Publications
- Acosta, K, Appenroth, KJ, Borisjuk, L, Edelman, M, Heinig, U, Jansen, MAK, Oyama, T, Pasaribu, B, Schubert, I, Sorrels, S, Sree, KS, Xu, S, Michael, TP, and Lam, E. . “Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era.” The Plant cell koab189. doi: 10.1093/plcell/koab189.
- Li, J, Halitschke, R, Li, D, Paetz, C, Su, H, Heiling, S, Xu, S, and Baldwin, IT. . “Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity.” Science 371 (6526): 255–260.
- Heiling, S, Llorca, LC, Li, J, Gase, K, Schmidt, A, Schäfer, M, Schneider, B, Halitschke, R, Gaquerel, E, and Baldwin, IT. . “Specific decorations of 17-hydroxygeranyllinalool diterpene glycosides solve the autotoxicity problem of chemical defense in Nicotiana attenuata.” The Plant cell 2021. doi: 10.1093/plcell/koab048.
- Ke, L, Wang, Y, Schäfer, M, Städler, T, Zeng, R, Fabian, J, Pulido, H, De, Moraes CM, Song, Y, and Xu, S. . “Transcriptomic profiling reveals shared signalling networks between flower development and herbivory-induced responses in tomato.” Frontiers in Plant Science 12: 722810.. doi: 10.3389/fpls.2021.722810.
- Zeng, X, Xu, T, Ling, Z, Wang, Y, Li, X, Xu, S, Xu, Q, Zha, S, Qimei, W, Basang, Y, Dunzhu, J, Yu, M, Yuan, H, and Nyima, T. . “An improved high-quality genome assembly and annotation of Tibetan hulless barley.” Scientific data 7 (1): 139. doi: 10.1038/s41597-020-0480-0.
- Hauslage, Jens, Görög, Mark, Krause, Lars, Schüler, Oliver, Schäfer, Martin, Witten, Anika, Kesseler, Leona, Böhmer, Maik, and Hemmersbach, Ruth. . “ARABIDOMICS—A new experimental platform for molecular analyses of plants in drop towers, on parabolic flights, and sounding rockets.” Review of Scientific Instruments 91 (3). doi: 10.1063/1.5120573.
- Cortés, Llorca L, Li, R, Yon, F, Schäfer, M, Halitschke, R, Robert, CA, Kim, S‐G, and Baldwin, IT. . “ZEITLUPE facilitates the rhythmic movements of Nicotiana attenuata flowers.” The Plant journal 2020. doi: 10.1111/tpj.14732.
- Bog, M, Xu, S, Himmelbach, A, Brandt, R, Wagner, F, Appenroth, K, and Sree, KS. . “Genotyping-by-Sequencing for Species Delimitation in Lemna Section Uninerves Hegelm. (Lemnaceae).” in The Duckweed Genomes, edited by XH Cao, P Fourounjian and W Wang. Cham. doi: 10.1007/978-3-030-11045-1_11.
- Xu, S, Kreitzer, C, McGale, E, Lackus, ND, Guo, H, Köllner, TG, Schuman, MC, Baldwin, IT, and Zhou, W. . “Allelic differences of clustered terpene synthases contribute to correlated intra-specific variation of floral and herbivory-induced volatiles in a wild tobacco.” New Phytologist na (na). doi: 10.1111/nph.16739.
- Guo, H, Lackus, ND, Köllner, TG, Li, R, Bing, J, Wang, Y, Baldwin, IT, and Xu, S. . “Evolution of a novel and adaptive floral scent in wild tobacco.” Molecular Biology and Evolution 2019. doi: 10.1093/molbev/msz292.
- Ling, Z, Brockmöller, T, Baldwin, IT, and Xu, S. . “Evolution of Alternative Splicing in Eudicots.” Frontiers in Plant Science 10: 707. doi: 10.3389/fpls.2019.00707.
