Publications

 

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, 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, Baldwin IT. . ‘Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity.’ Science 371, No. 6526: 255–260.
  • Heiling S, Llorca LC, Li J, Gase K, Schmidt A, Schäfer M, Schneider B, Halitschke R, Gaquerel E, 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, 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, Nyima T. . ‘An improved high-quality genome assembly and annotation of Tibetan hulless barley.’ Scientific data 7, No. 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, 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, No. 3. doi: 10.1063/1.5120573.
  • Cortés Llorca L, Li R, Yon F, Schäfer M, Halitschke R, Robert CA, Kim S‐G, 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, Sree KS. . ‘Genotyping-by-Sequencing for Species Delimitation in Lemna Section Uninerves Hegelm. (Lemnaceae).’ In The Duckweed Genomes, edited by Cao XH, Fourounjian P, Wang W, 115–123. 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, 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, No. na. doi: 10.1111/nph.16739.

  • Guo H, Lackus ND, Köllner TG, Li R, Bing J, Wang Y, Baldwin IT, Xu S. . ‘Evolution of a novel and adaptive floral scent in wild tobacco.’ Molecular Biology and Evolution 2019. doi: 10.1093/molbev/msz292. [online first]
  • Ling Z, Brockmöller T, Baldwin IT, 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, Ma Y. . ‘Efficient genetic transformation and CRISPR/Cas9-mediated genome editing in Lemna aequinoctialis.’ Plant Biotechnology Journal , No. ja. doi: 10.1111/pbi.13128.
  • Xu S, Stapley J, Gablenz S, Boyer J, Appenroth KJ, Sree KS, Gershenzon J, Widmer A, Huber M. . ‘Low genetic variation is associated with low mutation rate in the giant duckweed.’ Nature Communications 10, No. 1: 1243. doi: 10.1038/s41467-019-09235-5.
  • Mindt E, Wang M, Schäfer M, Halitschke R, Baldwin IT. . ‘Quantification of Blumenol Derivatives as Leaf Biomarkers for Plant-AMF Association.’ Bio-protocol 9, No. 14: e3301. doi: 10.21769/BioProtoc.3301.

  • Brütting C, Crava CM, Schäfer M, Schuman MC, Meldau S, Adam N, Baldwin IT. . ‘Cytokinin transfer by a free-living mirid to Nicotiana attenuata recapitulates a strategy of endophytic insects.’ eLife 7, No. 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, 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, Meldau S. . ‘Changes in cytokinins are sufficient to alter developmental patterns of defense metabolites in Nicotiana attenuata.’ The Plant Journal 89, No. 1: 15–30. doi: 10.1111/tpj.13316.
  • Schäfer M, 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 Dandekar T., Naseem M. (eds), 127–139. 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, Baldwin IT. . ‘Flower-specific jasmonate signaling regulates constitutive floral defenses in wild tobacco.’ Proceedings of the National Academy of Sciences 114, No. 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, 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, No. 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, Xu S. . ‘Tissue-specific emission of (E)-alpha-bergamotene helps resolve the dilemma when pollinators are also herbivores.’ Current biology 27, No. 9: 1336–1341. doi: 10.1016/j.cub.2017.03.017.
  • Machado RAR, Zhou W, Ferrieri AP, Arce CCM, Baldwin IT, Xu S, Erb M. . ‘Species-specific regulation of herbivory-induced defoliation tolerance is associated with jasmonate inducibility.’ Ecology and Evolution 7, No. 11: 3703–3712. doi: 10.1002/ece3.2953.
  • Luu VT, Weinhold A, Ullah C, Dressel S, Schoettner M, Gase K, Gaquerel E, Xu S, Baldwin IT. . ‘O-Acyl sugars protect a wild tobacco from both native fungal pathogens and a specialist herbivore.’ Plant Physiology 174, No. 1: 370–386. doi: 10.1104/pp.16.01904.
  • Brockmoller T, Ling Z, Li D, Gaquerel E, Baldwin IT, Xu S. . ‘Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.’ BMC Genomics 18, No. 1: 79. doi: 10.1186/s12864-016-3465-9.
  • Schäfer M, Brütting C, Xu S, Ling Z, Steppuhn A, Baldwin IT, Schuman MC. . ‘NaMYB8 regulates distinct, optimally distributed herbivore defense traits.’ Journal of Integrative Plant Biology 59, No. 12: 844–850. doi: 10.1111/jipb.12593.
  • Byers KJ, Xu S, Schluter PM. . ‘Molecular mechanisms of adaptation and speciation: why do we need an integrative approach?’ Molecular Ecology 26, No. 1: 277–290. doi: 10.1111/mec.13678.
  • Rogers SM, Xu S, Schluter PM. . ‘Introduction: integrative molecular ecology is rapidly advancing the study of adaptation and speciation.’ Molecular Ecology 26, No. 1: 1–6. doi: 10.1111/mec.13947.
  • Durrant M, Boyer J, Zhou W, Baldwin IT, Xu S. . ‘Evidence of an evolutionary hourglass pattern in herbivory-induced transcriptomic responses.’ New Phytologist 215, No. 3: 1264–1273. doi: 10.1111/nph.14644.
  • Wang M, Schoettner M, Xu S, Paetz C, Wilde J, Baldwin IT, 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, No. 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, Horvath P. . ‘Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.’ Cell Syst 4, No. 6: 651–655.e5. doi: 10.1016/j.cels.2017.05.012.

