{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T16:07:58Z","timestamp":1769011678025,"version":"3.49.0"},"reference-count":87,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2014,5,23]],"date-time":"2014-05-23T00:00:00Z","timestamp":1400803200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0098376","type":"journal-article","created":{"date-parts":[[2014,5,23]],"date-time":"2014-05-23T20:31:09Z","timestamp":1400877069000},"page":"e98376","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":49,"title":["Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling"],"prefix":"10.1371","volume":"9","author":[{"given":"M\u00f3nica","family":"Sebastiana","sequence":"first","affiliation":[]},{"given":"Bruno","family":"Vieira","sequence":"additional","affiliation":[]},{"given":"Teresa","family":"Lino-Neto","sequence":"additional","affiliation":[]},{"given":"Filipa","family":"Monteiro","sequence":"additional","affiliation":[]},{"given":"Andreia","family":"Figueiredo","sequence":"additional","affiliation":[]},{"given":"Lisete","family":"Sousa","sequence":"additional","affiliation":[]},{"given":"Maria Salom\u00e9","family":"Pais","sequence":"additional","affiliation":[]},{"given":"Rui","family":"Tavares","sequence":"additional","affiliation":[]},{"given":"Oct\u00e1vio S.","family":"Paulo","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,5,23]]},"reference":[{"key":"ref1","unstructured":"Smith S, Read D (1997) Mycorrhizal symbiosis, Academic Press, London."},{"key":"ref2","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1046\/j.1469-8137.2002.00397.x","article-title":"Coevolution of roots and mycorrhizas of land plants","volume":"154(2)","author":"MC Brundrett","year":"2002","journal-title":"New Phytol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.phytochem.2006.09.024","article-title":"Sugar for my honey: carbohydrate partitioning in ectomycorrhizal symbiosis","volume":"68(1)","author":"U Nehls","year":"2007","journal-title":"Phytochem"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1991","DOI":"10.1104\/pp.109.147231","article-title":"The ectomycorrhizal fungus <italic>Laccaria bicolor<\/italic> stimulates lateral root formation in poplar and <italic>Arabidopsis<\/italic> through auxin transport and signaling","volume":"151(4)","author":"J Felten","year":"2009","journal-title":"Plant Physiol"},{"key":"ref5","first-page":"1902","article-title":"Upgrading root physiology for stress tolerance by ectomycorrhizas: insights from metabolite and transcriptional profiling into reprogramming for stress anticipation","volume":"151(4)","author":"ZB Luo","year":"2009","journal-title":"Plant Physiol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1007\/s004250000342","article-title":"Root hair elongation is inhibited by hypaphorine, the indole alkaloid from the ectomycorrhizal fungus <italic>Pisolithus tinctorius<\/italic>, and restored by indole-3-acetic acid","volume":"211(5)","author":"FA Ditengou","year":"2000","journal-title":"Planta"},{"key":"ref7","first-page":"02","article-title":"Transcriptional responses of <italic>Paxillus involutus<\/italic> and <italic>Betula pendula<\/italic> during formation of ectomycorrhizal root tissue","volume":"17(2)","author":"T Johansson","year":"2004","journal-title":"Mol Plant Microbe Interact"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1111\/j.1469-8137.2004.01248.x","article-title":"Transcript patterns associated with ectomycorrhiza development in <italic>Eucalyptus globulus<\/italic> and <italic>Pisolithus microcarpus<\/italic>","volume":"165(2)","author":"S Duplessis","year":"2005","journal-title":"New Phytol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1094\/MPMI-18-0659","article-title":"Global patterns of gene regulation associated with the development of ectomycorrhiza between birch (<italic>Betula pendula<\/italic> Roth.) and <italic>Paxillus involutus<\/italic> (Batsch) Fr","volume":"18(7)","author":"A Le Qu\u00e9r\u00e9","year":"2005","journal-title":"Mol Plant Microbe Interact"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1471-2229-8-19","article-title":"Transcriptional analysis of <italic>Pinus sylvestris<\/italic> roots challenged with the ectomycorrhizal fungus <italic>Laccaria bicolor<\/italic>","volume":"8","author":"G Heller","year":"2008","journal-title":"BMC Plant Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/nature06556","article-title":"The genome of <italic>Laccaria bicolor<\/italic> provides insights into mycorrhizal symbiosis","volume":"452(7183)","author":"F Martin","year":"2008","journal-title":"Nature"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nature08867","article-title":"Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis","volume":"464(7291)","author":"F Martin","year":"2010","journal-title":"Nature"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1007\/s005720050172","article-title":"Interactions between <italic>Pisolithus