Publication list
Publications – 2018 |
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Characterization of indole-3-acetic acid biosynthesis and the effects of this phytohormone on the proteome of the plant-associated microbe Pantoea sp. YR343Kasey Estenson, Greg Hurst, Robert F. Standaert, Amber N. Bible, David Garcia, Karuna Chourey, Mitchel J. Doktycz, and Jennifer L. Morrell-Falvey. Journal of Proteome Research |
Bacterial-Fungal interactions: ecology, mechanisms, and challengesAurélie Deveau, Gergory Bonito, Jessie Uehling, Matthias Becker, Saskia Bindschedler, Mathieu Paoletti, Stephane Hacquard, Vincent Hervé, Jessy Labbé, Olga Lastovetsky, Sophie Mieszkin, Larry Millet, Balázs Vajna, Paola Bonfante, Bastiaan P. Krom, Stefan Olsson, Jan Dirk van Elsas and Lukas Y. Wick. FEMS Microbiology Reviews |
Secretome analysis from the ectomycorrhizal ascomycete Cenococcum geophilumMaira de Freitas Pereira, Claire Veneault-Fourrey, Patrice Vion, Fréderic Guinet, Emmanuelle Morin, Kerrie W. Barry, Anna Lipzen, Vasanth Singan, Stephanie Pfister, Hyunsoo Na, Megan Kennedy, Simon Egli, Igor Grigoriev, Francis Martin, Annegret Kohler, and Martina Peter. Frontiers in Microbiology |
Elucidating duramycin’s bacterial selectivity and mode of action on the bacterial cell envelopeSahar Hasim, David Allison, Berlin Mendez, Abigail Farmer, Dale A. Pelletier, Scott Retterer, Shawn Campagna, Todd B. Reynolds, and Mitchel J. Doktycz. Frontiers in Microbiology |
The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiomeMelissa A Cregger, Allison M. Veach, Zamin K. Yang, Miranda J. Crouch, Rytas Vilgalys, Gerald A. Tuskan and Christopher W. Schadt. Microbiome |
Abiotic stresses shift belowground Populus-associated bacteria toward a core stress microbiomeCollin M. Timm, Kelsey R. Carter, Alyssa A. Carrell, Se-Ran Jun, Sara S. Jawdy, Jessica M. Vélez, Lee E. Gunter, Zamin Yang, Intawat Nookaew, Nancy L. Engle, Tse-Yuan Lu, Christopher W. Schadt, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, Dale A. Pelletier, and David J. Weston. M Systems |
Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their treeBrian Looney, Peter Meidl, Marek Piatek, Otto Miettinen, Francis Martin, Brandon P. Matheny, and Jessy Labbé. New Phytologist |
High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularisEric C. H. Chen, Emmanuelle Morin, Denis Beaudet, Jessica Noel, Gokalp Yildirir, Steve Ndikumana, Philippe Charron, Camille St-Onge, John Giorgi, Manueala Krüger, Timea Marton, Jeanne Ropars, Igor V. Grigoriev, Matthieu Hainaut, Bernard Henrissat, Christophe Roux, Francis Martin and Nicolas Corradi. New Phytologist |
Publications – 2017 |
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Quantitative proteomic profile of water-deficient stress responses in eastern cottonwood (Populus deltoides) leavesPaul E. Abraham, Ben Garcia, Lee E Gunter, Sara S. Jawdy, Dan A Jacobson, Nancy L Engle, Xiaohan Yang, Robert L. Hettich, Gerald A. Tuskan and Timothy J. Tschaplinski. PLoS One |
Genomic features of bacterial adaptation to plantsAsaf Levy, Isai Salas Gonzalez, Maximilan Mittelviefhaus, Scott Clingenpeel, Sur Herrera Paredes, Jiamin Miao, Kunru Wang, Giulia Devescovi, Kyra Stillman, Freddy Monteiro, Bryan Rangel Alvarez, Derek S. Lundberg, Tse-Yuan Lu, Sarah Lebeis, Zhao Jin, Meredith McDonald, Andrew P. Klein, Meghan E. Feltcher, Tijana Glavina del Rio, Sarah R. Gran, Sharon Doty, Ruth Ley, Bingyu Zhao, Vittorio Venturi, Dale A. Pelletier, Julia A. Vorholt, Susannah G. Tringe, Tanja Woyke, and Jeffery L. Dangl. Nature Genetics; DOI: 10.1038/s41588-017-0012-9 |
Progress in and promise of bacterial quorum sensing researchMarvin Whitely, Stephen P. Diggle, and E. Peter Greenberg. Nature 551: 313-320; DOI:10.1038/nature24624 |
Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry DataAnton Ievlev, Alex Belianinov, Stephen Jesse, David Allison, Mitch Doktycz, Scott Retterer, Sergei V. Kalinin, and Olga S. Ochinnikova Scientific Reports; DOI: 10.1038/s41598-017-17049-y |
Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systemsJessie Uehling, Aurélie Deveau and M. Paoleetti. Pearls in PLoS Pathogens |