  • Schäfer M, Brütting C, Baldwin IT, 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, No. 1: 30. doi: 10.1186/s13007-016-0130-x.
  • Zhou W, Brockmoller T, Ling Z, Omdahl A, Baldwin IT, 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, Erb M. . ‘Auxin is rapidly induced by herbivore attack and regulates a subset of systemic, jasmonate-dependent defenses.’ Plant Physiology 172, No. 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, Meldau S. . ‘The role of cis-zeatin-type cytokinins in plant growth regulation and mediating responses to environmental interactions.’ Journal of Experimental Botany 66, No. 16: 4873–4884. doi: 10.1093/jxb/erv214.
  • Schäfer M, Meza-Canales ID, Brütting C, Baldwin IT, 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, No. 3: 645–658. doi: 10.1111/nph.13404.
  • Schäfer M, Meza-Canales ID, Navarro-Quezada A, Brütting C, Vanková R, Baldwin IT, Meldau S. . ‘Cytokinin levels and signaling respond to wounding and the perception of herbivore elicitors in Nicotiana attenuata.’ Journal of Integrative Plant Biology 57, No. 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, others. . ‘Dynamic maize responses to aphid feeding are revealed by a time series of transcriptomic and metabolomic assays.’ Plant Physiology 169, No. 3: 1727–1743. doi: 10.1104/pp.15.01039.
  • Groten K, Pahari NT, Xu S, Miloradovi vDM, 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, No. 8: e0136234. doi: 10.1371/journal.pone.0136234.
  • Xu S, Zhou W, Baldwin IT. . ‘The rapidly evolving associations among herbivore associated elicitor-induced phytohormones in Nicotiana.’ Plant Signal and Behaviour 10, No. 7: e1035850. doi: 10.1080/15592324.2015.1035850.
  • Xu S, 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, No. 2: 493–502. doi: 10.1002/ece3.1378.
  • Ling Z, Zhou W, Baldwin IT, Xu S. . ‘Insect herbivory elicits genome-wide alternative splicing responses in Nicotiana attenuata.’ The Plant journal 84, No. 1: 228–243. doi: 10.1111/tpj.12997.
  • Xu S, Zhou W, Pottinger S, 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, Kutay U. . ‘Genome-wide RNAi Screening Identifies Protein Modules Required for 40S Subunit Synthesis in Human Cells.’ Cell Rep 13, No. 12: 2879. doi: 10.1016/j.celrep.2015.11.061.

  • Schäfer M, Reichelt M, Baldwin IT, Meldau S. . ‘Cytokinin analysis: sample preparation and quantification.’ Bio-protocol 4, No. 13: 1–8. doi: 10.21769/BioProtoc.1167.

  • Schäfer M, Brütting C, Gase K, Reichelt M, Baldwin I, Meldau S. . ‘'Real time' genetic manipulation: a new tool for ecological field studies.’ The Plant Journal 76, No. 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, Schluter PM. . ‘Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids.’ PloS one 8, No. 5: e64621. doi: 10.1371/journal.pone.0064621.
  • Breitkopf H, Schluter PM, Xu S, Schiestl FP, Cozzolino S, Scopece G. . ‘Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence?’ Journal of Evolutionary Biology 26, No. 10: 2197. doi: 10.1111/jeb.12216.

  • Xu S, Schluter PM, Grossniklaus U, Schiestl FP. . ‘The genetic basis of pollinator adaptation in a sexually deceptive orchid.’ PLoS Genetics 8, No. 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, 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, No. 12: 5679–5693. doi: 10.1093/nar/gks223.

  • Schäfer M, Fischer C, Baldwin IT, Meldau S. . ‘Grasshopper oral secretions increase salicylic acid and abscisic acid levels in wounded leaves of Arabidopsis thaliana.’ Plant Signaling & Behavior 6, No. 9: 1256–1258. doi: 10.4161/psb.6.9.16552.
  • Schäfer M, Fischer C, Meldau S, Seebald E, Oelmüller R, Baldwin IT. . ‘Lipase activity in insect oral secretions mediates defense responses in Arabidopsis.’ Plant Physiology 156, No. 3: 1520–1534. doi: 10.1104/pp.111.173567.
  • Xu S, Schlüter PM, 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, 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, No. 14: 5696. doi: 10.1073/pnas.1013313108.
  • Xu S, Schluter PM, Scopece G, Breitkopf H, Gross K, Cozzolino S, Schiestl FP. . ‘Floral isolation is the main reproductive barrier among closely related sexually deceptive orchids.’ Evolution 65, No. 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, 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, Zheng X. . ‘High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome.’ Journal of Genetics and Genomics 34, No. 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, 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, No. 1: 34–42. doi: 10.1016/j.jcv.2007.01.002.

  • Tong XM, Liang Y, Wang W, Xu SQ, Zheng XG, Wang J, Yu J. . ‘Complete sequence and gene organization of the Tibetan chicken mitochondrial genome.’ Yi Chuan 28, No. 7: 769–777.

  • Xu SQ, Yang YZ, Zhou J, Jing GE, Chen YT, Wang J, Yang HM, Wang J, Yu J, Zheng XG, Ge RL. . ‘A mitochondrial genome sequence of the Tibetan antelope (Pantholops hodgsonii).’ Genomics Proteomics and Bioinformatics 3, No. 1: 5–17.