- Liu, Y, Wang, Y, Xu, S, Tang, X, Zhao, J, Yu, C, Zhou, G, He, G, Xu, H, Wang, S, Tang, Y, Fu, C, and Ma, Y. . “Efficient genetic transformation and CRISPR/Cas9-mediated genome editing in Lemna aequinoctialis.” Plant Biotechnology Journal, № ja. doi: 10.1111/pbi.13128.
- Xu, S, Stapley, J, Gablenz, S, Boyer, J, Appenroth, KJ, Sree, KS, Gershenzon, J, Widmer, A, and Huber, M. . “Low genetic variation is associated with low mutation rate in the giant duckweed.” Nature Communications 10 (1): 1243. doi: 10.1038/s41467-019-09235-5.
- Mindt, E, Wang, M, Schäfer, M, Halitschke, R, and Baldwin, IT. . “Quantification of Blumenol Derivatives as Leaf Biomarkers for Plant-AMF Association.” Bio-protocol 9 (14): e3301.. doi: 10.21769/BioProtoc.3301.
- Brütting, C, Crava, CM, Schäfer, M, Schuman, MC, Meldau, S, Adam, N, and Baldwin, IT. . “Cytokinin transfer by a free-living mirid to Nicotiana attenuata recapitulates a strategy of endophytic insects.” eLife 7 (e36268). doi: 10.7554/eLife.36268.
- Wang, M, Schäfer, M, Li, D, Halitschke, R, Dong, C, McGale, E, Paetz, C, Song, Y, Li, S, Dong, J, Heiling, S, Groten, K, Franken, P, Bitterlich, M, Harrison, MJ, Paszkowski, U, and Baldwin, IT. . “Blumenols as shoot markers of root symbiosis with arbuscular mycorrhizal fungi.” eLife 7: e37093.. doi: 10.7554/eLife.37093.
- Brütting, C, Schäfer, M, Vanková, R, Gase, K, Baldwin, IT, and Meldau, S. . “Changes in cytokinins are sufficient to alter developmental patterns of defense metabolites in Nicotiana attenuata.” The Plant Journal 89 (1): 15–30. doi: 10.1111/tpj.13316.
- Schäfer, M, and Meldau, S. . “Real-Time Genetic Manipulations of the Cytokinin Pathway: A Tool for Laboratory and Field Studies.” in Auxins and Cytokinins in Plant Biology: Methods and Protocols, edited by T. Dandekar and M.(eds) Naseem. doi: 10.1007/978-1-4939-6831-2_10.
- Li, R, Wang, M, Wang, Y, Schuman, MC, Weinhold, A, Schäfer, M, Jiménez-Alemán, GH, Barthel, A, and Baldwin, IT. . “Flower-specific jasmonate signaling regulates constitutive floral defenses in wild tobacco.” Proceedings of the National Academy of Sciences 114 (34): E7205–E7214.. doi: 10.1073/pnas.1703463114.
- Xu, S, Brockmoller, T, Navarro-Quezada, A, Kuhl, H, Gase, K, Ling, Z, Zhou, W, Kreitzer, C, Stanke, M, Tang, H, Lyons, E, Pandey, P, Pandey, SP, Timmermann, B, Gaquerel, E, and Baldwin, IT. . “Wild tobacco genomes reveal the evolution of nicotine biosynthesis.” Proceedings of the National Academy of Sciences of the United States of America 114 (23): 6133–6138. doi: 10.1073/pnas.1700073114.
- Zhou, W, Kugler, A, McGale, E, Haverkamp, A, Knaden, M, Guo, H, Beran, F, Yon, F, Li, R, Lackus, N, Kollner, TG, Bing, J, Schuman, MC, Hansson, BS, Kessler, D, Baldwin, IT, and Xu, S. . “Tissue-specific emission of (E)-alpha-bergamotene helps resolve the dilemma when pollinators are also herbivores.” Current biology 27 (9): 1336–1341. doi: 10.1016/j.cub.2017.03.017.