Proteomics-based tools for evaluation of cell-free protien synthesisGregory B. Hurst, Keiji G. Asano, Charles J. Doktycz, Elliot J. Consoli, William L. Doktycz, Carmen M. Foster, Jennifer L. Morrell-Falvey, Robert F. Standaert, and Mitchel J. Doktycz. Analytical Chemistry |
Regulatory networks underlying mycorhizzal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolorDaguerre, Y., Levati, E., Ruytinx, J., Tisserant, E., Morin, E., Kohler, A., Montanini, B., Ottonello, S., Brun, A., Veneault-Fourrey, C., and Martin, F. BMC Genomics |
Assessment of genome annotation using gene function similarity within the gene neighborhoodSe-Ran Jun, Intawat Nookaew, Loren Hauser and Andrey Gorin BMC Bioinformatics |
Imaging the root hair morphology of Arabidopsis seedlings in a two-layer microfluidic platformJayde A. Aufrecht, Jennifer M. Ryan, Sahar Hasim, David P. Allison, Andreas Nebenführ, Mitchel J. Doktycz and Scott T. Retterer J. Vis. Exp Aug 15 (126); DOI:10.3791/55971 |
A case study into microbial genome assembly gap sequences and finishing strategiesSagar Utturkar, Dawn M. Klingeman, Richard A. Hurt and Steven D. Brown. Frontiers in Microbiology 18-July-2017; https://doi.org/10.3389/fmicb.2017.01272 |
Ancestral Alliances: Plant mutualistic symbioses with fungi and bacteriaFrancis Martin, Stéphane Uroz and David G. Barker. Science 356 (6340): eaad4501 |
“Hot Stuff”: The many uses of a radiolabel assay in detecting acyl-homoserine lacone quourum sensing signalsAmy Schaefer, Caroline S. Harwood, E. Peter Greenberg. Quorum Sensing: Methods and Protocols. Springer Publishing, Giordano Rampioni and Livia Leoni, Eds. |
Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus treesJessica M. Vélez,Timothy J. Tschaplinski,Rytas Vilgalys,Christopher W. Schadt,Gregory Bonito,Khalid Hameed,Nancy Engle,Cyd E. Hamilton Fungal Ecology 27 Part A: 78-86 |
Populus trichocarpa encodes small, effector-like secreted proteins that are highly induces during mutualistic symbiosisJonathan M. Plett,Hengfu Yin,Ritesh Mewalal,Rongbin Hu,Ting Li,Priya Ranjan,Sara Jawdy,Henrique C. De Paoli,George Butler,Tessa Maureen Burch-Smith,Hap-Bo Guo,Chun Ju Chen,Annegret Kohler,Ian C. Anderson,Jessy L. Labbé,Francis Martin,Gerald A. Tuskan,Xiaohan Yang Scientific Reports 7(1): 382 |
The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiationJeanne Doré,Annegret Kohler,Audrey Dubost,Hope Hundley,Vasanth Singan,Yi Peng,Alan Kuo,Igor V. Grigoriev,Francis Martin,Roland Marmeisse,Gilles Gay Environmental Microbiology DOI: 10.1111/1462-2920.13670 |
Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant GrowthYuan Qin,Xueyu Pan,Christian Kubicek,Irina Druzhinina,Komal Chenthamara,Jessy Labbé,Zhilin Yuan Front. Microbiology 8(158): 1-14 https://doi.org/10.3389/fmicb.2017.00158 |
The Identification of Phytohormone Receptor Homologs in Early Diverging Fungi Suggests a Role for Plant Sensing in Land Colonization by FungiAnaïs Hérivaux,Thomas Dugé de Bernonville,Christophe Roux,Marc Clastre,Vincent Courdavault,Amandine Gastebois,Jean-Philippe Bouchara,Timothy Y. James,Jean-Paul Latgé,Francis Martin,Nicolas Papon mBio vo.8 no.1 e01739-16 |
Comparative and Functional Genomics of Ectomycorrhizal SymbiosisJoske Ruytinx and Francis Martin in “The Fungal Community: Its Organization and Role in the Ecosystem, Fourth Edition. CRC Press, ed. JOhn Dighton and James F. White pp 27-36 |
Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network TopologyDeborah A. Weighill,Daniel A. Jacobson Advances in Biochemical Engineering/Biotechnology DOI: 10.1007/10_2016_46 |
Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigensJessie Uehling,A. Gryganskyi,K Hameed,Tim Tschaplinski,P. K. Misztal,S. Uw,A. Desiró,N. Pol Vande,Z. Du,Z. Zienkiewicz,K. Zienkiewicz,E. Morin,E. Tisserant,R. Splivallo,M. Hainaut,B. Henrissat,R. Ohn,A. Kuo,J. Yan,A. Lipzen,M. Nolan,K. LaButti,K. Barry,A. H. Goldstein,J. Labbé,C. Schadt,G. Tuskan,I. Grigoriev,F. Martin,R. Vilgalys,Gregory Bonito Environmental Microbiology, doi:10.1111/1462-2920.13669 |
Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomesF. Rineau, H. Lmalem, D. Ahre, F. Shah, T. Johansson, L. Coninx, J. Ruytinx, H. Nguyen, I. Grigoriev, A. Kuo, A. Kohler, E. Morin, J. Vangronsveld, F. Martin and J. V. Colpaert Mychorriza 27(4): 383-396; DOI: 10.1007/s00572-016-0758-4 |
Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial SystemZhou Li,Qiuming Yao,Stephen P. Dearth,Matthew R. Entler,Hector F. Castro Gonzalez,Jessie K. Uehling,Rytas J. Vilgalys,Gregory B. Hurst,Shawn R. Campagna,Jessy L. Labbé,Chongle Pan Environmental Microbiology, |
Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-merQian Zhang,Se-Ran Jun,Michael Leuze,David Ussery,Intawat Nookaew Scientific Reports 7, Article number: 40712 (2017) |
Atractiella rhizophila sp. nov., an endorrhizal fungus isolated from the Populus root microbiomeGregory Bonito,Khalid Hameed,Merje Toome-Heller,Rosanne Healy,Chantal Reid,Hui-Ling Liao,M. Catherine Aime,Christopher Schadt,Rytas Vilgalys Mycologia 109(1); 18-26 |
Publications – 2016 |
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A New Method for Qualitative Multiscale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron MicroscopyCora Miquel Guennoc,Christophe Rose,Frédéric Guinnet,Igor Miquel,Jessy Labbé,Aurélie Deveau Journal of Visualized Experiments |
Signaling pathways driving the development of ectomycorrhizal symbiosisYohann Daguerre,Jonathan M. Plett,Claire Veneault-Fourrey Molecular Mycorrhizal Symbiosis DOI: 10.1002/9781118951446.ch9 |
Harnessing mycorrhizal genomics for biological insightsFrancis Martin Molecular Mycorrhizal Symbiosis, ed. Francis Martin |
The evolution of the mycorrhizal lifestyles – a genomic perspectiveAnnegret Kohler,Francis Martin Molecular Mycorrhizal Symbiosis Ed. Francis Martin |
Mycorrhiza helper bacteriaAurélie Deveau,Jessy Labbé Molecular Mycorrhizal Symbiosis Ed. Francis Martin |
Molecular Mycorrhizal SymbiosisFrancis Martin |
Fungal and plant gene expression in the Tulasnella calospora–Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizasValeria Fochi,Walter Chitarra,Annegret Kohler,Samuele Voyron,Vasanth R. Singan,Erika A. Lindquist,Kerrie W. Barry,Marianglea Girlanda,Igor V. Grigoriev,Francis Martin,Raffaella Balestrini,Siliva Perotto New Phytologist 213: 365-379 |
Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype EvolutionLázló G. Nagy,Robert Riley,Philip J. Bergmann,Kirsztina Krizsán,Francis M. Martin,Igor V. Grigoriev,Dan Cullen,David S. Hibbett Mol Biol Evol (2016) 34 (1): 35-44 |
ß-glucan unmasking in some Candida albicans mutants correlates with increases in cell wall surface roughness and decreases in cell wall elasticitySahar Hasim,David P. Allison,Scott T. Retterer,Alex Hopke,Robert T. Wheeler,Mitchel J. Doktycz,Todd B. Reynolds Infection and Immunity doi: 10.1128/IAI.00601-16 |
Unearthing the roots of ectomycorrhizal symbiosesFrancis Martin,Annegret Kohler,Claude Murat,Claire Veneault-Fourrey,David S. Hibbett Nature Reviews Microbiology DOI: 10.1038/nrmicro.2016.149 |
Poplar PtabZIP1 positively regulates lateral root formation and flavonoid synthesis and enhance biomass growth under drought.Madhumita Dash,Yordan S. Yordanov,Tatyana Georgieva,Timothy J. Tschaplinski,Elena Yordanova,Victor Busov The Plant Journal; DOI: 10.111/tpj.13413 |
Root bacterial endophytes alter plant phenotype, but not physiologyJeremiah A. Henning,David J. Weston,Dale A. Pelletier,Collin M. Timm,Sara S. Jawdy,Aimée T. Classen Peer Journal 4:e2606 DOI: 10.7717/peerj.2606 |
Down-regulation of KORRIGAN-like endo-β-1,4-glucanase genes impacts carbon partitioning, mycorrhizal colonization and biomass production in PopulusUdaya C. Kalluri,Raja Payyavula,Jessy L. Labbé,Nancy Engle,Garima Bali,Sara S. Jawdy,Robert Sykes,Mark Davis,Arthur Ragauskas,Gerald A. Tuskan,Timothy Tschaplinski Frontiers in Plant Science |
Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilumMartina Peter,Annegret Kohler,Robin A. Ohm,Alan Kuo,Jennifer Krützmann,Emmanuelle Morin,Matthias Arend,Kerrie W. Barry,Manfred Binder,Cindy Choi,Alicia Clum,Alex Copeland,Nadine Grisel,Sajeet Haridas,Tabea Kipfer,Kurt LaButti,Erika Lindquist,Anna Lipzen,Renaud Maire,Barbara Meier,Sirma Mihalcheva,Virginie Molinier,Cluade Murat,Stefanie Pöggeler,C. Alisha Quandt,Christoph Sperisen,Andrew Tritt,Emilie Tisserant,Pedro W. Crous,Bernard Henrissat,Uwe Nehls,Simon Egli,Joseph W. Spatafora,Igor V. Grigoriev,Francis M. Martin Nature Communications 7, Article number: 12662 (2016) doi:10.1038/ncomms12662 |
Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to withstand Salinity.Zhilin Yuan,Irina S. Druzhinina,Jessy Labbe,Regina Redman,Yuan Qin,Russell Rodriguez,Chulong Zhang,Gerald A. Tuskan,Fucheng Lin Scientific Reports 6: 32467 |