tinctorius<\/italic> and its hosts: a review of current knowledge","volume":"7(3)","author":"JWG Cairney","year":"1997","journal-title":"Mycorrhiza"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1007\/s11056-013-9386-4","article-title":"Ectomycorrhizal inoculation with <italic>Pisolithus tinctorius<\/italic> increases the performance of <italic>Quercus suber<\/italic> L. (cork oak) nursery and field seedlings","volume":"44(6)","author":"M Sebastiana","year":"2013","journal-title":"New Forests"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/j.tplants.2010.06.005","article-title":"MYB transcription factors in <italic>Arabidopsis<\/italic>","volume":"15(10)","author":"C Dubos","year":"2010","journal-title":"Trends Plant Sci"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1104\/pp.112.195420","article-title":"Expression of the <italic>R2R3-MYB<\/italic> transcription factor <italic>TaMYB14<\/italic> from <italic>Trifolium arvense<\/italic> activates proanthocyanidin biosynthesis in the legumes <italic>Trifolium repens<\/italic> and <italic>Medicago sativa<\/italic>","volume":"159(3)","author":"KR Hancock","year":"2012","journal-title":"Plant Physiol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/nature02100","article-title":"APL regulates vascular tissue identity in <italic>Arabidopsis<\/italic>","volume":"426(6963)","author":"M Bonke","year":"2003","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1007\/s11103-005-0955-6","article-title":"<italic>AINTEGUMENTA-like<\/italic> (AIL) genes are expressed in young tissues and may specify meristematic or division-competent states","volume":"57(5)","author":"S Nole-Wilson","year":"2005","journal-title":"Plant Mol Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.tplants.2010.02.006","article-title":"<italic>WRKY<\/italic> transcription factors","volume":"15(5)","author":"PJ Rushton","year":"2010","journal-title":"Trends Plant Sci"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1016\/j.cub.2011.06.044","article-title":"A secreted fungal effector of <italic>Glomus<\/italic> intraradices promotes symbiotic biotrophy","volume":"21(14)","author":"S Kloppholz","year":"2011","journal-title":"Curr Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/1471-2164-8-125","article-title":"Transcriptional profiling of <italic>Arabidopsis<\/italic> heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways","volume":"8","author":"WR Swindell","year":"2007","journal-title":"BMC Genomics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1111\/j.1469-8137.1988.tb03720.x","article-title":"Time sequence of the infection process eucalypt ectomycorrhizas","volume":"109(4)","author":"DP Horan","year":"1988","journal-title":"New Phytol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/S136952660200002X","article-title":"Cell-fate specification in the epidermis: a common patterning mechanism in the root and shoot","volume":"6(1)","author":"J Schiefelbein","year":"2003","journal-title":"Curr Opin Plant Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1104\/pp.111.185785","article-title":"Cell fate in the <italic>Arabidopsis<\/italic> root epidermis is determined by competition between WEREWOLF and CAPRICE","volume":"157(3)","author":"SK Song","year":"2011","journal-title":"Plant Physiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1105\/tpc.107.056119","article-title":"The <italic>Arabidopsis<\/italic> Phosphatidylinositol Phosphate 5-Kinase PIP5K3 is a key regulator of root hair tip growth","volume":"20(2)","author":"H Kusano","year":"2008","journal-title":"Plant Cell"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.pbi.2007.01.006","article-title":"Living in harmony in the wood underground: ectomycorrhizal genomics","volume":"10","author":"F Martin","year":"2007","journal-title":"Curr Opin Plant Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1104\/pp.109.141325","article-title":"Truffles regulate plant root morphogenesis via the production of auxin and ethylene","volume":"150(4)","author":"R Splivallo","year":"2009","journal-title":"Plant Physiol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"3035","DOI":"10.1105\/tpc.105.035493","article-title":"Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT\/IAA14-mediated lateral root initiation in <italic>Arabidopsis thaliana<\/italic>","volume":"17(11)","author":"S Vanneste","year":"2005","journal-title":"Plant Cell"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1007\/s00572-011-0402-2","article-title":"Expression analysis of <italic>Clavata1-like<\/italic> and <italic>Nodulin21-like<\/italic> genes from <italic>Pinus sylvestris<\/italic> during ectomycorrhiza formation","volume":"22(4)","author":"G Heller","year":"2012","journal-title":"Mycorrhiza"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"864","DOI":"10.4161\/psb.5.7.11896","article-title":"Lateral root stimulation in the early interaction between Arabidopsis thaliana