Publications

Mann L. and Heitkam T. (2023): "Die Rückkehr der Ringe: Sequenzierung extra-chromosomaler zirkulärer DNA", Biospektrum 23(5), doi: 10.1007/s12268-023-1981-0.   read article

Heitkam T. and Garcia S. (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.   read book

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: https://doi.org/10.1007/978-1-0716-3226-0_8 read chapter

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: https://doi.org/10.1007/978-1-0716-3226-0_26    read chapter

Hartig N., Seibt K. M., Heitkam T. (2023): “How to start a LINE: 5’ switching rejuvenates LINE retrotransposons in tobacco and related Nicotiana species”, Plant Journal.   read article
Read the corresponding preprint: bioRxiv, doi: 10.1101/2022.11.04.512097.

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

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

Kazemi-Shahandashti S.-S., Mann L., El-nagish A., Harpke D., Nemati Z., Usadel B., Heitkam T. (2022): “Ancient artworks and crocus genetics both support saffron’s origin in early Greece”, Frontiers in Plant Science, doi: 10.3389/fpls.2022.834416.   read article

Sielemann K., Pucker B., Schmidt N., Viehöver P., Weisshaar B., Heitkam T., Holtgräwe D. (2022): “Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives”, BMC Genomics 23 (113), doi: 10.1186/s12864-022-08336-8.   read article
Read the corresponding preprint: bioRxiv, doi: 10.1101/2021.10.08.463637

Mann L., Seibt K. M., Weber B., Heitkam T. (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.    read article
Read the corresponding preprint: bioRxiv, doi: 10.1101/2021.06.08.447410

Sultana N., Menzel G., Seibt K. M., Garcia S., Weber B., Serçe S., and Heitkam T. (2022): „Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon“, Journal of Berry Research 12 (2), doi: 10.3233/JBR-211515.   read article
Read the corresponding open access preprint: bioRxiv, doi: 10.1101/2021.07.15.452536

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

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

Reiche B., Kögler A., Morgenstern K., Brückner M., Weber B., Heitkam T., Seibt K. M., Tröber U., Meyer M., Wolf H., Schmidt T., and Krabel D. (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.   read article

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.   read article (free access link)

Sultana N., Menzel G., Heitkam T., Kojima K. K., Bao W., Serçe S. (2020): Bioinformatic and molecular analysis of satellite repeat diversity in Vaccinium genomes. Genes 11(5): 527.   read article

Reiche B., Kögler A., Morgenstern K., Brückner M., Weber B., Heitkam T., Seibt K. M., Tröber U., Meyer M., Wolf H., Schmidt T., Krabel D. (2020): Anwendung des SINE-basierten Markersystems ISAP zur Identifizierung von Pappelklonen. In: Liesebach M (ed) Thünen Report 76: Forstpflanzenzüchtung für die Praxis. Johann Heinrich von Thünen-Institut, Braunschweig: 144-154.   read article

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

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

Seibt K. M., Schmidt T. and Heitkam T. (2020): The conserved 3’ Angio-domain defines a superfamily of short interspersed nuclear elements (SINEs) in higher plants. The Plant Journal 101:681-699.   read article

Heitkam T. (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    read article

Schmidt T., Heitkam T.,  Liedtke S., Schubert V. and Menzel G. (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 222:1965-1980   read article

Seibt K. M., Schmidt T. and Heitkam T. (2018): FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses. Bioinformatics 34:3575–3577  read article (this link grants pdf access)  FlexiDot software, documentation and examples

Sultana N., Serçe S., Menzel G., Heitkam T. and Schmidt T. (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 1:07-15  read article

Heitkam T., Petrasch S., Zakrzewski F., Kögler A., Wenke T., Wanke S. and Schmidt T. (2015): Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe's oldest Camellia japonica. Chromosome Research 23:791-806 read article

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

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

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

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

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