Genome-wide analysis of lectin receptorlike kinases in PopulusYongil Yang,Jessy Labbé,Wellington Muchero,Xiaohan Yang,Sara S. Jawdy,Megan Kennedy,Jenifer Johnson,Avinash Sreedasyam,Jeremy Schmutz,Gerald A. Tuskan,Jin-Gui Chen BMC Genomics 2016 17:699 |
Isolating a functionally relevant guild of fungi from the Populus rhizosphere.Gregory Bonito,Khalid Hameed,Rafael Ventura,Jay Krishnan,Christopher W. Schadt,Rytas Vilgalys Fungal Ecology 22(2016) 35-42 |
A LuxR homolog in a Cottonwood tree endophyte that activates gene expression in response to a plant signal or specific peptides.Amy L. Schaefer,Yasuhiro Oda,Bruna Goncalves Coutinho,Dale A. Pelletier,Justin Weiburg,Vittorio Venturi,E. Peter Greenberg,Caroline S. Harwood mBio 7(4): e01101-16, DOI: 10.1128/mBio.01101-16. |
While-you-wait proteins? Producing biomolecules at the point of need.Benjamin P. Mohr,Scott T. Retterer,Mitchel J. Doktycz Expert Reviews of Proteomics, 13:8, 707-709 |
Enrichment of root endophytic bacteria from Populus deltoides and single-cell genomics analysisSagar M. Utturkar,W. Nathan Cude,Michael S. Robeson,Zamin K. Yang,Dawn M. Klingeman,Miriam L. Land,Steve L. Allman,Tse-Yuan S. Lu,Steven D. Brown,Christopher W. Schadt,Mircea Podar,Mitchel J. Doktycz,Dale A. Pelletier Applied and Environmental Microbiology, DOI: 10.1128/AEM.01285-16 |
Transgenic soybean overexpressing GmSAMT1 exhibits resistance to multiple-HG types of soybean cyst nematode Heterodera glycinesJingyu Lin,Mitra Mazarei,Nan Zhao,Catherine N. Hatcher,Wegi A. Wuddineh,Mary Rudis,Timothy J. Tschaplinski,Vincent R. Pantalone,Prakash R. Arelli,Tarek Hewezi,Feng Cheng,Charles Neal Stewart Plant Biotechnology Journal |
Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron limited conditionsAurélie Deveau, Harald Gross, Béatrice Palin, Samina Mehnaz, Max Schnepf, Pierre Leblond, Pieter C. Dorrestein, and Bertrand Aigle FEMS Microbiology Ecology 92(8): 107 |
The Sphagnum microbiome: new insights from an ancient plant lineage.Joel E. Kostka,David J. Weston,Jennifer B. Glass,Erik A. Lilleskov,Jonathan A. Shaw,Merritt R. Turetsky New Phytologist 211: 57-64, DOI: 10.111/nph.13993 |
Two poplar-associated bacterial isolates induce additive favorable responses in a constructed plant-microbiome systemCollin M. Timm,Dale A. Pelletier,Sara S. Jawdy,Lee E. Gunter,Jeremiah Henning,Nancy Engle,Jayde Aufrecht,Emily Gee,Intawat Nookaew,Zamin Yang,Tse-Yuan Lu,Timothy J. Tschaplinski,Mitchel J. Doktycz,Gerald A. Tuskan,David J. Weston Frontiers in Plant Science 7:479 |
A carotenoid-deficient mutant in Pantoea sp. YR343, a bacteria isolated from the rhizosphere of Populus deltoides, is defective in root colonizationAmber N. Bible,Sarah J. Fletcher,Dale A. Pelletier,Christopher W. Schadt,Sara S. Jawdy,David J. WEston,Nancy L. Engle,Timothy J. Tschaplinski,Rachel Masyuko,Sneha Polisetti,Paul W. Bohn,Teresa A. Coutinho,Mitchel J. Doktycz,Jennifer L. Morell-Falvey Frontiers in Microbiology 7:491 |
Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarrayFabiano Sillo,Jonatan U. Fangel,Bernard Henrissat,Antonella Faccio,Paola Bonfante,Francis Martin,William G. T. Willats,Raffaella Balestrini,Andrey Gorin Planta 244: 347-359 |
Chapter Five: The Sphagnum Genome Project: A new model for ecological and evolutionary genomicsA.J. Shaw,J. Schmutz,N. Devos,S. Shu,A.A. Carrell,D.J. Weston Advances in Botanical Research 78: 167-187, DOI: 10.1016/bs.abr.2016.01.003 |
Characterization of DWARF14 genes in PopulusKaijie Zheng,Xiaoping Wang,Deborah A. Weighill,Hao-Bo Guo,Meng Xie,Yongil Yang,Jun Yang,Shucai Wang,Daniel A. Jacobson,Hong Guo,Wellington Muchero,Gerald A. Tuskan,Jin-Gui Chen Scientific Reports 6: 21593 |
Publications – 2015 |
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The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in ArabidopsisXiaoping Wang,Shanda Liu,Hainan Tian,Shucai Wang,Jin-Gui Chen Frontiers in Plant Science |
Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted ProteinsClement Pellegrin,Emmanuelle Morin,Francis M. Martin,Claire Veneault-Fourrey Frontiers in Microbiology (6): 1278 |
Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and RhizosphereDawn M. Klingeman,Sagar Utturkar,Tse-Yuan S. Lu,Christopher W. Schadt,Dale A. Pelletier,Steven D. Brown Genome Announcements 3(6): e01344-15 DOI: 10.1128/genomeA.01344-15 |
Microstencils to generate defined, multi-species patterns of bacteriaCollin T Timm,Ryan R Hansen,Mitch J Doktycz,Scott T Retterer,Dale A Pelletier Biomicrofluidics |
Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestorsFiroz Shah,César Nicolás,Johan Bentzer,Magnus Ellström,Mark Smits,François Rineau,Björn Canbäck,dimitrios Floudas,Robert Carleer,Gerald Lackner,Jana Braesel,Dirk Hoffmeister,Bernard Henrissat,Dag Ahrén,Tomas Johansson,Davis S. Hibbett,Francis Martin,Per Persson,Anders Tunlid New Phytologist |
Diversity of Pseudomonas genomes, including Populus-associated isolates, as revealed by comparative genome analysis.Se-Ran Jun,Trudy M. Wassenaar,Intawat Nookaew,Loren Hauser,Visanu Wanchai,Miriam Land,collin M. Timm,Tse-Yuan Lu,Christopher W. Schadt,Mitchel J. Doktycz,Dale A. Pelletier,David W. Ussery Applied and Environmental Microbiology 82: 375-383. |
Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartmentCollin M. Timm,Alisha G. Campbell,Sagar M. Utturkar,Se Ran Jun,Rebecca E. Parales,Watumesa Tan,Michael S. Robeson,Tse-Yuan Lu,Sara Jawdy,Steven D. Brown,David W. Ussery,Christopher W. Schadt,Gerald A. Tuskan,Mitchel J. Doktycz,David J. Weston,Dale A. Pelletier Frontiers in Microbiology |
PanFP: Pangenome-based functional profiles for microbial communities.Se-Ran Jun,Michael S. Robeson,Loren J Hauser,Christopher W. Schadt,Andrey A. Gorin BMC Research Notes |
Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylinddrosporum and its involvement in ectomycorrhizal symbiosis.Jeanne Doré,Marie Perraud,Cindy Dieryckx,Annegret Kohler,Emmanuelle Morin,Bernard Henrissat,Erika Lindquist,Sabine D. Zimmermann,Vincent Girard,Alan Kuo,Igor V. Grigoriev,Francis Martin,Roland Marmeisse,Gilles Gay New Phytologist |
Reconsidering mutualistic plant-fungal interactions through the lens of effector biologyJonathan M. Plett,Francis Martin Current Opinion in Plant Biology 2015 26: 45-50 |
Development of the Poplar-Laccaria bicolor ectomycorrhiza Modifies Root Auxin Metabolism, Signaling, and Response.Alice Vassières,Ales Pencík,Judith Felten,Annegret Kohler,Karin Ljung,Francis Martin,Valérie Legué Plant Physiology 169(1): 890-902 September 2015 |
Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistryJennifer M. Talbot,Francis Martin,Annegret Kohler,Bernard Henrissat,Kabir G. Peay Soil Biology & Biochemistry 88 (2015) 441-456 |
Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomychorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiomeC. Alisha Quandt,Annegret Kohler,Cedar N. Hesse,Thomas J. Sharpton,Francis Martin,Joseph W. Spatafora Enivronmental Microbiology 8(17): 2952-2968 |
Phosphorylation of RACK1 in plantsJin-Gui Chen Plant Signaling and Behavior 10(8): |
Sequence data for Clostridium autoehanogenum using three generations of sequencing technologiesSagar Utturkar,Dawn M Klingeman,José M Bruno-Barcena,Mari S. Chinn,Amy M. Grunden,Michael Köpke,Steven D. Brown Scientific Data 2, Article number: 150014 |
ALD1 regulates the basal immune components and early inducible defense responses in Arabidopsis.Nicolás M. Cecchini,Ho Won Jung,Nancy L. Engle,Timothy J. Tschaplinski,Jean T. Greenberg Molecular Plant-Microbe Interactions 28(4): 455-466 |
3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics.Deborah A. Weighill,Daniel A. Jacobson PLoS Computational Biology |
The mutualist Laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defensesJonathan M. Plett,Emilie Tisserant,Annick Burn,Emmanuelle Morin,Igor V. Grigoriev,Alan Kuo,Francis Martin,Annegret Kohler Molecular Plant-Microbe Interactions 28(3): 261-273 |
Insights from 20 years of bacterial genome sequencingMiriam Land,Loren Hauser,Se-Ran Jun,Intawat Nookaew,Michael R. Leuze,Tae-Hyuk Ahn,Tatiana Karpinets,Ole Lund,Guruprasad Kora,Trudy Wassenaar,Suresh Poudel,David W. Ussery Functional and Integrative Genomics 15(2): 141-161 |
