Smith SE, Read DJ. Mycorrhizal symbiosis. London: Academic Press; 2008.
Hibbett DS, Gilbert L-B, Donoghue MJ. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature. 2000;407:506–8.
Article
CAS
PubMed
Google Scholar
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, et al. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet. 2015;47:410–5.
Article
CAS
PubMed
Google Scholar
Agerer R. Exploration types of ectomycorrhizae. Mycorrhiza. 2001;11:107–14.
Article
Google Scholar
Burgess T, Dell B, Malajczuk N. Variation in mycorrhizal development and growth stimulation by 20 Pisolithus isolates inoculated on to Eucalyptus grandis W. Hill ex Maiden New Phytologist. 1994;127:731-9.
Lu X, Malajczuk N, Dell B. Mycorrhiza formation and growth of Eucalyptus globulus seedlings inoculated with spores of various ectomycorrhizal fungi. Mycorrhiza. 1998;8:81–6.
Article
Google Scholar
Pena R, Polle A. Attributing functions to ectomycorrhizal fungal identities in assemblages for nitrogen acquisition under stress. ISME J. 2014;8:321–30.
Article
CAS
PubMed
Google Scholar
Plett JM, Tisserant E, Brun A, Morin E, Grigoriev IV, Kuo A, et al. The mutualist Laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses. MPMI. 2014;28:261–73.
Article
CAS
Google Scholar
Tisserant E, Silva CD, Kohler A, Morin E, Wincker P, Martin F. Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome. New Phytol. 2011;189:883–91.
Article
CAS
PubMed
Google Scholar
Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, et al. The genome of Eucalyptus grandis. Nature. 2014;510:356–62.
Article
CAS
PubMed
Google Scholar
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497:579–84.
Article
CAS
PubMed
Google Scholar
Plomion C, Aury J-M, Amselem J, Leroy T, Murat F, Duplessis S, et al. Oak genome reveals facets of long lifespan. Nature Plants. 2018;4:440.
Article
CAS
PubMed
PubMed Central
Google Scholar
Staton M, Zhebentyayeva T, Olukolu B, Fang GC, Nelson D, Carlson JE, et al. Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics. 2015;16:744.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, et al. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 2014;196:875–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barker SJ, Tagu D, Delp G. Regulation of root and fungal morphogenesis in mycorrhizal symbioses. Plant Physiol. 1998;116:1201–7.
Article
CAS
Google Scholar
Laurans F, Pepin R, Gay G. Fungal auxin overproduction affects the anatomy of Hebeloma cylindrosporum–Pinus pinaster ectomycorrhizas. Tree Physiol. 2001;21:533–40.
Article
CAS
PubMed
Google Scholar
Herrmann S, Munch J-C, Buscot F. A gnotobiotic culture system with oak microcuttings to study specific effects of mycobionts on plant morphology before, and in the early phase of, ectomycorrhiza formation by Paxillus involutus and Piloderma croceum. New Phytol. 1998;138:203–12.
Article
PubMed
Google Scholar
Buscot F, Herrmann S. At the frontier between basiodiomycotes and plants: reciprocal interactions between mycorrhiza formation and root development in an in vitro system with oaks and hymenomycetes. In: Agerer R, Piepenbring M, Blanz P (eds), Frontiers in Basidiomycote mycology. Eching IHW-Verlag; 2004. pp. 361-76.
Sarjala T, Niemi K, Häggman H. Mycorrhiza formation is not needed for early growth induction and growth-related changes in polyamines in scots pine seedlings in vitro. Plant Physiol Biochem. 2010;48:596–601.
Article
CAS
PubMed
Google Scholar
Duplessis S, Courty P-E, Tagu D, Martin F. Transcript patterns associated with ectomycorrhiza development in Eucalyptus globulus and Pisolithus microcarpus. New Phytol. 2005;165:599–611.
Article
CAS
PubMed
Google Scholar
Plett JM, Kohler A, Khachane A, Keniry K, Plett KL, Martin F, et al. The effect of elevated carbon dioxide on the interaction between Eucalyptus grandis and diverse isolates of Pisolithus sp. is associated with a complex shift in the root transcriptome. New Phytol. 2015;206:1423–36.
