Publications

Plant Biotechnology and Bioinformatics

2024

• Wolff K.*, Friedhoff R.*, Horz J. M.*, Pucker B. (2024). Genome sequence of the medicinal and ornamental plant Digitalis purpurea reveals the molecular basis of flower color variation. bioRxiv 2024.02.14.580303; doi: 10.1101/2024.02.14.580303.

• Pucker, B. (2024). Functional Annotation – How to Tackle the Bottleneck in Plant Genomics. Preprints. doi: 10.20944/preprints202402.0645.v1.

• Baasner J.-S., Rempel A. Howard D., Pucker B. (2024). NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction. bioRxiv 596718; doi: 10.1101/596718.

• Frommann J.-F., Pucker B., Sielmann L. M., Muller C., Weisshaar B., Stracke R., Schweiger R. (2024). Metabolic fingerprinting reveals roles of Arabidopsis thaliana BGLU1, BGLU3 and BGLU4 in glycosylation of various flavonoids. bioRxiv 2024.01.30.577901; doi: 10.1101/2024.01.30.577901.

• Choudhary N. & Pucker B. (2024). Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR. bioRxiv 2023.11.05.565693; doi: 10.1101/2023.11.05.565693.
• Hafner, A.; DeLeo, V.; Deng, C.; Elsik, C.G.; Fleming, D.; Harrison, P.W.; Kalbfleisch, T.S.; Petry, B.; Pucker, B.; Quezada-Rodríguez, E.H.; Tuggle, C.K.; Koltes, J. Data Reuse in Agricultural Genomics Research: Present Challenges and Future Solutions. Preprints 2024, 2024010780. https://doi.org/10.20944/preprints202401.0780.v1.
• Pucker, B.*, Walker-Hale, N.*, Dzurlic, J., Yim, W.C., Cushman, J.C., Crum, A., Yang, Y. and Brockington, S.F. (2024), Multiple mechanisms explain loss of anthocyanins from betalain-pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme. New Phytol., 241: 471-489. doi: 10.1111/nph.19341.

2023

• Schmidt N., Sielemann K., Breitenbach S., Fuchs J., Pucker B., Weisshaar B., Holtgräwe D., Heitkam T. (2023). Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets. Plant J. doi: 10.1111/tpj.16599.

• Thoben C. and Pucker B. (2023). Automatic annotation of the bHLH gene family in plants. BMC Genomics 24, 780 (2023). doi: 10.1186/s12864-023-09877-2.

• Wolff, K.; Friedhoff, R.; Schwarzer, F.; Pucker, B. (2023). Data Literacy in Genome Research. Journal of Integrative Bioinformatics, 2023, pp. 20230033. doi: 10.1515/jib-2023-0033.

• Sielemann, K.*, Pucker, B.*, Orsini, E. et al. Genomic characterization of a nematode tolerance locus in sugar beet. BMC Genomics 24, 748 (2023). doi: 10.1186/s12864-023-09823-2.

• Rempel A., Choudhary N. and Pucker B. (2023). KIPEs3: Automatic annotation of biosynthesis pathways. PLOS ONE 18(11): e0294342. doi: 10.1371/journal.pone.0294342.

• Naik J., Tyagi S., Rajput R., Kumar P., Pucker B., Bisht N. C., Misra P., Stracke R., Pandey A. Flavonols have opposite effects on the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana, Journal of Experimental Botany, 2023;, erad391, doi: 10.1093/jxb/erad391.

• Natarajan, S., Pucker, B. & Srivastava, S. Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409. Sci Rep 13, 14614 (2023). doi: 10.1038/s41598-023-41738-6.

• Movahedi A, Pucker B and Kadkhodaei S (2023) Editorial: Genomics and gene editing of orphan plants. Front. Plant Sci. 14:1277625. doi: 10.3389/fpls.2023.1277625.

• Meckoni, S.N., Nass, B. & Pucker, B. (2023). Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data. BMC Res Notes 16, 187. doi: 10.1186/s13104-023-06459-z.

• Siadjeu, C. & Pucker, B. (2023). Medicinal plant genomics. BMC Genomics 24, 429 (2023). doi: 10.1186/s12864-023-09542-8.

• Feng, T.*, Pucker, B.*, Kuang, T.*, Song B.*, Yang Y., Lin N., Zhang H., Moore M.J., Brockington S.F., Wang Q., Deng T., Wang H. and Sun H. (2023). The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation. Commun Biol 6, 706 (2023). doi: 10.1038/s42003-023-05044-1.