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualistsAnnegret Kohler,Alan Kuo,Laszlo G. Nagy,Emmanuelle Morin,Kerrie W. Barry,Francois Buscot,Björn Canbäck,Cindy Choi,Nicolas Cichocki,Alicia Clum,Jan Colpaert,Alex Copeland,Mauricio D. Costa,Jeanne Doré,Dimitrios Floudas,Gilles Gay,Mariangela Girlanda,Bernard Henrissat,Sylvie Herrmann,Jaqueline Hess,Nils Högberg,Tomas Johansson,Hassine-Radhouane Khouja,Kurt LaButti,Urs Lahrmann,Anthony Levasseur,Erika A. Lindquist,Anna Lipszen,Roland Marmeisse,Elena Martino,Cluade Murat,Chew Y. Ngan,Uwe Nehls,Jonathan M. Plett,Anne Pringle,robin A. Ohm,Silvia Perotto,Martina Peter,Robert Riley,Francois Rineau,Joske Ruytinx,Asaf Salamov,Firoz Shah,Hui Sun,Mika Tarkka,Andrew Tritt,Claire Veneault-Fourrey,Alga Zuccaro,Mycorrhizal Genomics Initiative Consortium,Anders Tunlid,Igor V. Grigoriev,David S. Hibbett,Francis Martin Nature Genetics. doi:10.1038/ng.3223 |
Evolving insights to understanding mycorrhizasIan A. Dickie, Ian Alexander, Sarah Lennon, Maarja Opik, Marc-André Selosse, Marcel G.A. van der Heijden, and Francis Martin New Phytologist 205: 1369-1374 Feb 2015 |
Mycorrhizal ecology and evolution: the past, the present and the future – Tansley Reveiw –Marcel GA van der Heijden, Frances Martin, Marc-André, Selosse and Ian R. Sanders New Phytologist 205: 1406-1423 Feb 2015 |
Prospects and challenges for fungal metatranscriptomics of complex communitiesCheryl R. Kuske,Cedar N. Hesse,Jean F. Challacombe,Daniel Cullen,Joshua R. Herr,Rebecca C. Mueller,Adrian Tsang,Rytas Vilgalys Fungal Ecology 14: 133-137 April 2015 |
Publications – 2014 |
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Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem functionDavid J. Weston,Collin M. Timm,Anthony P. Walker,Lianhong Gu,Wellington Muchero,Jeremy Schmutz,A. Johathan Shaw,Gerald A. Tuskan,Jeffrey M. Warren,Stan D. Wullschleger Plant, Cell and Environment 2014; doi: 10.1111-pce.12458 |
Towards a holistic understanding of the beneficial interactions across the Populus microbiomeStéphane Hacquard,Christopher W. Schadt New Phytologist, doi: 10.1111/nph.13133 |
Expanding genomics of mycorrhizal symbiosisAlan Kuo, Annegret Kohler, Francis M. Martin, and Igor V. Grigoriev Frontiers in Microbiology. doi: 10.3389/fmicb.2014.00582 |
Quality scores for 32,000 genomesMiriam L. Land,Doug Hyatt,Se-Ran Jun,Guruprasad H. Kora,Loren J. Hauser,Oksana Lukjancenko,David W. Ussery Standards in Genomic Sciences 2014, 9:20 doi:10.1186/1944-3277-9-20 |
Newly identified helper bacteria stimulate ectomycorrhizal formation in PopulusJessy L. Labbé,David J. Weston,Nora Dunkirk,Dale A. Pelletier,Gerald A. Tuskan Frontiers in Plant Science 5(579): 1-10 |
Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishmentClaire Veneault-Fourrey,Carine Commun,Annegret Kohler,Emmanuelle Morin,Raffaella Balestrini,Jonathan Plett,Etienne Danchin,Pedro Coutinho,Ad Wiebenga,Ronald P. de Vries,Bernard Henrissat,Francis Martin Fungal Genetics and Biology Volume 72, November 2014, Pages 168–181 |
Selective herbivory by an invasive cyprinid, the rudd Scardinius erythrophthalmusKevin L. Kapuscinksi,John M. Farrell,Stephen V. Stehman,Gregory L. Boyer,Danilo D. Fernando,Mark A. Teece,Timothy J. Tschaplinski Freshwater Biology |
MIDAS: A Database-Searching Algorithm for Metabolite Identification in MetabolomicsYinfeng Wang,Guruprasad Kora,Benjamin P Bowen,Chongle Pan Analytical Chemistry DOI: 10.1021/ac5014783 |
Characterization of MORE AXILLARY GROWTH Genes in PopulusOlaf Czarnecki,Jun Yang,Xiaoping Wang,Shucai Wang,Wellington Muchero,Gerald A. Tuskan,Jin-Gui Chen PLoS One |
Latent homology and convergent regulatory evolution underlies the repeated emergence of yeastsLászló G. Nagy,Robin A. Ohm,Gábor M. Kovács,Dimitrios Floudas,Robert Riley,Attila Gácser,Mátyás Sipiczki,John M. Davis,Sharon L. Doty,G Sybren de Hoog,B. Franz Lang,Joseph W. Spatafora,Francis M. Martin,Igor V. Grigoriev,David S. Hibbett Nature Communications 5(4471); doi:10.1038/ncomms5471 |
Duplications and losses in gene families of rust pathogens highlight putative effectors.Amanda L. Pendleton,Katherine E. Smith,Nicolas Feau,Francis M. Martin,Igor V. Grigoriev,Richard Hamelin,C. Dana Nelson,J. Gordon Burleigh,John M. Davis Front Plant Sci. 2014 Jun 26;5:299. doi: 10.3389/fpls.2014.00299. eCollection 2014. |
Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plantsGregory Bonito,Hannah Reynolds,Michael S. Robeson,Jessica Nelson,Brendan P. Hodkinson,Gerald Tuskan,Christopher W. Schadt,Rytas Vilgalys Molecular Ecology (2014) 23, 3356–3370 |