Article
CAS
PubMed
Google Scholar
Sebastiana M, Vieira B, Lino-Neto T, Monteiro F, Figueiredo A, Sousa L, et al. Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling. PLoS One. 2014;9:e98376.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tarkka MT, Herrmann S, Wubet T, Feldhahn L, Recht S, Kurth F, et al. OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis. New Phytol. 2013;199:529–40.
Article
CAS
PubMed
Google Scholar
Garcia K, Delaux P-M, Cope KR, Ané J-M. Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses. New Phytol. 2015;208:79–87.
Article
PubMed
Google Scholar
Herrmann S, Recht S, Boenn M, Feldhahn L, Angay O, Fleischmann F, et al. Endogenous rhythmic growth in oak trees is regulated by internal clocks rather than resource availability. J Exp Bot. 2015;66:7113-27.
Kaling M, Schmidt A, Moritz F, Rosenkranz M, Witting M, Kasper K, et al. Mycorrhiza-triggered transcriptomic and metabolomic networks impinge on herbivore fitness. Plant Physiol. 2018;176:2639–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurth F, Feldhahn L, Bönn M, Herrmann S, Buscot F, Tarkka MT. Large scale transcriptome analysis reveals interplay between development of forest trees and a beneficial mycorrhiza helper bacterium. BMC Genomics. 2015;16:658.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu J, Maldonado-Mendoza I, Lopez-Meyer M, Cheung F, Town CD, Harrison MJ. Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots. Plant J. 2007;50:529–44.
Article
CAS
PubMed
Google Scholar
Loewe A, Einig W, Shi L, Dizengremel P, Hampp R. Mycorrhiza formation and elevated CO2 both increase the capacity for sucrose synthesis in source leaves of spruce and aspen. New Phytol. 2000;145:565–74.
Article
CAS
PubMed
Google Scholar
Luo Z-B, Li K, Gai Y, Göbel C, Wildhagen H, Jiang X, et al. The ectomycorrhizal fungus (Paxillus involutus) modulates leaf physiology of poplar towards improved salt tolerance. Environ Exp Bot. 2011;72:304–11.
Article
CAS
Google Scholar
Wright DP, Johansson T, Le Quéré A, Söderström B, Tunlid A. Spatial patterns of gene expression in the extramatrical mycelium and mycorrhizal root tips formed by the ectomycorrhizal fungus Paxillus involutus in association with birch (Betula pendula) seedlings in soil microcosms. New Phytol. 2005;167:579–96.
Article
CAS
PubMed
Google Scholar
Plett JM, Daguerre Y, Wittulsky S, Vayssières A, Deveau A, Melton SJ, et al. Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes. PNAS. 2014:201322671.
Ray P, Craven KD. Sebacina vermifera: a unique root symbiont with vast agronomic potential. World J Microbiol Biotechnol. 2016;32:16.
Article
PubMed
Google Scholar
Weiss M, Selosse M-A, Rexer K-H, Urban A, Oberwinkler F. Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential. Mycol Res. 2004;108:1003–10.
Article
PubMed
Google Scholar
Oberwinkler F, Riess K, Bauer R, Selosse M-A, Weiß M, Garnica S, et al. Enigmatic Sebacinales. Mycol Progress. 2013;12:1–27.
Article
Google Scholar
Wang Q, He XH, Guo L-D. Ectomycorrhizal fungus communities of Quercus liaotungensis Koidz of different ages in a northern China temperate forest. Mycorrhiza. 2012;22:461–70.
Article
PubMed
Google Scholar
Barazani O, von Dahl CC, Baldwin IT. Sebacina vermifera promotes the growth and fitness of Nicotiana attenuata by inhibiting ethylene signaling. Plant Physiol. 2007;144:1223–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ghimire SR, Charlton ND, Craven KD. The mycorrhizal fungus, Sebacina vermifera, enhances seed germination and biomass production in switchgrass (Panicum virgatum L). Bioenerg Res. 2009;2:51–8.
Article
Google Scholar
Lahrmann U, Strehmel N, Langen G, Frerigmann H, Leson L, Ding Y, et al. Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity. New Phytol. 2015;207:841–57.
Article
CAS
PubMed
Google Scholar
Herrmann S, Buscot F. Cross talks at the morphogenetic, physiological and gene regulation levels between the mycobiont Piloderma croceum and oak microcuttings (Quercus robur) during formation of ectomycorrhizas. Phytochemistry. 2007;68:52–67.