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

• Bartas M., Volna A., Cerven J. and Pucker B. (2023). Identification of annotation artifacts concerning the CHALCONE SYNTHASE (CHS). BMC Res Notes 16, 109 (2023). doi: 10.1186/s13104-023-06386-z.
• Busche M., Pucker B., Weisshaar B., Stracke R. Three R2R3-MYB transcription factors from banana (Musa spp.) activate structural anthocyanin biosynthesis genes as part of an MBW complex. BMC Res Notes 16, 103 (2023). doi: 10.1186/s13104-023-06375-2.
• Marin M. F. & Pucker B. (2023). Genetic factors explaining anthocyanin pigmentation differences. bioRxiv 2023.06.05.543820; doi: 10.1101/2023.06.05.543820.
• Albert N. W., Iorizzo M., Mengist M.F., Montanari S., Zalapa J., Maule A., Edger P. P., Yocca A. E., Platts A. E., Pucker B., Espley R. V. (2023). Vaccinium as a comparative system for understanding of complex flavonoid accumulation profiles and regulation in fruit. Plant Physiology. doi: 10.1093/plphys/kiad250.
• Göttl V.L., Pucker B., Wendisch V.F., Henke N.A. (2023). Screening of structurally distinct lycopene β-cyclases for production of the cyclic C40 carotenoids β-carotene and astaxanthin by Corynebacterium glutamicum. Journal of Agricultural and Food Chemistry. doi: 10.1021/acs.jafc.3c01492.
• Pucker B & Iorizzo M (2023). Apiaceae FNS I originated from F3H through tandem gene duplication. PLOS ONE 18(1): e0280155. doi: 10.1371/journal.pone.0280155.

2022

• Movahedi A, Wei H, Pucker B, Sun W, Li W, Yang L, Zhuge Q (2022). Regulation of poplar isoprenoid biosynthesis by methylerythritol phosphate and mevalonic acid pathways interactions. Front. Plant Sci. 13:968780. doi: 10.3389/fpls.2022.968780.

• Rajput, R., Tyagi, S., Naik, J. Pucker, B., Stracke, R., Pandey, A. The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat. Planta 256, 67 (2022). doi: 10.1007/s00425-022-03979-z.

• Mengist MF, Grace MH, Mackey T, Munoz B, Pucker B, Bassil N, Luby C, Ferruzzi M, Lila MA and Iorizzo M (2022) Dissecting the genetic basis of bioactive metabolites and fruit quality traits in blueberries (Vaccinium corymbosum L.). Front. Plant Sci. 13:964656. doi: 10.3389/fpls.2022.964656.

• Schilbert H. M.*, Pucker B.*, Ries D., Viehöver P., Micic Z., Dreyer F., Beckmann K., Wittkop B., Weisshaar B., Holtgräwe D.. Mapping-by-sequencing reveals genomic regions associated with seed quality parameters in Brassica napus. Genes 2022, 13(7), 1131; doi: 10.3390/genes13071131

• Ballmann, R.; Hotop, S.; Bertoglio, F.; Steinke, S.; Heine, P.A.; Chaudhry, M.; Jahn, D.; Pucker, B.; Baldanti, F.; Piralla, A.; Schubert, M.; Čičin-Šain, L.; Hust, M.; Dübel, S. ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-Cov-2 Spike Protein. Viruses 2022, 14, 1326. doi: 10.3390/v14061326.

• Pucker B (2022). Automatic identification and annotation of MYB gene family members in plants. BMC Genomics 23, 220 (2022). doi: 10.1186/s12864-022-08452-5.

• Pucker B, Irisarri I, de Vries J and Xu B (2022). Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. Quantitative Plant Biology, 3, E5. doi: 10.1017/qpb.2021.18

• Pucker B & Selmar D (2022). Biochemistry and Molecular Basis of Intracellular Flavonoid Transport in Plants. Plants 2022, 11, 963. doi: 10.3390/plants11070963

• Sielemann K, Pucker B, Schmidt N, Viehoever P, Weisshaar B, Heitkam T, Holtgraewe D (2021). Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 23, 113 (2022). doi: 10.1186/s12864-022-08336-8.

