{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T10:04:51Z","timestamp":1789207491869,"version":"build-2803163510"},"reference-count":80,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12864-015-1925-2","type":"journal-article","created":{"date-parts":[[2015,9,19]],"date-time":"2015-09-19T08:32:18Z","timestamp":1442651538000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":52,"title":["Bimodal dynamics of primary metabolism-related responses in tolerant potato-Potato virus Y interaction"],"prefix":"10.1186","volume":"16","author":[{"given":"Tja\u0161a","family":"Stare","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u017diva","family":"Ram\u0161ak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrej","family":"Blejec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katja","family":"Stare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ne\u017ea","family":"Turn\u0161ek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfram","family":"Weckwerth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Wienkoop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominik","family":"Vodnik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristina","family":"Gruden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,9,19]]},"reference":[{"key":"1925_CR1","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1111\/j.1364-3703.2011.00752.x","volume":"12","author":"K-BG Scholthof","year":"2011","unstructured":"Scholthof K-BG, Adkins S, Czosnek H, Palukaitis P, Jacquot E, Hohn T, et al. Top 10 plant viruses in molecular plant pathology. Mol Plant Pathol. 2011;12:938\u201354.","journal-title":"Mol Plant Pathol"},{"key":"1925_CR2","doi-asserted-by":"crossref","unstructured":"Kogovsek P, Ravnikar M: Physiology of the Potato\u2013Potato Virus Y Interaction. Volume 74. Edited by L\u00fcttge U, Beyschlag W, Francis D, Cushman J. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013. [Progress in Botany].","DOI":"10.1007\/978-3-642-30967-0_3"},{"key":"1925_CR3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00705-007-1059-1","volume":"153","author":"RP Singh","year":"2008","unstructured":"Singh RP, Valkonen JPT, Gray SM, Boonham N, Jones RAC, Kerlan C, et al. Discussion paper: The naming of Potato virus Y strains infecting potato. Arch Virol. 2008;153:1\u201313.","journal-title":"Arch Virol"},{"key":"1925_CR4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1111\/j.1364-3703.2004.00203.x","volume":"5","author":"DP Singh","year":"2004","unstructured":"Singh DP, Moore CA, Gilliland A, Carr JP. Activation of multiple antiviral defense mechanisms by salicylic acid. Mol Plant Pathol. 2004;5:57\u201363.","journal-title":"Mol Plant Pathol"},{"key":"1925_CR5","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1104\/pp.107.112029","volume":"146","author":"A Koornneef","year":"2008","unstructured":"Koornneef A, Pieterse CMJ. Cross talk in defense signaling. Plant Physiol. 2008;146:839\u201344.","journal-title":"Plant Physiol"},{"key":"1925_CR6","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1094\/MPMI-09-10-0224","volume":"24","author":"J Jovel","year":"2011","unstructured":"Jovel J, Walker M, Sanfa\u00e7on H. Salicylic acid-dependent restriction of Tomato ringspot virus spread in tobacco is accompanied by a hypersensitive response, local RNA silencing, and moderate systemic resistance. Mol Plant Microbe Interact. 2011;24:706\u201318.","journal-title":"Mol Plant Microbe Interact"},{"key":"1925_CR7","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1094\/MPMI-23-4-0394","volume":"23","author":"G S\u00e1nchez","year":"2010","unstructured":"S\u00e1nchez G, Gerhardt N, Siciliano F, Vojnov A, Malcuit I, Marano MR. Salicylic acid is involved in the Nb-mediated defense responses to Potato virus X in Solanum tuberosum. Mol Plant Microbe Interact. 