- Machado, RAR, Zhou, W, Ferrieri, AP, Arce, CCM, Baldwin, IT, Xu, S, and Erb, M. . “Species-specific regulation of herbivory-induced defoliation tolerance is associated with jasmonate inducibility.” Ecology and Evolution 7 (11): 3703–3712. doi: 10.1002/ece3.2953.
- Luu, VT, Weinhold, A, Ullah, C, Dressel, S, Schoettner, M, Gase, K, Gaquerel, E, Xu, S, and Baldwin, IT. . “O-Acyl sugars protect a wild tobacco from both native fungal pathogens and a specialist herbivore.” Plant Physiology 174 (1): 370–386. doi: 10.1104/pp.16.01904.
- Brockmoller, T, Ling, Z, Li, D, Gaquerel, E, Baldwin, IT, and Xu, S. . “Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.” BMC Genomics 18 (1): 79.. doi: 10.1186/s12864-016-3465-9.
- Schäfer, M, Brütting, C, Xu, S, Ling, Z, Steppuhn, A, Baldwin, IT, and Schuman, MC. . “NaMYB8 regulates distinct, optimally distributed herbivore defense traits.” Journal of Integrative Plant Biology 59 (12): 844–850. doi: 10.1111/jipb.12593.
- Byers, KJ, Xu, S, and Schluter, PM. . “Molecular mechanisms of adaptation and speciation: why do we need an integrative approach?” Molecular Ecology 26 (1): 277–290. doi: 10.1111/mec.13678.
- Rogers, SM, Xu, S, and Schluter, PM. . “Introduction: integrative molecular ecology is rapidly advancing the study of adaptation and speciation.” Molecular Ecology 26 (1): 1–6. doi: 10.1111/mec.13947.
- Durrant, M, Boyer, J, Zhou, W, Baldwin, IT, and Xu, S. . “Evidence of an evolutionary hourglass pattern in herbivory-induced transcriptomic responses.” New Phytologist 215 (3): 1264–1273. doi: 10.1111/nph.14644.
- Wang, M, Schoettner, M, Xu, S, Paetz, C, Wilde, J, Baldwin, IT, and Groten, K. . “Catechol, a major component of smoke, influences primary root growth and root hair elongation through reactive oxygen species-mediated redox signaling.” New Phytologist 213 (4): 1755–1770. doi: 10.1111/nph.14317.
- Piccinini, F, Balassa, T, Szkalisity, A, Molnar, C, Paavolainen, L, Kujala, K, Buzas, K, Sarazova, M, Pietiainen, V, Kutay, U, Smith, K, and Horvath, P. . “Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.” Cell Syst 4 (6): 651–655.e5.. doi: 10.1016/j.cels.2017.05.012.
- Schäfer, M, Brütting, C, Baldwin, IT, and Kallenbach, M. . “High-throughput quantification of more than 100 primary-and secondary-metabolites, and phytohormones by a single solid-phase extraction based sample preparation with analysis by UHPLC-HESI-MS/MS.” Plant Methods 12 (1): 30.. doi: 10.1186/s13007-016-0130-x.
- Zhou, W, Brockmoller, T, Ling, Z, Omdahl, A, Baldwin, IT, and Xu, S. . “Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana.” eLife 5. doi: 10.7554/eLife.19531.
- Machado, RA, Robert, CA, Arce, CC, Ferrieri, AP, Xu, S, Jimenez-Aleman, GH, Baldwin, IT, and Erb, M. . “Auxin is rapidly induced by herbivore attack and regulates a subset of systemic, jasmonate-dependent defenses.” Plant Physiology 172 (1): 521–532. doi: 10.1104/pp.16.00940.
- Schäfer, M. . “The role of cytokinins in plant-herbivore interactions: Response to herbivory and effects on plant defense.” Dissertation thesis, Friedrich-Schiller-Universität Jena.
- Schäfer, M, Brütting, C, Meza-Canales, ID, Großkinsky, DK, Vankova, R, Baldwin, IT, and Meldau, S. . “The role of cis-zeatin-type cytokinins in plant growth regulation and mediating responses to environmental interactions.” Journal of Experimental Botany 66 (16): 4873–4884. doi: 10.1093/jxb/erv214.