Publications by Boas Pucker (prior to start at TU Braunschweig)

2022

• Pucker B & Brockington S F. The evidence for anthocyanins in the betalain-pigmented genus Hylocereus is weak. BMC Genomics 23, 739 (2022). doi: 10.1186/s12864-022-08947-1.
  full text PDF
• Pellegrinelli, V., Rodriguez-Cuenca, S., Rouault, C., Schilbert, H., Virtue, S., Moreno-Navarrete, J. M., Bidault, G., Borrego, M. del C. V., Dias, A. R., Pucker, B., et al. (2022). Dysregulation of macrophage PEPD in obesity determines adipose tissue fibro-inflammation and insulin resistance. Nature Metabolism 4, 476-494. full text preprint

2021

• Chibani K., Pucker B., Dietz K.-J., Cavanagh A. (2021). Genome-wide analysis and transcriptional regulation of the typical and atypical thioredoxins in Arabidopsis thaliana. doi:10.1002/1873-3468.14197. full text PDF
• Schilbert H, Kleinbölting N, Weisshaar B, Pucker B. (2021). Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads. Bielefeld University. doi: 10.4119/unibi/2956654.
  full text PUB
• Pucker, B.*, Kleinbölting, N.* and Weisshaar, B. (2021). Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics 22, 599. doi: 10.1186/s12864-021-07877-8
  full text PDF preprint PUB github github *shared first authorship
• Pucker B., Singh H.B., Kumari M., Khan M.I., Brockington S.F. (2021) The report of anthocyanins in the betalain-pigmented genus Hylocereus is not well evidenced and is not a strong basis to refute the mutual exclusion paradigm. BMC Plant Biol 21, 297 (2021). doi: 10.1186/s12870-021-03080-9.
  full text PDF PUB data
• Montero, H., Lee, T., Pucker, B., Ferreras-Garrucho, G., Oldroyd, G., Brockington, S.F., Miyao, A. and Paszkowski, U. A mycorrhiza-associated receptor-like kinase with an ancient origin in the green lineage. PNAS (2021). doi:10.1073/pnas.2105281118
  full text(peer-reviewed) PDF PUB
• Naik, J., Rajput, R., Pucker, B., Stracke, R. and Pandey, A. The R2R3-MYB transcription factor MtMYB134 orchestrates flavonol biosynthesis in Medicago truncatula. Plant Mol Biol (2021). doi:10.1007/s11103-021-01135-x
  full text(peer-reviewed) PDF
• Sielemann, K., Weisshaar, B. and Pucker, B. (2021). Reference-based QUantification Of gene Dispensability (QUOD). Plant Methods 17, 18. doi: 10.1186/s13007-021-00718-5
  full text(peer-reviewed) bioRxiv PDF PUB github
• Xu B., Taylor L., Pucker B., Feng T., Glover B. J. and Brockington S. (2021). The land plant-specific MIXTA-MYB lineage is implicated in the early evolution of the plant cuticle and the colonization of land. New Phytologist. doi:10.1111/nph.16997.
  full text(peer-reviewed) PUB