and the ectomycorrhizal fungus <italic>Laccaria bicolor<\/italic>: is fungal auxin the trigger?","volume":"5(7)","author":"J Felten","year":"2010","journal-title":"Plant Signal Behav"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1111\/j.1744-7909.2010.00905.x","article-title":"Flavonoids: new roles for old molecules","volume":"52(1)","author":"CS Buer","year":"2010","journal-title":"J Integr Plant Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1104\/pp.110.155432","article-title":"The mysteries of proanthocyanidin transport and polymerization","volume":"153","author":"J Zhao","year":"2010","journal-title":"Plant Physiol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1007\/s00572-009-0242-5","article-title":"A <italic>Medicago truncatula<\/italic> mutant hyper-responsive to mycorrhiza and defective for nodulation","volume":"19(6)","author":"D Morandi","year":"2009","journal-title":"Mycorrhiza"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1051\/agro:19921012","article-title":"Effect of some plant flavonoids on in vitro behaviour of an arbuscular mycorrhizal fungus","volume":"12(10)","author":"D Morandi","year":"1992","journal-title":"Agronomie"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/1752-0509-5-70","article-title":"Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome","volume":"5","author":"PE Larsen","year":"2011","journal-title":"BMC Syst Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1007\/s00572-007-0131-8","article-title":"Flavonoids induce germination of basidiospores of the ectomycorrhizal fungus Suillus bovinus","volume":"17(7)","author":"K Kikuchi","year":"2007","journal-title":"Mycorrhiza"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1093\/pcp\/pcp190","article-title":"Sucrose synthase is an integral component of the cellulose synthesis machinery","volume":"51(2)","author":"S Fujii","year":"2010","journal-title":"Plant Cell Physiol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1006\/pmpp.1999.0254","article-title":"Ultrastructural changes and localization of chitin and callose in compatible and incompatible interactions between carnation callus and <italic>Fusarium oxysporum<\/italic>","volume":"56(3)","author":"MI Trillas","year":"2000","journal-title":"Physiol Mol Plant Pathol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.pbi.2004.03.006","article-title":"Glycosyltransferases and cell wall biosynthesis: novel players and insights","volume":"7(3)","author":"WR Scheible","year":"2004","journal-title":"Curr Opin Plant Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1038\/nrm1746","article-title":"Growth of the plant cell wall","volume":"6(11)","author":"DJ Cosgrove","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref41","doi-asserted-by":"crossref","unstructured":"Hobson G, Grierson D (1993) Tomato. <italic>In<\/italic>: G.Seymour, J.Taylor, and G.Tucker (eds). Biochemistry of fruit ripening: Chapman &amp; Hall, London. Pp 405\u2013442.","DOI":"10.1007\/978-94-011-1584-1_14"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1104\/pp.110.156844","article-title":"The <italic>XTH<\/italic> gene family: an update on enzyme structure, function, and phylogeny in xyloglucan remodeling","volume":"153(2)","author":"JM Eklof","year":"2010","journal-title":"Plant Physiol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1016\/S1360-1385(01)02045-3","article-title":"Pectin methylesterases: cell wall enzymes with important roles in plant physiology","volume":"6(9)","author":"F Micheli","year":"2001","journal-title":"Trends Plant Sci"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1093\/pcp\/pce061","article-title":"A large family of class III plant peroxidases","volume":"42(5)","author":"S Hiraga","year":"2001","journal-title":"Plant Cell Physiol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1104\/pp.110.155887","article-title":"The role of receptor-like kinases in regulating cell wall function","volume":"153(2)","author":"BJ Steinwand","year":"2010","journal-title":"Plant Physiol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1093\/jxb\/eri099","article-title":"Genes encoding ADP-ribosylation factors in <italic>Arabidopsis thaliana<\/italic> L. Heyn. genome analysis and antisense suppression","volume":"56(414)","author":"LK Gebbie","year":"2005","journal-title":"J Exp Bot"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.pbi.2003.09.003","article-title":"Expansins and cell growth","volume":"6(6)","author":"Y Li","year":"2003","journal-title":"Curr Opin Plant Biol"},{"key":"ref48","first-page":"637","article-title":"Identification of genes differentially expressed in ectomycorrhizal roots during the <italic>Pinus pinaster<\/italic>-<italic>Laccaria bicolor<\/italic> interaction","volume":"237(6)","author":"A Flores-Monterroso","year":"2013","journal-title":"Planta"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.tplants.2009.05.002","article-title":"<italic>Arabidopsis<\/italic> lateral