2010;23:394\u2013405.","journal-title":"Mol Plant Microbe Interact"},{"key":"1925_CR8","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1104\/pp.104.056028","volume":"137","author":"Z Huang","year":"2005","unstructured":"Huang Z, Yeakley JM, Garcia EW, Holdridge JD, Fan J, Whitham SA. Salicylic Acid-Dependent Expression of Host Genes in Compatible Arabidopsis-Virus Interactions 1. Plant Physiol. 2005;137:1147\u201359.","journal-title":"Plant Physiol"},{"key":"1925_CR9","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1093\/aob\/mcm079","volume":"100","author":"C Wasternack","year":"2007","unstructured":"Wasternack C. Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann Bot. 2007;100:681\u201397.","journal-title":"Ann Bot"},{"key":"1925_CR10","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1472-6785-4-11","volume":"4","author":"JA Zavala","year":"2004","unstructured":"Zavala JA, Baldwin IT. Fitness benefits of trypsin proteinase inhibitor expression in Nicotiana attenuata are greater than their costs when plants are attacked. BMC Ecol. 2004;4:11.","journal-title":"BMC Ecol"},{"key":"1925_CR11","doi-asserted-by":"crossref","first-page":"1597","DOI":"10.1111\/j.1365-3040.2010.02167.x","volume":"33","author":"DD Bilgin","year":"2010","unstructured":"Bilgin DD, Zavala JA, Zhu J, Clough SJ, Ort DR, DeLucia EH. Biotic stress globally downregulates photosynthesis genes. Plant Cell Environ. 2010;33:1597\u2013613.","journal-title":"Plant Cell Environ"},{"key":"1925_CR12","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1094\/MPMI-20-4-0358","volume":"20","author":"C Yang","year":"2007","unstructured":"Yang C, Guo R, Jie F, Nettleton D, Peng J, Carr T, et al. Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infection. Mol Plant Microbe Interact. 2007;20:358\u201370.","journal-title":"Mol Plant Microbe Interact"},{"key":"1925_CR13","doi-asserted-by":"crossref","first-page":"e29009","DOI":"10.1371\/journal.pone.0029009","volume":"6","author":"\u0160 Baebler","year":"2011","unstructured":"Baebler \u0160, Stare K, Kova\u010d M, Blejec A, Prezelj N, Stare T, et al. Dynamics of Responses in Compatible Potato - Potato virus Y Interaction Are Modulated by Salicylic Acid. PLoS One. 2011;6:e29009.","journal-title":"PLoS One"},{"key":"1925_CR14","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1055\/s-2006-924025","volume":"8","author":"VA Halim","year":"2006","unstructured":"Halim VA, Vess A, Scheel D, Rosahl S. The role of salicylic acid and jasmonic acid in pathogen defense. Plant Biol (Stuttg). 2006;8:307\u201313.","journal-title":"Plant Biol (Stuttg)"},{"key":"1925_CR15","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.plantsci.2011.06.008","volume":"181","author":"AL Vuorinen","year":"2011","unstructured":"Vuorinen AL, Kelloniemi J, Valkonen JPT. Why do viruses need phloem for systemic invasion of plants? Plant Sci. 2011;181:355\u201363.","journal-title":"Plant Sci"},{"key":"1925_CR16","doi-asserted-by":"crossref","first-page":"154","DOI":"10.3389\/fpls.2013.00154","volume":"4","author":"C Hipper","year":"2013","unstructured":"Hipper C, Brault V, Ziegler-Graff V, Revers F. Viral and cellular factors involved in Phloem transport of plant viruses. Front Plant Sci. 2013;4:154.","journal-title":"Front Plant Sci"},{"key":"1925_CR17","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1094\/MPMI-03-13-0062-R","volume":"26","author":"R Zavaliev","year":"2013","unstructured":"Zavaliev R, Levy A, Gera A, Epel BL. Subcellular dynamics and role of Arabidopsis \u03b2-1,3-glucanases in cell-to-cell movement of tobamoviruses. Mol Plant Microbe Interact. 