- Schäfer, M, Meza-Canales, ID, Brütting, C, Baldwin, IT, and Meldau, S. . “Cytokinin concentrations and CHASE-DOMAIN CONTAINING HIS KINASE 2 (NaCHK2)-and NaCHK3-mediated perception modulate herbivory-induced defense signaling and defenses in Nicotiana attenuata.” New Phytologist 207 (3): 645–658. doi: 10.1111/nph.13404.
- Schäfer, M, Meza-Canales, ID, Navarro-Quezada, A, Brütting, C, Vanková, R, Baldwin, IT, and Meldau, S. . “Cytokinin levels and signaling respond to wounding and the perception of herbivore elicitors in Nicotiana attenuata.” Journal of Integrative Plant Biology 57 (2): 198–212. doi: 10.1111/jipb.12227.
- Tzin, V, Fernandez-Pozo, N, Richter, A, Schmelz, EA, Schoettner, M, Schäfer, M, Ahern, KR, Meihls, LN, Kaur, H, Huffaker, A, and others. . “Dynamic maize responses to aphid feeding are revealed by a time series of transcriptomic and metabolomic assays.” Plant Physiology 169 (3): 1727–1743. doi: 10.1104/pp.15.01039.
- Groten, K, Pahari, NT, Xu, S, Miloradovi, vDM, and Baldwin, IT. . “Virus-induced gene silencing using tobacco rattle virus as a tool to study the interaction between Nicotiana attenuata and Rhizophagus irregularis.” PloS one 10 (8): e0136234.. doi: 10.1371/journal.pone.0136234.
- Xu, S, Zhou, W, and Baldwin, IT. . “The rapidly evolving associations among herbivore associated elicitor-induced phytohormones in Nicotiana.” Plant Signal and Behaviour 10 (7): e1035850.. doi: 10.1080/15592324.2015.1035850.
- Xu, S, and Schluter, PM. . “Modeling the two-locus architecture of divergent pollinator adaptation: how variation in SAD paralogs affects fitness and evolutionary divergence in sexually deceptive orchids.” Ecology and Evolution 5 (2): 493–502. doi: 10.1002/ece3.1378.
- Ling, Z, Zhou, W, Baldwin, IT, and Xu, S. . “Insect herbivory elicits genome-wide alternative splicing responses in Nicotiana attenuata.” The Plant journal 84 (1): 228–243. doi: 10.1111/tpj.12997.
- Xu, S, Zhou, W, Pottinger, S, and Baldwin, IT. . “Herbivore associated elicitor-induced defences are highly specific among closely related Nicotiana species.” BMC Plant Biology 15: 2.. doi: 10.1186/s12870-014-0406-0.
- Badertscher, L, Wild, T, Montellese, C, Alexander, LT, Bammert, L, Sarazova, M, Stebler, M, Csucs, G, Mayer, TU, Zamboni, N, Zemp, I, Horvath, P, and Kutay, U. . “Genome-wide RNAi Screening Identifies Protein Modules Required for 40S Subunit Synthesis in Human Cells.” Cell Rep 13 (12): 2879–91. doi: 10.1016/j.celrep.2015.11.061.
- Schäfer, M, Reichelt, M, Baldwin, IT, and Meldau, S. . “Cytokinin analysis: sample preparation and quantification.” Bio-protocol 4 (13): 1–8. doi: 10.21769/BioProtoc.1167.
- Schäfer, M, Brütting, C, Gase, K, Reichelt, M, Baldwin, I, and Meldau, S. . “'Real time' genetic manipulation: a new tool for ecological field studies.” The Plant Journal 76 (3): 506–518. doi: 10.1111/tpj.12301.
- Sedeek, KE, Qi, W, Schauer, MA, Gupta, AK, Poveda, L, Xu, S, Liu, ZJ, Grossniklaus, U, Schiestl, FP, and Schluter, PM. . “Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids.” PloS one 8 (5): e64621.. doi: 10.1371/journal.pone.0064621.