root development: an emerging story","volume":"14(7)","author":"B P\u00e9ret","year":"2009","journal-title":"Trends Plant Sci"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1093\/mp\/ssr053","article-title":"A highway for war and peace: the secretory pathway in plant-microbe interactions","volume":"4(4)","author":"D Wang","year":"2011","journal-title":"Mol Plant"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev-cellbio-101011-155716","article-title":"Diversity of clathrin function: new tricks for an old protein","volume":"28","author":"FM Brodsky","year":"2012","journal-title":"Annu Rev Cell Dev Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"4205","DOI":"10.1002\/j.1460-2075.1992.tb05514.x","article-title":"Fission yeast and a plant have functional homologues of the Sar1 and Sec12 proteins involved in ER to Golgi traffic in budding yeast","volume":"11(11)","author":"C d'Enfert","year":"1992","journal-title":"EMBO J"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"14550","DOI":"10.1074\/jbc.275.19.14550","article-title":"Mammalian Sec61 is associated with Sec62 and Sec63","volume":"275(19)","author":"HA Meyer","year":"2000","journal-title":"J Biol Chem"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1104\/pp.110.154872","article-title":"Straying off the highway: trafficking of secreted plant proteins and complexity in the plant cell wall proteome","volume":"153(2)","author":"JK Rose","year":"2010","journal-title":"Plant Physiol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.1365-313X.2011.04487.x","article-title":"<italic>Arabidopsis<\/italic> SNARE protein SEC22 is essential for gametophyte development and maintenance of Golgi-stack integrity","volume":"66(2)","author":"F El-Kasmi","year":"2011","journal-title":"Plant J"},{"key":"ref56","first-page":"299","article-title":"Integrative proteomic and cytological analysis of the effects of extracellular Ca(2+) influx on <italic>Pinus bungeana<\/italic> pollen tube development","volume":"7(10)","author":"X Wu","year":"2008","journal-title":"J Proteome Res"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"24189","DOI":"10.1074\/jbc.M110.212209","article-title":"Exocyst complex component 3-like 2 (EXOC3L2) associates with the exocyst complex and mediates directional migration of endothelial cells","volume":"286(27)","author":"I Barkefors","year":"2011","journal-title":"J Biol Chem"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1126\/science.1184096","article-title":"A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis","volume":"327(5969)","author":"D Wang","year":"2010","journal-title":"Science"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/nrn919","article-title":"Is there more to GABA than synaptic inhibition?","volume":"3(9)","author":"DF Owens","year":"2002","journal-title":"Nat Rev Neurosci"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"32","DOI":"10.4161\/psb.6.1.14318","article-title":"Does GABA increase the efficiency of symbiotic N2 fixation in legumes?","volume":"6(1)","author":"S Sulieman","year":"2011","journal-title":"Plant Signal Behav"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"13124","DOI":"10.1073\/pnas.0900689106","article-title":"Normal growth of <italic>Arabidopsis<\/italic> requires cytosolic invertase but not sucrose synthase","volume":"106(31)","author":"DH Barratt","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1111\/j.1469-8137.2009.02871.x","article-title":"Presymbiotic factors released by the arbuscular mycorrhizal fungus <italic>Gigaspora margarita<\/italic> induce starch accumulation in <italic>Lotus japonicus<\/italic> roots","volume":"183(1)","author":"C Gutjahr","year":"2009","journal-title":"New Phytol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1042\/BJ20110078","article-title":"The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs","volume":"436(1)","author":"B O'Leary","year":"2011","journal-title":"Biochem J"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1093\/pcp\/pcj028","article-title":"Phosphoenolpyruvate carboxylase plays a crucial role in limiting nitrogen fixation in <italic>Lotus japonicus<\/italic> nodules","volume":"47(5)","author":"M Nomura","year":"2006","journal-title":"Plant Cell Physiol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"2959","DOI":"10.1093\/jxb\/err009","article-title":"Nodulation enhances dark CO2 fixation and recycling in the model legume <italic>Lotus japonicus<\/italic>","volume":"62(8)","author":"MN Fotelli","year":"2011","journal-title":"J Exp Bot"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.phytochem.2006.09.021","article-title":"Nitrogen transport in the ectomycorrhiza association: the <italic>Hebeloma cylindrosporum-Pinus pinaster<\/italic> model","volume":"68(1)","author":"T Muller","year":"2007","journal-title":"Phytochem"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/gb-2006-7-4-212","article-title":"Plant