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.Robert Riley,Asaf A. Salamov,Daren W. Brown,Laszlo G. Nagy,Dimitrios Floudas,Benjamin W. Held,Anthony Levasseur,Vincent Lombard,Emmanuelle Morin,Robert Otillar,Erika A. Lindquist,Hui Sun,Kurt M. LaButti,Jeremy Schmutz,Dina Jabbour,Hong Luo,Scott E. Baker,Antonio G. Pisabarro,Jonathan D. Walton,Robert A. Blanchette,Bernard Henrissat,Francis Martin,Dan Cullen,David S. Hibbett,Igor V. Grigoriev Proceedings of the National Academy of Sciences, USA 2014: 1400592111v1-201400592 |
Fungal biology: compiling genomes and exploiting themJessy Labbé,Jessie Uehling,Thibaut Payen,Jonathan Plett The 12th European Conference on Fungal Genetics, March 2014 New Phytologist 203(2): 359-361 |
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequencesSagar M. Utturkar,Dawn M. Klingeman,Miriam L. Land,Christopher W. Schadt,Mitchel J. Doktycz,Dale A. Pelletier,Steven D. Brown Bioinformatics (2014) doi: 10.1093/bioinformatics/btu391 |
Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genesJonathan M. Plett,Yohann Daguerre,Sebastian Wittulsky,Alice Vayssiéres,Aurelie Deveau,Sarah J. Melton,Annegret Kohler,Jennifer L. Morell-Falvey,Annick Brun,Claire Veneault-Fourrey,Francis Martin Proceedings of the national Academy of Sciences, USA doi:10.1073/pnas.1322671111 |
Transgenic American chestnuts show enhanced blight resistance and transmit the trait to T1 progeny.Andrew E. Newhouse,Linda D. Polin-Guigan,Kathleen A. Baier,Kristia E.R. Valletta,William H. Rottmann,Timothy J. Tschaplinski,Charles A. Maynard,William A. Powell Plant Science, DOI: 10.1016/j.plantsci.2014.04.004 |
Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant ClostridiaSteven D. Brown,Shilpa Nagaraju,Sgar Utturkar,Sashini De Tissera,Simón Segovia,Wayne Michell,Miriam L. Land,Asela Dassanayake,Michael Köpke Biotechnology for Biofuels 2014, 7:40 |
Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and PlantsTatiana V. Karpinets,Byung H. Park,Mustafa H. Syed,Martin G. Klotz,Edward C. Uberbacher Molecular Plant-Microbe Interactions |
Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in ArabidopsisZhou Li,Olaf Czarnecki,Kaurna Chourey,Jun Yang,Gerald A. Tuskan,Gregory B. Hurst,Chongle Pan,Jin-Gui Chen J. Proteome Res., 2014, 13 (3), pp 1359–1372 DOI: 10.1021/pr400925t |
Populus trichocarpa and Populus deltoides Exhibit Different Metabolomic Responses to Colonization by the Symbiotic fungus Laccaria bicolorTimothy J. Tschaplinski,Jonathan M. Plett,Nancy L. Engle,Aurelie Deveau,Katherine C. Cushman,Madhavi Z. martin,Mitchel J. Doktycz,Gerald A. Tuskan,Annick Brun,Annegret Kohler,Francis Martin Molecular Plant-Microbe Interactions 27(6): 546-556 |
Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8A. Deveau, H. Gross, E. Morin, T. Karpinets, S. Utturkar, S. Mehnaz, F. Martin, P. Frey-Klett,J. Labbé Genome Announcement 2(1): e01152-13 |
Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus rootsJonthan M. Plett, Amit Khachane, Malika Ouassou,Björn Sundberg,Annegret Kohler,Francis Martin New Phytologist 202(1): 270-286 |
Genome resequencing in Populus. Revealing large-scale genome variation and implications on specialized-trait genomes.Wellington Muchero,Jessy Labbé,Priya Ranjan,Stephan DiFazio,Gerald A. Tuskan Challenges and Opportunities for the World’s Forests in the 21st Century. Series: Forestry Sciences, Vol. 81; pp. 587-595 |
Publications – 2013 |
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Single cell swimming dynamics of Listeria monocytogenes using a nanoporous microfluidic platformEvan Wright, Suresh Neethirajan, Ketih Warriner, Scott Retterer and Bernadeta Srijanto Lab Chip, 2014 14(5): 938-46 |
The Mycorrhizal Symbiosis GenomicsFrancis Martin and Annegret Kohler The Ecological Genomics of Fungi December 2013 |
The Ecological Genomics of FungiFrancis Martin The Ecological Genomics of Fungi December 2013 |