2013;26:1016\u201330.","journal-title":"Mol Plant Microbe Interact"},{"key":"1925_CR18","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1046\/j.1365-313x.2000.00658.x","volume":"21","author":"VA Iglesias","year":"2000","unstructured":"Iglesias VA, Meins F. Movement of plant viruses is delayed in a beta-1,3-glucanase-deficient mutant showing a reduced plasmodesmatal size exclusion limit and enhanced callose deposition. Plant J. 2000;21:157\u201366.","journal-title":"Plant J"},{"key":"1925_CR19","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1007\/s11816-013-0300-5","volume":"7","author":"D Dobnik","year":"2013","unstructured":"Dobnik D, Baebler S, Kogov\u0161ek P, Pompe-Novak M, Stebih D, Panter G, et al. \u03b2-1,3-glucanase class III promotes spread of PVY(NTN) and improves in planta protein production. Plant Biotechnol Rep. 2013;7:547\u201355.","journal-title":"Plant Biotechnol Rep"},{"key":"1925_CR20","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1007\/s00299-011-1211-y","volume":"31","author":"W Li","year":"2012","unstructured":"Li W, Zhao Y, Liu C, Yao G, Wu S, Hou C, et al. Callose deposition at plasmodesmata is a critical factor in restricting the cell-to-cell movement of Soybean mosaic virus. Plant Cell Rep. 2012;31:905\u201316.","journal-title":"Plant Cell Rep"},{"key":"1925_CR21","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1093\/jxb\/ert447","volume":"65","author":"\u0160 Baebler","year":"2014","unstructured":"Baebler \u0160, Witek K, Petek M, Stare K, Tu\u0161ek-\u017dnidari\u010d M, Pompe-Novak M, et al. Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potato. J Exp Bot. 2014;65:1095\u2013109.","journal-title":"J Exp Bot"},{"issue":"1-3","key":"1925_CR22","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/s11120-013-9880-8","volume":"117","author":"JO Berry","year":"2013","unstructured":"Berry JO, Yerramsetty P, Zielinski AM, Mure CM. Photosynthetic gene expression in higher plants. Photosynth Res. 2013;117(1-3):91\u2013120.","journal-title":"Photosynth Res"},{"key":"1925_CR23","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1007\/s00705-013-1778-4","volume":"158","author":"X Sun","year":"2013","unstructured":"Sun X, Li Y, Shi M, Zhang N, Wu G, Li T, et al. In vitro binding and bimolecular fluorescence complementation assays suggest an interaction between tomato mosaic virus coat protein and tobacco chloroplast ferredoxin I. Arch Virol. 2013;158:2611\u20135.","journal-title":"Arch Virol"},{"issue":"Pt 8","key":"1925_CR24","doi-asserted-by":"crossref","first-page":"2046","DOI":"10.1099\/vir.0.2008\/001271-0","volume":"89","author":"Y-Q Cheng","year":"2008","unstructured":"Cheng Y-Q, Liu Z-M, Xu J, Zhou T, Wang M, Chen Y-T, et al. HC-Pro protein of sugar cane mosaic virus interacts specifically with maize ferredoxin-5 in vitro and in planta. J Gen Virol. 2008;89(Pt 8):2046\u201354.","journal-title":"J Gen Virol"},{"issue":"August","key":"1925_CR25","doi-asserted-by":"crossref","first-page":"2809","DOI":"10.1105\/tpc.111.087346","volume":"23","author":"JW Moore","year":"2011","unstructured":"Moore JW, Loake GJ, Spoel SH. Transcription Dynamics in Plant Immunity. Plant Cell. 2011;23(August):2809\u201320.","journal-title":"Plant Cell"},{"key":"1925_CR26","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.cbpa.2012.05.002","volume":"16","author":"DC Ducat","year":"2012","unstructured":"Ducat DC, Silver PA. Improving carbon fixation pathways. Curr Opin Chem Biol. 2012;16:337\u201344.","journal-title":"Curr Opin Chem Biol"},{"key":"1925_CR27","doi-asserted-by":"crossref","first-page":"2877","DOI":"10.1073\/pnas.68.11.2877","volume":"68","author":"JA Bassham","year":"1971","unstructured":"Bassham JA. Photosynthetic Carbon Metabolism. Proc Nat Acad Sci USA. 1971;68:2877\u201382.","journal-title":"Proc Nat Acad Sci USA"},{"key":"1925_CR28","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/s11120-007-9225-6","volume":"94","author":"AR Portis","year":"2007","unstructured":"Portis AR, Parry MAJ. Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase\/oxygenase): A historical perspective. Photosynth Res. 2007;94:121\u201343.","journal-title":"Photosynth Res"},{"key":"1925_CR29","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/0968-0004(79)90212-3","volume":"4","author":"RJ Ellis","year":"1979","unstructured":"Ellis RJ. The most abundant protein in the world. Trends Biochem Sci. 1979;4:241\u20134.","journal-title":"Trends Biochem Sci"},{"key":"1925_CR30","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1146\/annurev.pp.32.060181.002025","volume":"32","author":"GH Lorimer","year":"1981","unstructured":"Lorimer GH. The Carboxylation and Oxygenation of Ribulose 1,5-Bisphosphate: The Primary Events in Photosynthesis and Photorespiration. Annu Rev Plant Physiol. 1981;32:349\u201382.","journal-title":"Annu Rev Plant Physiol"},{"key":"1925_CR31","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/BF00377192","volume":"78","author":"JR Evans","year":"1989","unstructured":"Evans JR. Photosynthesis and nitrogen relationships in leaves of C3 plants. Oecologia. 1989;78:9\u201319.","journal-title":"Oecologia"},{"key":"1925_CR32","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1104\/pp.100.4.1737","volume":"100","author":"A Makino","year":"1992","unstructured":"Makino A, Sakashita H, Hidema J, Mae T, Ojima K, Osmond B. Distinctive Responses of Ribulose-1,5-Bisphosphate Carboxylase and Carbonic Anhydrase in Wheat Leaves to Nitrogen Nutrition and their Possible Relationships to CO(2)-Transfer Resistance. Plant Physiol. 1992;100:1737\u201343.","journal-title":"Plant Physiol"},{"key":"1925_CR33","unstructured":"Berry JO, Patel M: Kranz Anatomy and the C4 Pathway. In eLS. John Wiley & Sons, Ltd, Chichester. http:\/\/www.els.net doi:[ 10.1002\/9780470015902.a0001295.pub2 ] 2008."},{"key":"1925_CR34","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1080\/07352680390243503","volume":"22","author":"A Tyagi","year":"2003","unstructured":"Tyagi A, Gaur T. Light Regulation of Nuclear Photosynthetic Genes in Higher Plants. CRC Crit Rev Plant Sci. 2003;22:417\u201352.","journal-title":"CRC Crit Rev Plant Sci"},{"key":"1925_CR35","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1104\/pp.112.209213","volume":"161","author":"J Zhao","year":"2013","unstructured":"Zhao J, Liu Q, Zhang H, Jia Q, Hong Y, Liu Y. The rubisco small subunit is involved in tobamovirus movement and Tm-22-mediated extreme resistance. Plant Physiol. 2013;161:374\u201383.","journal-title":"Plant Physiol"},{"key":"1925_CR36","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1007\/s11262-011-0596-6","volume":"43","author":"L Lin","year":"2011","unstructured":"Lin L, Luo Z, Yan F, Lu Y, Zheng H, Chen J. Interaction between potyvirus P3 and ribulose-1,5-bisphosphate carboxylase\/oxygenase (RubisCO) of host plants. Virus Genes. 2011;43:90\u20132.","journal-title":"Virus Genes"},{"key":"1925_CR37","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1094\/MPMI-22-5-0487","volume":"22","author":"MD Bolton","year":"2009","unstructured":"Bolton MD. Primary metabolism and plant defense--fuel for the fire. Mol Plant Microbe Interact. 2009;22:487\u201397.","journal-title":"Mol Plant Microbe Interact"},{"key":"1925_CR38","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1093\/jxb\/err402","volume":"63","author":"S Kangasj\u00e4rvi","year":"2012","unstructured":"Kangasj\u00e4rvi S, Neukermans J, Li S, Aro E-M, Noctor G. Photosynthesis, photorespiration, and light signalling in defense responses. J Exp Bot. 2012;63:1619\u201336.","journal-title":"J Exp Bot"},{"key":"1925_CR39","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1146\/annurev-cellbio-092910-154055","volume":"28","author":"CMJ Pieterse","year":"2012","unstructured":"Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM. Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol. 2012;28:489\u2013521.","journal-title":"Annu Rev Cell Dev Biol"},{"key":"1925_CR40","doi-asserted-by":"crossref","first-page":"17","DOI":"10.3389\/fpls.2014.00017","volume":"5","author":"CM Rojas","year":"2014","unstructured":"Rojas CM, Senthil-Kumar M, Tzin V, Mysore KS. Regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense. Front Plant Sci. 2014;5:17.","journal-title":"Front Plant Sci"},{"key":"1925_CR41","doi-asserted-by":"crossref","first-page":"3989","DOI":"10.1093\/jxb\/ers129","volume":"63","author":"MR Bolouri Moghaddam","year":"2012","unstructured":"Bolouri Moghaddam MR, Van den Ende W. Sugars and plant innate immunity. J Exp Bot. 2012;63:3989\u201398.","journal-title":"J Exp Bot"},{"key":"1925_CR42","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1094\/MPMI-20-7-0832","volume":"20","author":"J G\u00f3mez-Ariza","year":"2007","unstructured":"G\u00f3mez-Ariza J, Campo S, Rufat M, Estop\u00e0 M, Messeguer J, San Segundo B, et al. Sucrose-mediated priming of plant defense responses and broad-spectrum disease resistance by overexpression of the maize pathogenesis-related PRms protein in rice plants. Mol Plant Microbe Interact. 2007;20:832\u201342.","journal-title":"Mol Plant Microbe Interact"},{"key":"1925_CR43","doi-asserted-by":"crossref","first-page":"293","DOI":"10.3389\/fpls.2014.00293","volume":"5","author":"AS Tauzin","year":"2014","unstructured":"Tauzin AS, Giardina T. Sucrose and invertases, a part of the plant defense response to the biotic stresses. Front Plant Sci. 2014;5:293.","journal-title":"Front Plant Sci"},{"key":"1925_CR44","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.1111\/j.1742-4658.2010.07633.x","volume":"277","author":"MR Bolouri-Moghaddam","year":"2010","unstructured":"Bolouri-Moghaddam MR, Le Roy K, Xiang L, Rolland F, Van den Ende W. Sugar signalling and antioxidant network connections in plant cells. FEBS J. 2010;277:2022\u201337.","journal-title":"FEBS J"},{"key":"1925_CR45","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.1105\/tpc.9.10.1825","volume":"9","author":"R Ehness","year":"1997","unstructured":"Ehness R, Ecker M, Godt DE, Roitsch T. Glucose and Stress Independently Regulate Source and Sink Metabolism and Defense Mechanisms via Signal Transduction Pathways Involving Protein Phosphorylation. Plant Cell. 1997;9:1825\u201341.","journal-title":"Plant Cell"},{"key":"1925_CR46","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1046\/j.1469-8137.2001.00035.x","volume":"149","author":"P Reignault","year":"2002","unstructured":"Reignault P, Cogan A, Muchembled J, Lounes-Hadj Sahraoui A, Durand R, Sancholle M. Trehalose induces resistance to powdery mildew in wheat. New Phytol. 2002;149:519\u201329.","journal-title":"New Phytol"},{"key":"1925_CR47","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1046\/j.1364-3703.2000.00007.x","volume":"1","author":"K Herbers","year":"2000","unstructured":"Herbers K, Takahata Y, Melzer M, Mock HP, Hajirezaei M, Sonnewald U. Regulation of carbohydrate partitioning during the interaction of potato virus Y with tobacco. Mol Plant Pathol. 2000;1:51\u20139.","journal-title":"Mol Plant Pathol"},{"key":"1925_CR48","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/978-1-4020-3218-9_11","volume-title":"Chlorophyll fluorescence: A Signature of Photosynthesis","author":"U Schreiber","year":"2004","unstructured":"Schreiber U. 2004. In: Govindjee PG, editor. Chlorophyll fluorescence: A Signature of Photosynthesis, vol. 19. Netherlands: Springer; 2004. p. 279\u2013319 [Advances in Photosynthesis and Respiration]."},{"key":"1925_CR49","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1023\/B:PHOT.0000015459.22769.bf","volume":"41","author":"H Ry\u0161lav\u00e1","year":"2003","unstructured":"Ry\u0161lav\u00e1 H, M\u00fcller K, Semor\u00e1dov\u00e1 \u0160. Photosynthesis and activity of phosphoenolpyruvate carboxylase in Nicotiana tabacum L. leaves infected by Potato virus A and Potato virus Y. Photosynthetica. 