprint

Twitter thread explaining the paper

promoter mimicry of a transposon...

S. Maiwald, L. Mann, S. Garcia and T. Heitkam (2023): "Evolving together: Cassandra retrotransposons gradually mirror promoter mutations of the 5S rRNA genes", bioRxiv, doi: 10.1101/2023.07.14.548913. read preprint

Twitter thread explaining the paper

parentage of a tetraploid wild beet...

K. Sielemann, N. Schmidt, J. Guzik, N. Kalina, B. Pucker, P. Viehöver, S. Breitenbach, B. Weisshaar, T. Heitkam and D. Holtgräwe (2023): "Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet", bioRxiv, doi: 10.1101/2023.06.28.546919. read preprint

Twitter thread explaining the paper

Publications

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

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.