Article
CAS
PubMed
Google Scholar
Frettinger P, Derory J, Herrmann S, Plomion C, Lapeyrie F, Oelmüller R, et al. Transcriptional changes in two types of pre-mycorrhizal roots and in ectomycorrhizas of oak microcuttings inoculated with Piloderma croceum. Planta. 2007;225:331–40.
Article
CAS
PubMed
Google Scholar
Herrmann S, Oelmüller R, Buscot F. Manipulation of the onset of ectomycorrhiza formation by indole-3-acetic acid, activated charcoal or relative humidity in the association between oak microcuttings and Piloderma croceum: influence on plant development and photosynthesis. J Plant Physiol. 2004;161:509–17.
Article
CAS
PubMed
Google Scholar
Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11:R14.
Article
PubMed
PubMed Central
CAS
Google Scholar
Deeken R, Ache P, Kajahn I, Klinkenberg J, Bringmann G, Hedrich R. Identification of Arabidopsis thaliana phloem RNAs provides a search criterion for phloem-based transcripts hidden in complex datasets of microarray experiments. Plant J. 2008;55:746–59.
Article
CAS
PubMed
Google Scholar
Doering-Saad C, Newbury HJ, Couldridge CE, Bale JS, Pritchard J. A phloem-enriched cDNA library from Ricinus: insights into phloem function. J Exp Bot. 2006;57:3183–93.
Article
CAS
PubMed
Google Scholar
Kanehira A, Yamada K, Iwaya T, Tsuwamoto R, Kasai A, Nakazono M, et al. Apple phloem cells contain some mRNAs transported over long distances. Tree Genet Genomes. 2010;6:635–42.
Article
Google Scholar
Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, et al. Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nature Plants. 2015;1:15025.
Article
CAS
PubMed
Google Scholar
Parladé J, Pera J, Alvarez IF. Inoculation of containerized Pseudotsuga menziesii and Pinus pinaster seedlings with spores of five species of ectomycorrhizal fungi. Mycorrhiza. 1996;6:237–45.
Article
Google Scholar
Pellegrin C, Daguerre Y, Ruytinx J, Guinet F, Kemppainen M, Frey NF dit, et al. Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis. Environ Microbiol. 2019;21:3765–3779.
Kang H, Chen X, Kemppainen M, Pardo AG, Veneault-Fourrey C, Kohler A, et al. The small secreted effector protein MiSSP7.6 of Laccaria bicolor is required for the establishment of ectomycorrhizal symbiosis. Environ Microbiol. 2020;22:1435–46.
Article
CAS
PubMed
Google Scholar
Plett JM, Martin F. Poplar root exudates contain compounds that induce the expression of MiSSP7 in Laccaria bicolor. Plant Signal Behav. 2012;7:12–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang F, Anasontzis GE, Labourel A, Champion C, Haon M, Kemppainen M, et al. The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted β-1,4 endoglucanase that plays a key role in symbiosis development. New Phytol. 2018;220:1309–21.
Article
CAS
PubMed
Google Scholar
Plett JM, Plett KL, Bithell SL, Mitchell C, Moore K, Powell JR, et al. Improved Phytophthora resistance in commercial chickpea (Cicer arietinum) varieties negatively impacts symbiotic gene signalling and symbiotic potential in some varieties. Plant Cell Environ. 2016;39:1858–69.
Article
CAS
PubMed
Google Scholar
Kanter U, Usadel B, Guerineau F, Li Y, Pauly M, Tenhaken R. The inositol oxygenase gene family of Arabidopsis is involved in the biosynthesis of nucleotide sugar precursors for cell-wall matrix polysaccharides. Planta. 2005;221:243–54.
Article
CAS
PubMed
Google Scholar
Le Quéré A, Wright DP, Söderström B, Tunlid A, Johansson T. Global patterns of gene regulation associated with the development of ectomycorrhiza between birch (Betula pendula Roth.) and Paxillus involutus (Batsch) Fr. Mol Plant Microbe Interact. 2005;18:659–73.
Article
PubMed
CAS
Google Scholar
Felten J, Kohler A, Morin E, Bhalerao RP, Palme K, Martin F, et al. The ectomycorrhizal fungus Laccaria bicolor stimulates lateral root formation in poplar and Arabidopsis through auxin transport and signaling. Plant Physiol. 2009;151:1991–2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sukumar P, Legué V, Vayssières A, Martin F, Tuskan GA, Kalluri UC. Involvement of auxin pathways in modulating root architecture during beneficial plant–microorganism interactions. Plant Cell Environ. 2013;36:909–19.