2003;41:357\u201363.","journal-title":"Photosynthetica"},{"key":"1925_CR50","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.plantsci.2006.06.002","volume":"171","author":"H Synkov\u00e1","year":"2006","unstructured":"Synkov\u00e1 H, Semor\u00e1dov\u00e1 \u0160, Schnablov\u00e1 R, M\u00fcller K, Posp\u00ed\u0161ilov\u00e1 J, Ry\u0161lav\u00e1 H, et al. Effects of biotic stress caused by Potato virus Y on photosynthesis in ipt transgenic and control Nicotiana tabacum L. Plant Sci. 2006;171:607\u201316.","journal-title":"Plant Sci"},{"key":"1925_CR51","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s11099-013-0023-4","volume":"51","author":"P Spoustov\u00e1","year":"2013","unstructured":"Spoustov\u00e1 P, Synkov\u00e1 H, Valcke R, \u010ce\u0159ovsk\u00e1 N. Chlorophyll a fluorescence as a tool for a study of the Potato virus Y effects on photosynthesis of nontransgenic and transgenic Pssu-ipt tobacco. Photosynthetica. 2013;51:191\u2013201.","journal-title":"Photosynthetica"},{"key":"1925_CR52","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/0014-5793(89)80234-0","volume":"245","author":"RA Hodgson","year":"1989","unstructured":"Hodgson RA, Beachy RN, Pakrasi HB. Selective inhibition of photosystem II in spinach by tobacco mosaic virus: an effect of the viral coat protein. FEBS Lett. 1989;245:267\u201370.","journal-title":"FEBS Lett"},{"key":"1925_CR53","first-page":"713","volume":"2","author":"SF Elena","year":"2012","unstructured":"Elena SF, Rodrigo G. Towards an integrated molecular model of plant-virus interactions. Curr Opin Virol. 2012;2:713\u20138.","journal-title":"Curr Opin Virol"},{"key":"1925_CR54","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev.en.38.010193.000521","volume":"38","author":"JT Trumble","year":"1993","unstructured":"Trumble JT, Kolodny-Hirsch DMTI. Plant compensation for arthropod herbivory. Annu Rev Entomol. 1993;38:93\u2013119.","journal-title":"Annu Rev Entomol"},{"key":"1925_CR55","doi-asserted-by":"crossref","first-page":"3728","DOI":"10.1021\/pr300213k","volume":"11","author":"M Zhu","year":"2012","unstructured":"Zhu M, Dai S, Zhu N, Booy A, Simons B, Yi S, et al. Methyl jasmonate responsive proteins in Brassica napus guard cells revealed by iTRAQ-based quantitative proteomics. J Proteome Res. 2012;11:3728\u201342.","journal-title":"J Proteome Res"},{"key":"1925_CR56","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1111\/j.1364-3703.2008.00530.x","volume":"10","author":"S Baebler","year":"2009","unstructured":"Baebler S, Krecic-Stres H, Rotter A, Kogovsek P, Cankar K, Kok EJ, et al. PVY(NTN) elicits a diverse gene expression response in different potato genotypes in the first 12 h after inoculation. Mol Plant Pathol. 2009;10:263\u201375.","journal-title":"Mol Plant Pathol"},{"key":"1925_CR57","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1104\/pp.104.1.209","volume":"104","author":"R Vera-Estrella","year":"1994","unstructured":"Vera-Estrella R, Barkla BJ, Higgins VJ, Blumwald E. Plant Defense Response to Fungal Pathogens (Activation of Host-Plasma Membrane H\u2009+\u2009-ATPase by Elicitor-Induced Enzyme Dephosphorylation). Plant Physiol. 1994;104:209\u201315.","journal-title":"Plant Physiol"},{"key":"1925_CR58","doi-asserted-by":"crossref","first-page":"e1000606","DOI":"10.1371\/journal.pcbi.1000606","volume":"5","author":"C Dressaire","year":"2009","unstructured":"Dressaire C, Gitton C, Loubi\u00e8re P, Monnet V, Queinnec I, Cocaign-Bousquet M. Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis. PLoS Comput Biol. 2009;5:e1000606.","journal-title":"PLoS Comput Biol"},{"key":"1925_CR59","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/msb.2011.38","volume":"7","author":"T Maier","year":"2011","unstructured":"Maier T, Schmidt A, G\u00fcell M, K\u00fchner S, Gavin A-C, Aebersold R, et al. Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol. 2011;7:511.","journal-title":"Mol Syst Biol"},{"key":"1925_CR60","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1007\/s11033-010-0135-x","volume":"38","author":"H Yang","year":"2011","unstructured":"Yang H, Huang Y, Zhi H, Yu D. Proteomics-based analysis of novel genes involved in response toward soybean mosaic virus infection. Mol Biol Rep. 2011;38:511\u201321.","journal-title":"Mol Biol Rep"},{"key":"1925_CR61","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nrg3185","volume":"13","author":"C Vogel","year":"2012","unstructured":"Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet. 2012;13:227\u201332.","journal-title":"Nat Rev Genet"},{"key":"1925_CR62","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s00726-010-0669-1","volume":"41","author":"W Hoehenwarter","year":"2011","unstructured":"Hoehenwarter W, Chen Y, Recuenco-Munoz L, Wienkoop S, Weckwerth W. Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics. Amino Acids. 2011;41:329\u201341.","journal-title":"Amino Acids"},{"key":"1925_CR63","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1111\/j.1365-3059.2010.02340.x","volume":"59","author":"P Kogov\u0161ek","year":"2010","unstructured":"Kogov\u0161ek P, Pompe-Novak M, Baebler \u0160, Rotter A, Gow L, Gruden K, et al. Aggressive and mild Potato virus Y isolates trigger different specific responses in susceptible potato plants. Plant Pathol. 2010;59:1121\u201332.","journal-title":"Plant Pathol"},{"key":"1925_CR64","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s10142-008-0083-x","volume":"8","author":"B Kloosterman","year":"2008","unstructured":"Kloosterman B, De Koeyer D, Griffiths R, Flinn B, Steuernagel B, Scholz U, et al. Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Funct Integr Genomics. 2008;8:329\u201340.","journal-title":"Funct Integr Genomics"},{"key":"1925_CR65","first-page":"1","volume-title":"Agi4x44Preprocess","author":"P Lopez-romero","year":"2013","unstructured":"Lopez-romero P. Agi4x44Preprocess. 2013. p. 1\u201329."},{"key":"1925_CR66","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1093\/bioinformatics\/bti270","volume":"21","author":"GK Smyth","year":"2005","unstructured":"Smyth GK, Michaud J, Scott HS. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics. 2005;21:2067\u201375.","journal-title":"Bioinformatics"},{"key":"1925_CR67","doi-asserted-by":"crossref","first-page":"e11","DOI":"10.1093\/nar\/gkm1075","volume":"36","author":"SM Lin","year":"2008","unstructured":"Lin SM, Du P, Huber W, Kibbe WA. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 2008;36:e11.","journal-title":"Nucleic Acids Res"},{"key":"1925_CR68","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Stat Soc Ser B. 1995;57:289\u2013300.","journal-title":"J R Stat Soc Ser B"},{"key":"1925_CR69","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1111\/j.1365-313X.2004.02016.x","volume":"37","author":"O Thimm","year":"2004","unstructured":"Thimm O, Bl\u00e4sing O, Gibon Y, Nagel A, Meyer S, Kr\u00fcger P, et al. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004;37:914\u201339.","journal-title":"Plant J"},{"key":"1925_CR70","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1746-4811-3-10","volume":"3","author":"A Rotter","year":"2007","unstructured":"Rotter A, Usadel B, Baebler S, Stitt M, Gruden K. Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods. 2007;3:10.","journal-title":"Plant Methods"},{"key":"1925_CR71","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102:15545\u201350.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1925_CR72","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jviromet.2008.01.025","volume":"149","author":"P Kogovsek","year":"2008","unstructured":"Kogovsek P, Gow L, Pompe-Novak M, Gruden K, Foster GD, Boonham N, et al. Single-step RT real-time PCR for sensitive detection and discrimination of Potato virus Y isolates. J Virol Methods. 