Recent Publications

2017

Alvarez, M. F., Angarita, M., Delgado, M. C., Garcia, C., Jimenez-Gomez, J. M., Gebhardt, C., & Mosquera, T. (2017). Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja. Frontiers in Plant Science, 8: 1040. doi:10.3389/fpls.2017.01040. open access

Ariga H, Katori T, Tsuchimatsu T, Hirase T, Tajima Y, Parker JE, Alcázar R, Koornneef M, Hoekenga O, Lipka AE, Gore MA, Sakakibara H, Kojima M, Kobayashi Y, Iuchi S, Kobayashi M, Shinozaki K, Sakata Y, Hayashi T, Saijo Y and Taji T. (2017) NLR locus-mediated trade-off between abiotic and biotic stress adaptation in Arabidopsis. Nature Plants 26;3:17072, doi: 10.1038/nplants.2017.72. open access

Birkenbihl, R.P., Liu, S., and Somssich, I.E. (2017). Transcriptional events defining plant immune responses. Curr. Opin. Plant Biol. 38, 1-9, 10.1016/j.pbi.2017.04.004.

Birkenbihl, R.P., Kracher, B., Roccaro, M. and Somssich, I.E. (2017). Induced genome-wide binding of three WRKY transcription factors during early MAMP-triggered immunity. Plant Cell 29, 20-38. open access

Chandrasekar, B., Tram Hong, N., & Van der Hoorn, R. A. L. (2017). Inhibitor Discovery by Convolution ABPP. ACTIVITY-BASED PROTEOMICS: METHODS AND PROTOCOLS, 47-56. doi:10.1007/978-1-4939-6439-0_4.

Chao, Y., Li, L., Girodat, D., Foerstner, K. U., Said, N., Corcoran, C., Smiga, M., Papenfort, K., Reinhardt, R., Wieden, H.-J., Luisi, B. F., & Vogel, J. (2017). In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. Molecular Cell, 65(1), 39-51. doi:10.1016/j.molcel.2016.11.002.

Cui, H., Gobbato, E., Kracher, B., Qiu, J., Bautor, J., Parker, J. E.: A core function of EDS1 with PAD4 is to protect the salicylic acid defense sector in Arabidopsis immunity. New Phytologist 213: 1802-1817, doi: 10.1111/nph.14302 (2017) open access

De Montaigu, A., Oeljeklaus, J., Krahn, J., Suliman, M., Halder, V., de Ansorena, E., Nickel, S., Schlicht, M., Plihal, O., Kubiasova, K., Radova, L., Kracher, B., Toth, R., Kaschani, F., Coupland G., Kombrink, E. and Kaiser, M. (2017) The root growth-regulating brevicompanine natural products modulate the plant circadian clock. ACS Chemical Biology, 12 (6), 1466–1471. open access

Dombrowski, N., Schlaeppi, K., Agler, M., Hacquard, S., Kemen, E., Garrido Oter, R., Wunder, J., Coupland, G. and Schulze-Lefert, P., Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time. ISME Journal 11, 43-55, doi:10.1038/ismej.2016.109 (2017). open access

Duarte-Delgado, D., Juyo, D., Gebhardt, C., Sarmiento, F., & Mosquera-Vasquez, T. (2017). Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja. BMC Medical Genetics, 18: 23. doi:10.1186/s12863-017-0489-3. open access

Durvasula, A., Fulgione, A, Gütaker, R, , Alacakaptan, S, Flood, P, Neto, C, Tsuchimatsu, T, Burbano, HA, Pico, XA, Alonso-Blanco, C, Hancock, AM. African genomes illuminate the early history of Arabidopsis thaliana, Proceedings of the National Academy of Sciences USA, doi:10.1073/pnas.1616736114. open access

Ejaz M and von Korff M (2016) Genetic control of reproductive development under high ambient temperature. Plant Physiology, 173,1: 294-306, doi: 10.​1104/​pp.​16.​01275. open access

Engelhorn, J., Turck, F.: Meta-analysis of Genome-Wide Chromatin Data (2017) In: Methods in Molecular Biology 1456: Plant Epigenetics, pp 33-50, doi: 10.1007/978-1-4899-7708-3_3.

