TY - BOOK AU - Smith, S. E. AU - Read, D. J. PY - 2008 DA - 2008// TI - Mycorrhizal symbiosis PB - Elsevier Academic Pres CY - Amsterdam ID - Smith2008 ER - TY - JOUR AU - Cumming, J. R. AU - Zawaski, C. AU - Desai, S. AU - Collart, F. R. PY - 2015 DA - 2015// TI - Phosphorus disequilibrium in the tripartite plant-ectomycorrhiza-plant growth promoting rhizobacterial association JO - J Soil Sci Plant Nutr VL - 15 ID - Cumming2015 ER - TY - JOUR AU - Compant, S. AU - Clement, C. AU - Sessitsch, A. PY - 2010 DA - 2010// TI - Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization JO - Soil Biol Biochem VL - 42 UR - https://doi.org/10.1016/j.soilbio.2009.11.024 DO - 10.1016/j.soilbio.2009.11.024 ID - Compant2010 ER - TY - JOUR AU - Finlay, R. D. PY - 2008 DA - 2008// TI - Ecological aspects of mycorrhizal symbiosis: with special emphasis on the functional diversity of interactions involving the extraradical mycelium JO - J Exp Bot VL - 59 UR - https://doi.org/10.1093/jxb/ern059 DO - 10.1093/jxb/ern059 ID - Finlay2008 ER - TY - STD TI - Dimkpa C, Weinand T, Asch F. Plant-rhizobacteria interactions alleviate abiotic stress conditions. Plant Cell Environ. 2009;32(12):1682–94. ID - ref5 ER - TY - JOUR AU - Podila, G. K. AU - Sreedasyam, A. AU - Muratet, M. A. PY - 2009 DA - 2009// TI - Populus rhizosphere and the ectomycorrhizal interactome JO - Crit Rev Plant Sci VL - 28 UR - https://doi.org/10.1080/07352680903241220 DO - 10.1080/07352680903241220 ID - Podila2009 ER - TY - JOUR AU - Ortiz-Castro, R. AU - Contreras-Cornejo, H. A. AU - Macias-Rodriguez, L. AU - Lopez-Bucio, J. PY - 2009 DA - 2009// TI - The role of microbial signals in plant growth and development JO - Plant Signal Behav VL - 4 UR - https://doi.org/10.4161/psb.4.8.9047 DO - 10.4161/psb.4.8.9047 ID - Ortiz-Castro2009 ER - TY - JOUR AU - Garcia, K. AU - Delaux, P. M. AU - Cope, K. R. AU - Ane, J. M. PY - 2015 DA - 2015// TI - Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses JO - New Phytol VL - 208 UR - https://doi.org/10.1111/nph.13423 DO - 10.1111/nph.13423 ID - Garcia2015 ER - TY - JOUR PY - 1994 DA - 1994// JO - Acta Botanica Gallica VL - 141 UR - https://doi.org/10.1080/12538078.1994.10515192 DO - 10.1080/12538078.1994.10515192 ID - ref9 ER - TY - JOUR AU - Deveau, A. AU - Palin, B. AU - Delaruelle, C. AU - Peter, M. AU - Kohler, A. AU - Pierrat, J. C. PY - 2007 DA - 2007// TI - The mycorrhiza helper Pseudomonas fluorescens BBc6R8 has a specific priming effect on the growth, morphology and gene expression of the ectomycorrhizal fungus Laccaria bicolor S238N JO - New Phytol VL - 175 UR - https://doi.org/10.1111/j.1469-8137.2007.02148.x DO - 10.1111/j.1469-8137.2007.02148.x ID - Deveau2007 ER - TY - STD TI - Labbe JL, Weston DJ, Dunkirk N, Pelletier DA, Tuskan GA. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus. Front Plant Sci. 2014;5. ID - ref11 ER - TY - JOUR AU - Navarro-Rodenas, A. AU - Berna, L. M. AU - Lozano-Carrillo, C. AU - Andrino, A. AU - Morte, A. PY - 2016 DA - 2016// TI - Beneficial native bacteria improve survival and mycorrhization of desert truffle mycorrhizal plants in nursery conditions JO - Mycorrhiza VL - 26 UR - https://doi.org/10.1007/s00572-016-0711-6 DO - 10.1007/s00572-016-0711-6 ID - Navarro-Rodenas2016 ER - TY - JOUR AU - Roesti, D. AU - Ineichen, K. AU - Braissant, O. AU - Redecker, D. AU - Wiemken, A. AU - Aragno, M. PY - 2005 DA - 2005// TI - Bacteria associated with spores of the arbuscular mycorrhizal fungi Glomus geosporum and Glomus constrictum JO - Appl Environ Microbiol VL - 71 UR - https://doi.org/10.1128/AEM.71.11.6673-6679.2005 DO - 10.1128/AEM.71.11.6673-6679.2005 ID - Roesti2005 ER - TY - JOUR AU - Frey-Klett, P. AU - Burlinson, P. AU - Deveau, A. AU - Barret, M. AU - Tarkka, M. AU - Sarniguet, A. PY - 2011 DA - 2011// TI - Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists JO - Microbiol Mol Biol Rev VL - 75 UR - https://doi.org/10.1128/MMBR.00020-11 DO - 10.1128/MMBR.00020-11 ID - Frey-Klett2011 ER - TY - JOUR AU - Frey-Klett, P. AU - Garbaye, J. AU - Tarkka, M. PY - 2007 DA - 2007// TI - The mycorrhiza helper bacteria revisited JO - New Phytol VL - 176 UR - https://doi.org/10.1111/j.1469-8137.2007.02191.x DO - 10.1111/j.1469-8137.2007.02191.x ID - Frey-Klett2007 ER - TY - JOUR AU - Miransari, M. PY - 2011 DA - 2011// TI - Interactions between arbuscular mycorrhizal fungi and soil bacteria JO - Appl Microbiol Biot VL - 89 UR - https://doi.org/10.1007/s00253-010-3004-6 DO - 10.1007/s00253-010-3004-6 ID - Miransari2011 ER - TY - JOUR AU - Mosse, B. PY - 1962 DA - 1962// TI - The establishment of vesicular-arbuscular mycorrhiza under aseptic conditions JO - J Gen Microbiol VL - 27 UR - https://doi.org/10.1099/00221287-27-3-509 DO - 10.1099/00221287-27-3-509 ID - Mosse1962 ER - TY - STD TI - Kurth F, Feldhahn L, Bonn 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. ID - ref18 ER - TY - JOUR AU - Martin, F. AU - Duplessis, S. AU - Ditengou, F. AU - Lagrange, H. AU - Voiblet, C. AU - Lapeyrie, F. PY - 2001 DA - 2001// TI - Developmental cross talking in the ectomycorrhizal symbiosis: signals and communication genes JO - New Phytol VL - 151 UR - https://doi.org/10.1046/j.1469-8137.2001.00169.x DO - 10.1046/j.1469-8137.2001.00169.x ID - Martin2001 ER - TY - STD TI - Plett JM, Martin F. Mutualistic effectors: architects of symbiosis. In: Martin F, Kamoun S, editors. Effectors in plant-microbe interactions. Hoboken: Wiley; 2012. p. 295–326. ID - ref20 ER - TY - JOUR AU - Schrey, S. D. AU - Schellhammer, M. AU - Ecke, M. AU - Hampp, R. AU - Tarkka, M. T. PY - 2005 DA - 2005// TI - Mycorrhiza helper bacterium Streptomyces AcH 505 induces differential gene expression in the ectomycorrhizal fungus amanita muscaria JO - New Phytol VL - 168 UR - https://doi.org/10.1111/j.1469-8137.2005.01518.x DO - 10.1111/j.1469-8137.2005.01518.x ID - Schrey2005 ER - TY - JOUR AU - Noirot-Gros, M. F. AU - Shinde, S. AU - Larsen, P. E. AU - Zerbs, S. AU - Korajczyk, P. J. AU - Kemner, K. M. PY - 2018 DA - 2018// TI - Dynamics of aspen roots colonization by pseudomonads reveals strain-specific and mycorrhizal-specific patterns of biofilm formation JO - Front Microbiol VL - 9 UR - https://doi.org/10.3389/fmicb.2018.00853 DO - 10.3389/fmicb.2018.00853 ID - Noirot-Gros2018 ER - TY - STD TI - Shinde S, Cumming JR, Collart FR, Noirot PH, Larsen PE. Pseudomonas fluorescens transportome is linked to strain-specific plant growth promotion in aspen seedlings under nutrient stress. Front Plant Sci. 2017;8:348. ID - ref23 ER - TY - JOUR AU - Larsen, P. E. AU - Collart, F. R. PY - 2012 DA - 2012// TI - BowStrap v1.0: assigning statistical significance to expressed genes using short-read transcriptome data JO - BMC Res Notes VL - 5 UR - https://doi.org/10.1186/1756-0500-5-275 DO - 10.1186/1756-0500-5-275 ID - Larsen2012 ER - TY - JOUR AU - Lugtenberg, B. AU - Kamilova, F. PY - 2009 DA - 2009// TI - Plant-growth-promoting rhizobacteria JO - Annu Rev Microbiol VL - 63 UR - https://doi.org/10.1146/annurev.micro.62.081307.162918 DO - 10.1146/annurev.micro.62.081307.162918 ID - Lugtenberg2009 ER - TY - JOUR AU - Plett, J. M. AU - Daguerre, Y. AU - Wittulsky, S. AU - Vayssieres, A. AU - Deveau, A. AU - Melton, S. J. PY - 2014 DA - 2014// TI - Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1322671111 DO - 10.1073/pnas.1322671111 ID - Plett2014 ER - TY - STD TI - Martin G. Suppression and activation of the plant immune system by Pseudomonas syringae effectors AvrPto and AvrPtoB. In: Martin F, Kamoun S, editors. Effectors in plant-microbe interactions. Hoboken: Wiley; 2012. p. 123–54. ID - ref27 ER - TY - JOUR AU - Jones, J. D. G. AU - Dangl, J. L. PY - 2006 DA - 2006// TI - The plant immune system JO - Nature VL - 444 UR - https://doi.org/10.1038/nature05286 DO - 10.1038/nature05286 ID - Jones2006 ER - TY - JOUR AU - Knox, R. B. PY - 1976 DA - 1976// TI - Cell recognition in plants: determinants of the stigma surface and their pollen interactions JO - Proc Natl Acad Sci U S A VL - 8 UR - https://doi.org/10.1073/pnas.73.8.2788 DO - 10.1073/pnas.73.8.2788 ID - Knox1976 ER - TY - JOUR AU - Hiscock, S. J. PY - 2002 DA - 2002// TI - Pollen recognition during the self-incompatibility response in plants JO - Genome Biol VL - 3 UR - https://doi.org/10.1186/gb-2002-3-2-reviews1004 DO - 10.1186/gb-2002-3-2-reviews1004 ID - Hiscock2002 ER - TY - STD TI - Phytozome. Available from: https://phytozome.jgi.doe.gov. UR - https://phytozome.jgi.doe.gov ID - ref31 ER - TY - JOUR AU - Wilkins, K. A. AU - Poulter, N. S. AU - Franklin-Tong, V. E. PY - 2014 DA - 2014// TI - Taking one for the team: self-recognition and cell suicide in pollen JO - J Exp Bot VL - 65 UR - https://doi.org/10.1093/jxb/ert468 DO - 10.1093/jxb/ert468 ID - Wilkins2014 ER - TY - JOUR AU - Franceschi, P. AU - Dondini, L. AU - Sanzol, J. PY - 2012 DA - 2012// TI - Molecular bases and evolutionary dynamics of self-incompatibility in the Pyrinae (Rosaceae) JO - J Exp Bot VL - 63 UR - https://doi.org/10.1093/jxb/ers108 DO - 10.1093/jxb/ers108 ID - Franceschi2012 ER - TY - JOUR AU - Watanabe, M. AU - Suwabe, K. AU - Suzuki, G. PY - 2012 DA - 2012// TI - Molecular genetics, physiology and biology of self-incompatibility in Brassicaceae JO - P Jpn Acad B-Phys VL - 88 UR - https://doi.org/10.2183/pjab.88.519 DO - 10.2183/pjab.88.519 ID - Watanabe2012 ER - TY - JOUR AU - Slavov, G. T. AU - DiFazio, S. P. AU - Martin, J. AU - Schackwitz, W. AU - Muchero, W. AU - Rodgers-Melnick, E. PY - 2012 DA - 2012// TI - Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa JO - New Phytol VL - 196 UR - https://doi.org/10.1111/j.1469-8137.2012.04258.x DO - 10.1111/j.1469-8137.2012.04258.x ID - Slavov2012 ER - TY - JOUR AU - Vigue, L. M. AU - Lindroth, R. L. PY - 2010 DA - 2010// TI - Effects of genotype, elevated CO2 and elevated O3 on aspen phytochemistry and aspen leaf beetle Chrysomela crotchi performance JO - Agric For Entomol VL - 12 ID - Vigue2010 ER - TY - JOUR AU - Wullschleger, S. D. AU - Weston, D. J. AU - DiFazio, S. P. AU - Tuskan, G. A. PY - 2013 DA - 2013// TI - Revisiting the sequencing of the first tree genome: Populus trichocarpa JO - Tree Physiol VL - 33 UR - https://doi.org/10.1093/treephys/tps081 DO - 10.1093/treephys/tps081 ID - Wullschleger2013 ER - TY - JOUR AU - Tuskan, G. A. AU - Difazio, S. AU - Jansson, S. AU - Bohlmann, J. AU - Grigoriev, I. AU - Hellsten, U. PY - 2006 DA - 2006// TI - The genome of black cottonwood, Populus trichocarpa (Torr. & gray) JO - Science VL - 313 UR - https://doi.org/10.1126/science.1128691 DO - 10.1126/science.1128691 ID - Tuskan2006 ER - TY - JOUR AU - Martin, F. AU - Aerts, A. AU - Ahren, D. AU - Brun, A. AU - Danchin, E. G. J. AU - Duchaussoy, F. PY - 2008 DA - 2008// TI - The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis JO - Nature VL - 452 UR - https://doi.org/10.1038/nature06556 DO - 10.1038/nature06556 ID - Martin2008 ER - TY - STD TI - Mycosm J. Available from: https://genome.jgi.doe.gov/programs/fungi/index.jsf. UR - https://genome.jgi.doe.gov/programs/fungi/index.jsf ID - ref40 ER - TY - JOUR AU - Silby, M. W. AU - Cerdeno-Tarraga, A. M. AU - Vernikos, G. S. AU - Giddens, S. R. AU - Jackson, R. W. AU - Preston, G. M. PY - 2009 DA - 2009// TI - Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-5-r51 DO - 10.1186/gb-2009-10-5-r51 ID - Silby2009 ER - TY - JOUR AU - Preston, G. M. AU - Bertrand, N. AU - Rainey, P. B. PY - 2001 DA - 2001// TI - Type III secretion in plant growth-promoting Pseudomonas fluorescens SBW25 JO - Mol Microbiol VL - 41 UR - https://doi.org/10.1046/j.1365-2958.2001.02560.x DO - 10.1046/j.1365-2958.2001.02560.x ID - Preston2001 ER - TY - STD TI - NCBI. Available from: https://www.ncbi.nlm.nih.gov/genome. UR - https://www.ncbi.nlm.nih.gov/genome ID - ref43 ER - TY - JOUR AU - Cumming, J. R. AU - Swiger, T. D. AU - Kurnik, B. S. AU - Panaccione, D. G. PY - 2001 DA - 2001// TI - Organic acid exudation by Laccaria bicolor and Pisolithus tinctorius exposed to aluminum in vitro JO - Can J For Res VL - 31 ID - Cumming2001 ER - TY - STD