2008;149:1\u201311.","journal-title":"J Virol Methods"},{"key":"1925_CR73","doi-asserted-by":"crossref","first-page":"2853","DOI":"10.1128\/AEM.66.7.2853-2858.2000","volume":"66","author":"SA Weller","year":"2000","unstructured":"Weller SA, Elphinstone JG, Smith NC, Boonham N, Stead DE. Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay. Appl Environ Microbiol. 2000;66:2853\u20138.","journal-title":"Appl Environ Microbiol"},{"key":"1925_CR74","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/1471-2164-10-460","volume":"10","author":"M Hren","year":"2009","unstructured":"Hren M, Nikoli\u0107 P, Rotter A, Blejec A, Terrier N, Ravnikar M, et al. \u201cBois noir\u201d phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine. BMC Genomics. 2009;10:460.","journal-title":"BMC Genomics"},{"key":"1925_CR75","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.mimet.2008.01.006","volume":"73","author":"FW-F Lee","year":"2008","unstructured":"Lee FW-F, Lo SC-L. The use of Trizol reagent (phenol\/guanidine isothiocyanate) for producing high quality two-dimensional gel electrophoretograms (2-DE) of dinoflagellates. J Microbiol Methods. 2008;73:26\u201332.","journal-title":"J Microbiol Methods"},{"key":"1925_CR76","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/0003-2697(76)90527-3","volume":"72","author":"MM Bradford","year":"1976","unstructured":"Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976;72:248\u201354.","journal-title":"Anal Biochem"},{"key":"1925_CR77","doi-asserted-by":"crossref","first-page":"285","DOI":"10.3389\/fpls.2012.00285","volume":"3","author":"C Staudinger","year":"2012","unstructured":"Staudinger C, Mehmeti V, Turetschek R, Lyon D, Egelhofer V, Wienkoop S. Possible Role of Nutritional Priming for Early Salt and Drought Stress Responses in Medicago truncatula. Front Plant Sci. 2012;3:285.","journal-title":"Front Plant Sci"},{"issue":"Database issue","key":"1925_CR78","doi-asserted-by":"crossref","first-page":"D1167","DOI":"10.1093\/nar\/gkt1056","volume":"42","author":"\u017d Ramsak","year":"2014","unstructured":"Ramsak \u017d, Baebler \u0160, Rotter A, Korbar M, Mozetic I, Usadel B, et al. GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic Acids Res. 2014;42(Database issue):D1167\u201375.","journal-title":"Nucleic Acids Res"},{"key":"1925_CR79","doi-asserted-by":"crossref","first-page":"1495","DOI":"10.1104\/pp.107.101618","volume":"144","author":"E Larrainzar","year":"2007","unstructured":"Larrainzar E, Wienkoop S, Weckwerth W, Ladrera R, Arrese-Igor C, Gonz\u00e1lez EM. Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress. Plant Physiol. 2007;144:1495\u2013507.","journal-title":"Plant Physiol"},{"key":"1925_CR80","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/nature10158","volume":"475","author":"X Xu","year":"2011","unstructured":"Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, et al. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475:189\u201395.","journal-title":"Nature"}],"updated-by":[{"DOI":"10.1186\/s12864-017-3611-z","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2017,3,13]],"date-time":"2017-03-13T00:00:00Z","timestamp":1489363200000}}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-015-1925-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T06:48:25Z","timestamp":1718088505000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.biomedcentral.com\/1471-2164\/16\/716"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,9,19]]},"references-count":80,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["1925"],"URL":"https:\/\/doi.org\/10.1186\/s12864-015-1925-2","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,9,19]]},"article-number":"716"}}