Flood, P., & Hancock, A. (2017). The genomic basis of adaptation in plants. Current Opinion in Plant Biology, 36, 88-94. doi:10.1016/j.pbi.2017.02.003.

Frantzeskakis, L., Courville, K. J., Pluecker, L., Kellner, R., Kruse, J., Brachmann, A., Feldbrügge, M., & Göhre, V. (2017). The plant-dependent life cycle of Thecaphora thlaspeos: a smut fungus adapted to Brassicaceae. Molecular Plant-Microbe Interactions. doi:10.1094/MPMI-08-16-0164-R.

Fukunaga, S., Sogame, M., Hata, M., Singkaravanit-Ogawa, S., Piślewska-Bednarek, M., Onozawa-Komori, M., Nishiuchi, T., Hiruma, K., Saitoh, H., Terauchi, R., Kitakura, S., Inoue, Y., Bednarek, P., Schulze-Lefert, P., Takano, Y. Dysfunction of Arabidopsis MACPF domain protein activates programmed cell death via tryptophan metabolism in MAMP-triggered immunity. Plant Journal 89, 381-393, doi: 10.1111/tpj.13391 (2016). open access

Gol L, Tomé F, von Korff M (2017) Floral transitions in wheat and barley: interactions between photoperiod, abiotic stresses and nutrient status. J. Exp. Bot., doi: 10.1093/jxb/erx055. open access

Hacquard, S., Spaepen, S., Garrido‐Oter R. and Schulze‐Lefert, P. Interplay between innate immunity and the plant microbiota. Annu. Rev. Phytopathol. 55, doi: 10.1146/annurev-phyto-080516-035623 (2017).

Hacquard, S. (2017). Commentary: Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions. Frontiers in Microbiology, 8:1. doi:10.3389/fmicb.2017.00001. open access

Hayama, R., Sarid-Krebs, L., Richter, R., Fernández, V., Jang, S. and G. Coupland (2017). PSEUDO RESPONSE REGULATORs stabilize CONSTANS protein to promote flowering in response to day length. EMBO Journal. doi:10.15252/embj.201693907. open access

Hillmer R, Tsuda K, Rallapalli G, Asai S, Truman W, Papke MD, Sakakibara H, Jone JDG, Myers CL, Katagiri F: The Highly Buffered Arabidopsis Immune Signaling Network Conceals the Functions of its Components. PLoS Genetics 13(5), e1006639 (2017). open acces

Hofhuis, H. and Hay, A. (2017), Explosive seed dispersal. New Phytol. doi:10.1111/nph.14541. open acces

Horvath, M., Steinbiss, H. H., & Reiss, B. (2017). Gene Targeting Without DSB Induction Is Inefficient in Barley. Frontiers in Plant Science, 7: 1973. doi:10.3389/fpls.2016.01973. open access

Hyun, Y., Richter, R. and Coupland, G. (2017) Competence to Flower: Age-Controlled Sensitivity to Environmental Cues. Plant Physiology 173, 36-46, doi: 10.1104/pp.16.01523. open access

Imprialou, M., Kahles, A., Steffen, J. G., Osborne, E. J., Gan, X., Lempe, J., Bhomra, A., Belfield, E., Visscher, A., Greenhalgh, R., Harberd, N. P., Goram, R., Hein, J., Robert-Seilaniantz, A., Jones, J., Stegle, O., Kover, P., Tsiantis, M., Nordborg, M., Rätsch, G., Clark, R. M., Mott, R.: Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics 205(4), 1425-1441, doi: 10.1534/genetics.116.192823 (2017).