NBS-LRR proteins: adaptable guards","volume":"7(4)","author":"L McHale","year":"2006","journal-title":"Genome Biol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1146\/annurev.phyto.42.040803.140421","article-title":"Systemic acquired resistence","volume":"42","author":"WE Durrant","year":"2004","journal-title":"An Rev Phytopatol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1016\/S0092-8674(03)00429-X","article-title":"Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes","volume":"113(7)","author":"Z Mou","year":"2003","journal-title":"Cell"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"e 8399","DOI":"10.1371\/journal.pone.0008399","article-title":"NPR1 protein regulates pathogenic and symbiotic interactions between <italic>Rhizobium<\/italic> and legumes and non-legumes","volume":"4(12)","author":"S Peleg-Grossman","year":"2009","journal-title":"PLoS One"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.tplants.2009.08.002","article-title":"One for all: the receptor-associated kinase BAK1","volume":"14(10)","author":"D Chinchilla","year":"2009","journal-title":"Trends Plant Sci"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.chom.2008.05.017","article-title":"Bacterial effectors target the common signaling partner BAK1 to disrupt multiple MAMP receptor-signaling complexes and impede plant immunity","volume":"4(1)","author":"L Shan","year":"2008","journal-title":"Cell Host Microbe"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1016\/j.cub.2011.05.033","article-title":"A secreted effector protein of <italic>Laccaria bicolor<\/italic> is required for symbiosis development","volume":"21(14)","author":"JM Plett","year":"2011","journal-title":"Curr Biol"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1038\/nature00842","article-title":"A receptor kinase gene regulating symbiotic nodule development","volume":"417(6892)","author":"G Endre","year":"2002","journal-title":"Nature"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"14348","DOI":"10.1073\/pnas.1107912108","article-title":"Nuclear membranes control symbiotic calcium signaling of legumes","volume":"108(34)","author":"W Capoen","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1741-7007-7-13","article-title":"The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses","volume":"7","author":"DS Hibbett","year":"2009","journal-title":"BMC Biol"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1111\/j.1365-313X.2010.04411.x","article-title":"From defense to symbiosis: limited alterations in the kinase domain of LysM receptor-like kinases are crucial for evolution of legume\u2013<italic>Rhizobium<\/italic> symbiosis","volume":"65","author":"T Nakagawa","year":"2011","journal-title":"Plant J"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1006\/abio.1994.1538","article-title":"A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (<italic>Gossypium hirsutum<\/italic> L.)","volume":"223(1)","author":"CY Wan","year":"1994","journal-title":"Anal Biochem"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1101\/gr.1917404","article-title":"Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs","volume":"14(6)","author":"B Chevreux","year":"2004","journal-title":"Genome Res"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1186\/1471-2105-9-386","article-title":"The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes","volume":"9","author":"F Meyer","year":"2008","journal-title":"BMC Bioinform"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215(3)","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research","volume":"21(18)","author":"A Conesa","year":"2005","journal-title":"Bioinform"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1186\/1471-2105-12-480","article-title":"GC-content normalization for RNA-Seq data","volume":"12","author":"D Risso","year":"2011","journal-title":"BMC Bioinform"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26(1)","author":"MD Robinson","year":"2010","journal-title":"Bioinform"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40(10)","author":"DJ McCarthy","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57(1)","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Series B (Methodological)"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method","volume":"25","author":"KJ Livak","year":"2001","journal-title":"Methods"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0098376","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,4]],"date-time":"2022-04-04T14:06:27Z","timestamp":1649081187000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0098376"}},"subtitle":[],"editor":[{"given":"Richard A.","family":"Wilson","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,5,23]]},"references-count":87,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2014,5,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0098376","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,23]]}}}