TI - Molina R, Palmer J. Isolation, maintenance and pure culture manipulation of ectomycorrhizal fungi. In: Schenck N, editor. Methods and principles of mycorrhizal research. St. Paul: APS Press; 1982. p. 115–29. ID - ref45 ER - TY - JOUR AU - Baum, C. AU - Weih, M. AU - Verwijst, T. AU - Makeschin, F. PY - 2002 DA - 2002// TI - The effects of nitrogen fertilization and soil properties on mycorrhizal formation of Salix viminalis JO - Forest Ecol Manag VL - 160 UR - https://doi.org/10.1016/S0378-1127(01)00470-4 DO - 10.1016/S0378-1127(01)00470-4 ID - Baum2002 ER - TY - JOUR AU - Brundrett, M. C. AU - Piche, Y. AU - Peterson, R. L. PY - 1984 DA - 1984// TI - A new method for observing the morphology of vesicular-arbuscular mycorrhizae JO - Can J Bot VL - 62 UR - https://doi.org/10.1139/b84-290 DO - 10.1139/b84-290 ID - Brundrett1984 ER - TY - CHAP AU - Brundrett, M. C. AU - Bougher, N. AU - Dell, B. AU - Grove, T. AU - Malajczuk, N. ED - Lynch, P. PY - 1996 DA - 1996// TI - Examining mycorrhizal associations BT - Mycorrhizas for forestry and agriculture: ACIAR ID - Brundrett1996 ER - TY - STD TI - QIAGEN. Available from: https://www.qiagen.com/us/resources. UR - https://www.qiagen.com/us/resources ID - ref49 ER - TY - STD TI - Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3). ID - ref50 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate - a practical and powerfula to multiple testing JO - J R Stat Soc Ser B Methodol VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Bolstad, B. M. AU - Irizarry, R. A. AU - Astrand, M. AU - Speed, T. P. PY - 2003 DA - 2003// TI - A comparison of normalization methods for high density oligonucleotide array data based on variance and bias JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/19.2.185 DO - 10.1093/bioinformatics/19.2.185 ID - Bolstad2003 ER - TY - JOUR AU - Rousseeuw, P. J. PY - 1987 DA - 1987// TI - Silhouettes - a graphical aid to the interpretation and validation of cluster-analysis JO - J Comput Appl Math VL - 20 UR - https://doi.org/10.1016/0377-0427(87)90125-7 DO - 10.1016/0377-0427(87)90125-7 ID - Rousseeuw1987 ER - TY - JOUR AU - Carbon, S. AU - Dietze, H. AU - Lewis, S. E. AU - Mungall, C. J. AU - Munoz-Torres, M. C. AU - Basu, S. PY - 2017 DA - 2017// TI - Expansion of the gene ontology knowledgebase and resources JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1108 DO - 10.1093/nar/gkw1108 ID - Carbon2017 ER - TY - STD TI - Rice J. Mathematical statistics and data analysis (third ed.). Boston: Cengage Learning; 2013. ID - ref55 ER - TY - JOUR AU - Smith, V. A. AU - Yu, J. AU - Smulders, T. V. AU - Hartemink, A. J. AU - Jarvis, E. D. PY - 2006 DA - 2006// TI - Computational inference of neural information flow networks JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020161 DO - 10.1371/journal.pcbi.0020161 ID - Smith2006 ER - TY - STD TI - BANJO. Available from: https://users.cs.duke.edu/~amink/software/banjo/. UR - https://users.cs.duke.edu/~amink/software/banjo/ ID - ref57 ER -