Jiao, W.-B., Accinelli, G.G., Hartwig, B., Kiefer, C., Baker, D., Severing, E., Willing, E.-M., Piednoel, M., Woetzel, S., Madrid-Herrero, E.M., Huettel, B., Hümann, U., Reinhard, R., Koch, M.A., Swan, D., Clavijo, B., Coupland, G. and Schneeberger, K. (2017) Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Research, doi: 10.1101/gr.213652.116. open access

Jiao, W.-B., Schneeberger, K. (2017) The impact of third generation genomic technologies on plant genome assembly, Current Opinion in Plant Biology, Volume 36, April 2017, Pages 64-70 doi: 10.1016/j.pbi.2017.02.002. open access

Jung, C., Pillen, K., Staiger, D., Coupland, G., & von Korff, M. (2017). Editorial: Recent Advances in Flowering Time Control. Frontiers in Plant Science, 7: 2011. doi:10.3389/fpls.2016.02011. open access

Kiefer, C., Severing, E., Karl, R., Bergonzi, S., Koch, M., Tresch, A., & Coupland, G. (2017). Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at FLC orthologues. Molecular Ecology. doi:10.1111/mec.14084.

Kovacs, J., Poor, P., Kaschani, F., Chandrasekar, B., Hong, T. N., Misas-Villamil, J. C., et al. (2017). Proteasome Activity Profiling Uncovers Alteration of Catalytic beta 2 and beta 5 Subunits of the Stress-Induced Proteasome during Salinity Stress in Tomato Roots. Frontiers in Plant Science, 8: 107. doi:10.3389/fpls.2017.00107. open access

Kroll, S., Agler, M. T., Kemen, E. (2017) Genomic dissection of host–microbe and microbe–microbe interactions for advanced plant breeding, Current Opinion in Plant Biology 36, 71-78, doi: 10.1016/j.pbi.2017.01.004.

Kuhn, H., Lorek, J., Kwaaitaal, M., Consonni, C., Becker, K., Micali, C., Ver Loren van Themaat, E., Bednarek, P., Raaymakers, T.., Appiano, M., Bai, Y., Meldau, D., Baum, S., Conrath, U., Feussner, I., & Panstruga, R. (2017). Key Components of Different Plant Defense Pathways Are Dispensable for Powdery Mildew Resistance of the Arabidopsis mlo2 mlo6 mlo12 Triple Mutant. Frontiers in Plant Science, 8: 1006. doi:10.3389/fpls.2017.01006. open access

Liller CB, Walla A,  Boer MP, Hedley P, Macaulay M, Effgen S, von Korff M, van Esse GW, Koornneef M (2017) Fine mapping of a major QTL for awn length in barley using a multiparent mapping population. Theoretical and Applied Genetics, 130: 269–281, doi: 10.1007/s00122-016-2807-y. open access

Liu, S., Ziegler, J., Zeier, J., Birkenbihl, R.P., Somssich, I.E. (2017). Botrytis cinerea B05.10 promotes disease development in Arabidopsis by suppressing WRKY33-mediated host immunity. Plant Cell Environ., in press; doi: 10.1111/pce.13022.

Maekawa, T., Schulze-Lefert, P. (2017) Caught in the jump. Science 357, 31-32, doi: 10.1126/science.aan8287.

Merini, W., Romero-Campero, F. J., Gomez-Zambrano, A., Zhou, Y., Turck, F., & Calonje, M. (2017). The Arabidopsis Polycomb Repressive Complex 1 (PRC1) components AtBMI1A, B and C impact gene networks throughout all stages of plant development. Plant Physiology, 173, 627-641. doi:10.1104/pp.16.01259.

Mine, A., Nobori, T., Salazar-Rondon, M. C., Winkelmüller, T. M., Anver, S., Becker, D., & Tsuda, K. (2017). An incoherent feed-forward loop mediates robustness and tunability in a plant immune network. EMBO Reports. doi:10.15252/embr.201643051.

Misas-Villamil, J., van der Burgh, A. M., Grosse-Holz, F., Bach-Pages, M., Kovács, J., Kaschani, F., Schilasky, S., Emon, A. E. K., Ruben, M., Kaiser, M., Overkleeft, H. S., & Van der Hoorn, R. A. L. (2017). Subunit-selective proteasome activity profiling uncovers uncoupled proteasome subunit activities during bacterial infections. The Plant Journal, 90(2), 418-430. doi:10.1111/tpj.13494.