- Breitkopf, H, Schluter, PM, Xu, S, Schiestl, FP, Cozzolino, S, and Scopece, G. . “Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence?” Journal of Evolutionary Biology 26 (10): 2197–208. doi: 10.1111/jeb.12216.
- Xu, S, Schluter, PM, Grossniklaus, U, and Schiestl, FP. . “The genetic basis of pollinator adaptation in a sexually deceptive orchid.” PLOS Genetics 8 (8): e1002889.. doi: 10.1371/journal.pgen.1002889.
- Holub, P, Lalakova, J, Cerna, H, Pasulka, J, Sarazova, M, Hrazdilova, K, Arce, MS, Hobor, F, Stefl, R, and Vanacova, S. . “Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.” Nucleic Acids Res 40 (12): 5679–5693.. doi: 10.1093/nar/gks223.
- Schäfer, M, Fischer, C, Baldwin, IT, and Meldau, S. . “Grasshopper oral secretions increase salicylic acid and abscisic acid levels in wounded leaves of Arabidopsis thaliana.” Plant Signaling & Behavior 6 (9): 1256–1258. doi: 10.4161/psb.6.9.16552.
- Schäfer, M, Fischer, C, Meldau, S, Seebald, E, Oelmüller, R, and Baldwin, IT. . “Lipase activity in insect oral secretions mediates defense responses in Arabidopsis.” Plant Physiology 156 (3): 1520–1534. doi: 10.1104/pp.111.173567.
- Xu, S, Schlüter, PM, and Schiestl, FP. . “Pollinator-driven speciation in sexually deceptive orchids.” International Journal of Ecology 2012. doi: 10.1155/2012/285081.
- Schluter, PM, Xu, S, Gagliardini, V, Whittle, E, Shanklin, J, Grossniklaus, U, and Schiestl, FP. . “Stearoyl-acyl carrier protein desaturases are associated with floral isolation in sexually deceptive orchids.” Proceedings of the National Academy of Sciences of the United States of America 108 (14): 5696–701. doi: 10.1073/pnas.1013313108.
- Xu, S, Schluter, PM, Scopece, G, Breitkopf, H, Gross, K, Cozzolino, S, and Schiestl, FP. . “Floral isolation is the main reproductive barrier among closely related sexually deceptive orchids.” Evolution 65 (9): 2606–2620. doi: 10.1111/j.1558-5646.2011.01323.x.
- Xu, S, Clark, T, Zheng, H, Vang, S, Li, R, Wong, GK, Wang, J, and Zheng, X. . “Gene conversion in the rice genome.” BMC Genomics 9: 93.. doi: 10.1186/1471-2164-9-93.
- Xu, S, Luosang, J, Hua, S, He, J, Ciren, A, Wang, W, Tong, X, Liang, Y, Wang, J, and Zheng, X. . “High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome.” Journal of Genetics and Genomics 34 (8): 720–729. doi: 10.1016/S1673-8527(07)60081-2.
- Wang, W, Wang, C, Xu, S, Chen, C, Tong, X, Liang, Y, Dong, X, Lei, Y, Zheng, X, Yu, J, and Wang, J. . “Detection of HPV-2 and identification of novel mutations by whole genome sequencing from biopsies of two patients with multiple cutaneous horns.” Journal of Clinic Virology 39 (1): 34–42. doi: 10.1016/j.jcv.2007.01.002.
- Tong, XM, Liang, Y, Wang, W, Xu, SQ, Zheng, XG, Wang, J, and Yu, J. . “Complete sequence and gene organization of the Tibetan chicken mitochondrial genome.” Yi Chuan 28 (7): 769–777.
- Xu, SQ, Yang, YZ, Zhou, J, Jing, GE, Chen, YT, Wang, J, Yang, HM, Wang, J, Yu, J, Zheng, XG, and Ge, RL. . “A mitochondrial genome sequence of the Tibetan antelope (Pantholops hodgsonii).” Genomics Proteomics and Bioinformatics 3 (1): 5–17.