2020

• Pucker B., Schwandner A., Becker S., Hausmann L., Viehöver P., Töpfer R., Weisshaar B., Holtgräwe D. (2020). RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile. Plants 2020, 9(11), 1548; doi:10.3390/plants9111548.
  full text(peer-reviewed) preprint PDF PUB
• Pucker B., Pandey A., Weisshaar B. and Stracke R. (2020). The R2R3-MYB gene family in banana (Musa acuminata): genome-wide identification, classification and expression patterns. PLOS ONE 15(10): e0239275. doi:10.1371/journal.pone.0239275 full text(peer-reviewed) preprint PDF PUB github
• Sielemann, K.*, Hafner, A.* and Pucker B. (2020). The Reuse of Public Datasets in the Life Sciences: Potential Risks and Rewards. PeerJ 8:e9954. doi: 10.7717/peerj.9954
  full text(peer-reviewed) PDF preprint PUB *shared first authorship
• Pucker, B., Reiher, F. and Schilbert, H. M. Automatic identification of players in the flavonoid biosynthesis with application on the biomedicinal plant Croton tiglium. Plants 2020, 9, 1103. doi:10.3390/plants9091103.
  full text(peer-reviewed) PDF bioRxiv PUB github
• Choi, J., Lee, T., Cho, J., Servante, E., Pucker, B., Summers, W., et al. The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. Nature Communications 11, 2114 (2020). doi:10.1038/s41467-020-16021-1.
  full text(peer-reviewed) Apollo (free full text) PUB
• Schilbert H. M., Rempel A. and Pucker, B. (2020). Comparison of read mapping and variant calling tools for the analysis of plant NGS data. Plants. doi:10.3390/plants9040439.
  full text(peer-reviewed) bioRxiv PDF PUB data
• Siadjeu C.*, Pucker B.*, Viehoever P., Albach D. and Weisshaar B. (2020). High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing. Genes. doi:10.3390/genes11030274.
  full text(peer-reviewed) bioRxiv PDF PUB github DNA extraction protocol data (PUB)
  *shared first authorship
• Frey K. & Pucker, B. (2020). Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. Cells. doi:10.3390/cells9020458.
  full text(peer-reviewed) PDF bioRxiv PUB github data (fungi) data (animals)
• Holtgräwe, D., Rosleff Sörensen, T., Hausmann, L., Pucker, B., Viehöver, P., Töpfer, R., Weisshaar, B. (2020). A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia x Vitis cinerea) and its Exploitation for Marker Development and Targeted Mapping. Front. Plant Sci. doi:10.3389/fpls.2020.00156.
  full text(peer-reviewed) PDF bioRxiv PUB data set 1 data set 2 data set 3
• Busche M*, Pucker B*, Viehöver P, Weisshaar B, Stracke R. (2020). Genome Sequencing of Musa acuminata Dwarf Cavendish Reveals a Duplication of a Large Segment of Chromosome 2. G3: Genes|Genomes|Genetics. doi:10.1534/g3.119.400847.
  full text(peer-reviewed) PDF PUB bioRxiv github genome assemblies sequence variants
  *shared first authorship
• Sheehan, H., Feng, T., Walker-Hale, N., Lopez-Nieves, S., Pucker, B., Guo, R., Yim, W. C., Badgami, R., Timoneda, A., Zhao, L., Tiley, H., Copetti, D., Sanderson, M. J., Cushman, J. C., Moore, M. J., Smith, S. A., Brockington, S. F. Evolution of L-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales. New Phytologist. 2020. doi:10.1111/nph.16089
  full text(peer-reviewed) PDF PubMed PUB Apollo

2019

• Pucker B & Schilbert H. Genomics and Transcriptomics Advance in Plant Sciences. Molecular Approaches in Plant Biology and Environmental Challenges. Springer. 2019. ISBN 978-981-15-0690-1. doi:10.1007/978-981-15-0690-1
  springer(peer-reviewed book chapter) PUB
• Pucker B, Rückert C, Stracke R, Viehöver P, Kalinowski J, Weisshaar B. Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome. Genes. 2019. doi:10.3390/genes10090671
  full text(peer-reviewed) PDF bioRxiv PubMed PUB github
• Timoneda, A., Feng, T., Sheehan, H., Walker-Hale, N., Pucker, B., Lopez-Nieves, S., Guo, R., Brockington, S. (2019). The evolution of betalain biosynthesis in Caryophyllales. New Phytologist. doi:10.1111/nph.15980
  full text(peer-reviewed) PDF PubMed PUB
• Pucker, B. Schilbert, H.M., Schumacher, S.F. (2019). Integrating Molecular Biology and Bioinformatics Education. Journal of Integrative Bioinformatics. doi:10.1515/jib-2019-0005.
  full text(peer-reviewed) PDF PubMed preprint PUB
  Applied Genome Research (github) Molecular Methods in Genome Research (github)
• Pucker, B., Feng, T., Brockington, S. (2019). Next generation sequencing to investigate genomic diversity in Caryophyllales. bioRxiv 646133; doi:10.1101/646133.
  full text PDF PUB data github
• Pucker, B., Holtgraewe, D., Stadermann, K. B., Frey, K., Huettel, B., Reinhardt, R., & Weisshaar, B. (2019). A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set. PLOS ONE: e0216233. doi: 10.1371/journal.pone.0216233.
  full text(peer-reviewed) PDF PubMed bioRxiv PUB data github
• Pucker, B. (2019). Mapping-based genome size estimation. bioRxiv. doi:10.1101/607390.
  full text PDF PUB github (MGSE)
• Pucker, B. (2019). De novo Nd-1 genome assembly reveals genomic diversity of Arabidopsis thaliana and facilitates genome-wide non-canonical splice site analyses across plant species. Dissertation. doi:10.4119/unibi/2935794.
  PDF PUB DOI