Monniaux, M., McKim, S. M., Cartolano, M., Thévenon, E., Parcy, F., Tsiantis, M. and Hay, A. (2017), Conservation vs divergence in LEAFY and APETALA1 functions between Arabidopsis thaliana and Cardamine hirsuta. New Phytolgist, doi:10.1111/nph.14419. open access

Nakano, R.T., Pilewska-Bednarek, M., Yamada, K., Edger, P., Miyahara, M., Kondo, M., Böttcher, C., Mori, M., Nishimura, M., Schulze-Lefert*, P., Hara-Nishimura*, I. and Bednarek* P. PYK10 Myrosinase Reveals a Functional Coordination between ER Bodies and Glucosinolates in Arabidopsis thaliana. Plant Journal 89: 204–220, DOI: 10.1111/tpj.13377 (2017). *co-corresponding author. open access

Née, G.; Kramer, K.; Nakabayashi, K.; Yuan, B.; Xiang, Y.; Miatton, E.; Finkemeier, I.; Soppe, W.: Delay of germination requires PP2C phosphatases of the ABA signalling pathway to control seed dormancy (2017) Nature Communications 8:72 doi:10.1038/s41467-017-00113-6. open access

Née, G., Xiang, Y., & Soppe, W. (2017). The release of dormancy, a wake-up call for seeds to germinate. Current Opinion in Plant Biology, Special Issue: Growth and development, SI: 35, 8-14. doi:10.1016/j.pbi.2016.09.002. open access

Nikolov, L. A., & Tsiantis, M. (2017). Using mustard genomes to explore the genetic basis of evolutionary change. Current Opinion in Plant Biology 36, 119-128, doi:10.1016/j.pbi.2017.02.005.

Oka, R.*, Zicola, J.*, Weber, B.*, Anderson, S.N., Hodgman, C., Gent, J. I., Wesselink, J.-J., Springer, N. M., Hoefsloot, H.C.J., Turck, F. and M. Stam (2017) Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biology 18:137, doi: 10.1186/s13059-017-1273-4. *contributed equally, ** joint corresponding authors open access

Oral, M., Colleter, J., Bekaert, M., Taggart, J. B., Palaiokostas, C., McAndrew, B. J., Vandeputte, M., Chatain, B., Kuhl, H., Reinhardt, R., Peruzzi, S., & Penman, D. J. (2017). Gene-centromere mapping in meiotic gynogenetic European seabass. BMC Genomics, 18: 449. doi:10.1186/s12864-017-3826-z.

Pankin, A. & von Korff, M. (2017). Co-evolution of methods and thoughts in cereal domestication studies: a tale of barley (Hordeum vulgare). Current Opinion in Plant Biology, 36, 15-21. doi:10.1016/j.pbi.2016.12.001. open access

Pruzinska, A., Shindo, T., Niessen, S., Kaschani, F., Toth, R., Millar, A. H., & Van der Hoorn, R. A. L. (2017) Major Cys protease activities are not essential for senescence in individually darkened Arabidopsis leaves. BMC Plant Biology, 17: 4. doi:10.1186/s12870-016-0955-5. open access

Rast, P., Gloeckner, I., Boedeker, C., Jeske, O., Wiegand, S., Reinhardt, R., Schumann, P., Rohde, M., Spring, S., Gloeckner, F. O., Jogler, C., & Jogler, M. (2017). Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov in the Family Opitutaceae of the Verrucomicrobial Subdivision 4. Frontiers in Microbiology, 8: 202. doi:10.3389/fmicb.2017.00202. open access

Riedlmeier M, Ghirardo A, Wenig M, Knappe C, Koch K, Georgii E, Dey S, Parker JE, Schnitzler JP, Vlot AC. (2017) Monoterpenes support systemic acquired resistance within and between plants. Plant Cell, doi: 10.1105/tpc.16.00898. open access

Rishmawi, L., Bühler, J., Jaegle, B., Hülskamp, M., & Koornneef, M. (2017). Quantitative trait loci controlling leaf venation in Arabidopsis. Plant, Cell and Environment, 40, 1429-1441 doi:10.1111/pce.12938.