Article
CAS
PubMed
Google Scholar
Vayssières A, Pěnčík A, Felten J, Kohler A, Ljung K, Martin F, et al. Development of the poplar-Laccaria bicolor ectomycorrhiza modifies root auxin metabolism, signaling, and response. Plant Physiol. 2015;169:890–902.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cope KR, Bascaules A, Irving TB, Venkateshwaran M, Maeda J, Garcia K, et al. The ectomycorrhizal fungus Laccaria bicolor produces lipochitooligosaccharides and uses the common symbiosis pathway to colonize Populus roots. Plant Cell. 2019;31:2386–410.
Article
CAS
PubMed
PubMed Central
Google Scholar
Plett JM, Gibon J, Kohler A, Duffy K, Hoegger PJ, Velagapudi R, et al. Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor. Fungal Genet Biol. 2012;49:199–209.
Article
CAS
PubMed
Google Scholar
Morel M, Jacob C, Kohler A, Johansson T, Martin F, Chalot M, et al. Identification of genes differentially expressed in extraradical mycelium and ectomycorrhizal roots during Paxillus involutus-Betula pendula ectomycorrhizal symbiosis. Appl Environ Microbiol. 2005;71:382–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Santner A, Estelle M. Recent advances and emerging trends in plant hormone signalling. Nature. 2009;459:1071–8.
Article
CAS
PubMed
Google Scholar
Hause B, Mrosk C, Isayenkov S, Strack D. Jasmonates in arbuscular mycorrhizal interactions. Phytochemistry. 2007;68:101–10.
Article
CAS
PubMed
Google Scholar
Luo Z-B, Li K, Jiang X, Polle A. Ectomycorrhizal fungus (Paxillus involutus) and hydrogels affect performance of Populus euphratica exposed to drought stress. Ann For Sci. 2009;66:106p1–10.
Article
CAS
Google Scholar
Kurth F, Mailänder S, Bönn M, Feldhahn L, Herrmann S, Große I, et al. Streptomyces-induced resistance against oak powdery mildew involves host plant responses in defense, photosynthesis, and secondary metabolism pathways. MPMI. 2014;27:891–900.
Article
CAS
PubMed
Google Scholar
Perotto S, Rodda M, Benetti A, Sillo F, Ercole E, Rodda M, et al. Gene expression in mycorrhizal orchid protocorms suggests a friendly plant–fungus relationship. Planta. 2014;239:1337–49.
Article
CAS
PubMed
Google Scholar
Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nürnberger T, Jones JDG, et al. A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature. 2007;448:497–500.
Article
CAS
PubMed
Google Scholar
Saijo Y, Loo EP, Yasuda S. Pattern recognition receptors and signaling in plant–microbe interactions. Plant J. 2018;93:592–613.
Article
CAS
PubMed
Google Scholar
Strullu-Derrien C, Selosse M-A, Kenrick P, Martin FM. The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. New Phytol. 2018;220:1012–30.
Article
PubMed
Google Scholar
Martin F, Kohler A, Murat C, Veneault-Fourrey C, Hibbett DS. Unearthing the roots of ectomycorrhizal symbioses. Nat Rev Microbiol. 2016;14:760–73.
Article
CAS
PubMed
Google Scholar
Marx DH. The influence of ectotrophic mycorrhizal fungi on the resistance of pine roots to pathogenic infections. I. Antagonism of mycorrhizal fungi to root pathogenic fungi and soil bacteria. Phytopathology. 1969;59:153–63.
Google Scholar
R Core Team. R: A language and environment for statistical computing. 2013.
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Article
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Article
CAS
PubMed
Google Scholar
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36:3420–35.
Article
PubMed
PubMed Central
CAS
Google Scholar
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32(suppl_1):D258–61.
CAS
PubMed
Google Scholar
Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2014;42:D699–704.
Article
CAS
PubMed
Google Scholar
Shah F, Nicolás C, Bentzer J, Ellström M, Smits M, Rineau F, et al. Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. New Phytol. 2016;209:1705–19.
Article
CAS
PubMed
Google Scholar
Pfaffl MW, Horgan GW, Dempfle L. Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res. 2002;30:e36.
Article
PubMed
PubMed Central
Google Scholar