2018

• Pucker, B. and Brockington, S.F. (2018). Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5360-z.
  full text(peer-reviewed) PDF PubMed bioRxiv PUB Apollo data github
• Schilbert, H.M., Pellegrinelli, V., Rodriguez-Cuenca, S., Vidal-Puig, A. & Pucker, B. (2018). Harnessing natural diversity to identify key amino acid residues in prolidase. bioRxiv 423475; doi:10.1101/423475.
  full text PDF PUB github zenodo
• Brinkrolf, C., Henke, N. A., Ochel, L., Pucker, B., Kruse, O., and Lutter, P. (2018). Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics 15. doi:10.1515/jib-2018-0018.
  full text(peer-reviewed) PDF PubMed PUB VANESA
• Whitford, C. M., Dymek, S., Kerkhoff, D., März, C., Schmidt, O., Edich, M., Droste, J., Pucker, B., Rückert, C. and Kalinowski, J. (2018). Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. Journal of Biological Engineering, 12(1). doi:10.1186/s13036-018-0105-8.
  full text(peer-reviewed) PDF PubMed PUB Apollo iGEM
• Haak, M., Vinke, S., Keller, W., Droste, J., Rückert, C., Kalinowski, J., & Pucker, B. (2018). High Quality de novo Transcriptome Assembly of Croton tiglium. Frontiers in Molecular Biosciences, 5. doi:https://doi.org/10.3389/fmolb.2018.00062.
  full text(peer-reviewed) PDF PubMed PUB RNA-Seq data assembly
• Friedrich, A., & Pucker, B. (2018). Peer-review as a teaching method. Working Paper der AG Forschendes Lernen in der dghd, 2, 2018. Carl von Ossietzky Universität Oldenburg.
  full text(peer-reviewed) PDF PUB github

2017

• Pucker, B., Holtgräwe, D., & Weisshaar, B. (2017). Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes, 10, 667. doi:10.1186/s13104-017-2985-y.
  full text(peer-reviewed) PDF PubMed PUB
• Karsten, L., Bergen, D., Drake, C., Dymek, S., Edich, M., Haak, M., Kerkhoff, D., Kerkhoff, Y., Liebers, M., März, C., Schlüter, L., Schmidt, O., Vinke, S., Whitford, C.M., Pucker, B., Droste, J., Rückert, C., Müller, K.M., Kalinowski, J. (2017). Expanding The Genetic Code. Bielefeld University. doi:10.13140/RG.2.2.20342.91203.
  full text PUB
• Alkhateeb, R., Rückert, C., Rupp, O., Pucker, B., Hublik, G., Wibberg, D., Niehaus, K., Pühler, A., Vorhölter, F.J. (2017). Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. Journal of Biotechnology. doi:10.1016/j.jbiotec.2017.05.009.
  full text(peer-reviewed) PubMed PUB

2016

• Pucker, B., Holtgräwe, D., Rosleff Sörensen, T., Stracke, R., Viehöver, P., and Weisshaar, B. (2016). A de novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PloS-ONE 11:e0164321. doi:10.1371/journal.pone.0164321.
  full text(peer-reviewed) PDF PubMed PUB NCBI BioProject
• Frommer, B, Hain, C., Kampa, J., Königs, C., Linder, M., Perez Knoche, S., Sahin, M., Schmidt, P., Schöller, M., Kalinowski, J., Müller, K.M., Droste, J., Hoffmann, N., Roeloffs, F., Pucker, B. (2016). Generating Binding Proteins - via in vivo directed evolution in E. coli. doi:10.13140/RG.2.2.23164.95367.
  full text

2014

• Fust A., Hollmann B., Pucker, B., Wollborn D., Tiemann J., Droste J., Brosda S., Blunk S., Riedl S., Bleckwehl T. (2014). The Transformers. From Carbon Dioxide to Biofuel. doi:10.13140/RG.2.2.30504.98566.
  full text PUB PLOS Report
• Stracke, R., Holtgräwe, D., Schneider, J., Pucker, B., Sörensen, T.R., and Weisshaar, B. (2014). Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris). BMC Plant Biol. 14: 249. doi:10.1186/s12870-014-0249-8.
  full text(peer-reviewed) PDF PubMed PUB RNA-Seq data