Runions, A., Tsiantis, M., & Prusinkiewicz, P. (2017). A common developmental program can produce diverse leaf shapes. New Phytologist. doi:10.1111/nph.14449. open access

Rymen, B., Kawamura, A., Schaefer, S., Breuer, C., Iwase, A., Shibata, M., Ikeda, M., Mitsuda, N., Koncz, C., Ohme-Takagi, M., Matsui, M., & Sugimoto, K. (2017). ABA suppresses root hair growth via OBP4 transcriptional-regulator repression of the RSL2 promoter. Plant Physiology 173: 1750-1762, doi:10.1104/pp.16.01945. open access

Schiessl, S., Huettel, B., Kuehn, D., Reinhardt, R., & Snowdon, R. J. (2017). Targeted deep sequencing of flowering regulators in Brassica napus reveals extensive copy number variation. Scientific Data, 4: 170013. doi:10.1038/sdata.2017.13. open access

Schiessl, S., Huettel, B., Kuehn, D., Reinhardt, R., & Snowdon, R. (2017). Post-polyploidisation morphotype diversification associates with gene copy number variation. Scientific Reports, 7: 41845. doi:10.1038/srep41845. open access

Schneeberger, K., & Henderson, I. (2017). Editorial overview: Genome studies and molecular genetics. Current Opinion in Plant Biology, 36, IV-V. doi:10.1016/j.pbi.2017.03.017.

Sczyrba, A.*, Hofmann, P.*, Belmann, P*., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Sparholt Jørgensen, T., Shapiro, N., Blood, P. D., Gurevich, A., Bai, Y., Tuarev, D., DeMaere, M. Z., Chikhi, R., Nagarajan, N., Hestbjerg Hansen, L., Sørensen, S. J., Chia, B. K. H., Denis, B., Froula, J. L., Wang, Z., Egan, R., Don Kang, D., Cook, J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y.-W., Singer, S. W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M., Lingner, T., Lin, H.-H., Liao, Y.-C., Silva, G. G. Z., Cuevas, D. A., Edwards, R. A., Saha, S., Piro, V. C., Renard, B. Y., Hill, C. M., Pop, M., Klenk, H.-P., Goeker, M., Kyrpides, N., Woyke, T., Vorholt, J., Schulze-Lefert, P., Rubin, E. M., Darling, A. E., Rattei, T., McHardy, A. C. Critical Assessment of Metagenome Interpretation – a comprehensive benchmark of computational metagenomics software. Nature Methods, in press (2017). * contributed equally. abstract

Shin, J., Sánchez-Villarreal, A., Davis, A. M., Du, S. X., Berendzen, K. W., Koncz, C., Ding, Z., Li, C., & Davis, S. J. (2017). The metabolic sensor AKIN10 modulates the Arabidopsis circadian clock in a light-dependent manner. Plant, Cell and Environment. doi:10.1111/pce.12903

Stamm, P., Strauß, S., Montenegro-Johnson, T. D., Smith, R. S., & Bassel, G. W. (2017). In Silico Methods for Cell Annotation, Quantification of Gene Expression, and Cell Geometry at Single-Cell Resolution Using 3DCellAtlas. PLANT HORMONES: METHODS AND PROTOCOLS, 3RD EDITION, 99-123. doi:10.1007/978-1-4939-6469-7_11.

Templer SE, Ammon A, Pscheidt D, Ciobotea O, Schuy C, McCollum C, Sonnewald U, Hanemann A, Förster J, Ordon F, von Korff M, Voll LM. (2017) Metabolite profiling of barley flag leaves in drought and combined heat and drought stress reveals metabolic QTLs for metabolites associated with antioxidant defence. J. Exp. Bot., doi:10.1093/jxb/erx038. open access.

Vu, G. T. H., Cao, H. X., Reiss, B., & Schubert, I. (2017). Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage. New Phytologist, 214(4), 1712-1721. doi:10.1111/nph.14490.

*Zhou Y, *Romero-Campero FJ, Gómez-Zambrano Á, **Turck F, **Calonje M. H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity. Genome Biol. 2017, 18:69. doi: 10.1186/s13059-017-1197-z. open access. *shared first **shared correspondence

Zhou Y, Tergemina E, Cui H, Förderer A, Hartwig B, Velikkakam James G, Schneeberger K, Turck F. Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3 levels in dividing cells in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2017,  pii: 201620955. doi: 10.1073/pnas.1620955114. open access.