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosisEmilie Tisserant, Mathilde Malbreil, Alan Kuo, Annegret Kohler, Aikaterini Symeonidi, Raffaella Balestrini, Philippe Charron, Nina Duensing, Nicolas Frei dit Frey, Vivienne Gianinazzi-Pearson, Luz B. Gilbert, Yoshihiro Handa, Joshua R. Herr, Mohamed Hijri, Raman Koul, Masayoshi Kawaguchi, Franziska Krajinski, Peter J. Lammers, Frederic G. Masclaux, Claude Murat, Emmanuelle Morin, Steve Ndikumana, Marco Pagni, Denis Petitpierre, Natalia Requena, Pawel Rosikiewicz, Rohan Riley, Katsuharu Saito,Hélène San Clemente,Harris Shapiro,Diederik van Tuinen,Guillaume Bécard,Paola Bonfante,Uta Paszkowski,Yair Y. Shach ar-Hill,Gerald A. Tuskan,Peter W. Young,Ian R. Sanders,Bernard Henrissat,Stefan A. Rensing,Igor V. Grigoriev,Nicolas Corradi,Christophe Roux,Francis Martin PNAS 2013, doi: 10.1073/pnas.1313452110 |
A Multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.Migun Shakya, Neil Gottel, Hector Castro, Zamin K. Yang, Lee Gunter,Jessy Labbé,Wellington Muchero,Gregory Bonito,Rytas Vilgalys,Gerald A. Tuskan,Mircea Podar,Christopher W. Schadt PLoS ONE, DOI: 10.1371/journal.pone.0076382 |
Mycorrhizas and New Phytologist: une vraie historie d’amourMarc-André Selosse,Francis Martin New Phytologist (2013) 200, 587-589. |
Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populiPosy E. Busby,Naupaka Zimmerman,David J. Weston,Sara S. Jawdy,Jos Houbraken,George Newcombe Ecosphere 4(10):125. |
Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporusAleksandrina Patyshakuliyeva, Edita Jurak, Annegret Kohler, Adam Baker, Evy Battaglia, Wouter de Bruijn, Kerry S. Burton, Michael P. Challen, Pedro M. Coutinho, Daniel C. Eastwood, Birgit S. Gruben,Miia R. Mäkelä,Francis Martin,Marina Nadal,Joost van den Brink,Ad Wiebenga,Miaomiao Zhou,Bernard Henrissat,Mirjam Kabel,Harry Gruppen,Ronald P de Vries BMC Genomics 2013 14:663, doi:10.1186/1471-2164-14-663 |
Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay FungiClaude Murat, Thibaut Payen, Denis Petitpierre,Jessy Labbé The Ecological Genomics of Fungi (ed F. Martin), John Wiley & Sons, Inc, Hoboken, NJ. doi: 10.1002/9781118735893.ch2 |
Lectin-functionalized poly(glycidyl methacrylate)-block-poly(vinyldimethyl azlactone) surface scaffolds for high avidity microbial captureRyan R. Hansen, Juan Pablo Hinestrosa, Katherine R. Shubert, Jennifer L. Morrell-Falvey, Dale A. Pelletier, Jamie M. Messman, S. Michael Kilbey, Bradley S. Lokitz, and Scott T. Retterer Biomacromolecules, 2013, 14 (10), pp 3742â3748 DOI: 10.1021/bm4011358 |
Extreme diversification of the mating type-high mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungusRohan Riley, Philippe Charron, Alexander Idnum, Laurent Farinelli, Yolande Dalpé, Francis Martin and Nicolas Corradi New Phytologist 201: 254-268 |
New insights into ectomycorrhizal symbiosis evolution and functionClaire Veneault-Fourrey and Francis Martin Agricultural Applications The Mycota Volume 11, 2013, pp 273-293 |
LuxR- and LuxI-type quorum sensing circuits are prevalent in members of the Populus deltoides microbiomeAmy L. Schaefer,Colin R. Lappala,Ryan P. Morlen,Dale A. Pelletier,Tse-Yuan S. Lu,Patricia K. Lankford,Caroline S. Harwood,E. Peter Greenberg Applied and Environmental Microbiology 79(18): 5745-5752 |
Sipros/ProRata: a versatile informatics system for quantitative community proteomicsYingfeng Wang, Tae-Hyuk Ahn, Zhou Li, and Chongle Pan Bioinformatics 29(16): 2064-2065 |
Identification, characterization of an AP2/ERF transcriptiion factor that promotes adventitious, lateral root formation in Populus.Dalila Trupiano, Yordan Yordanov, Sharon Regan, Richard Meilan, Timothy J. Tschaplinski, Gabriella Stefania Scippa, Victor Busov Planta 238:271-282 |
Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-Like effectors into plant and animal cells is specific and reproducible.Brett M. Tyler, Shiv D. Kale, Qunqing Wang, Kai Tao, Helen R. Clark, Kelly Drews, Vincenzo Antignani, Amanda Rumore, Tristan Hayes, Jonathan M. Plett Isabelle Fudal, Biao Gu, Qinghe Chen, Katharyn J. Affeldt, Erwin Berthier, Gregory J. Fischer, Daolong Dou, Weixing Shan, Nancy P. Keller, Francis Martin, Thierry Rouxel, and Christopher B. Lawrence Molecular Plant Microbe Interactions 26(6): 611-616 |
A Dual Role of Strigolactones in Phosphate Acquisition and Utilization in PlantsOlaf Czarnecki, Jun Yang,David Weston,Gerald A. Tuskan,Jin-Gui Chen International Journal of Molecular Sciences 2013, 14(4): 7681-7701; doi:10.3390/ijms14047681 |
Heterotrimeric G protein signaling in the plant kingdomDaisuke Urano, Jin-Gui Chen,José Ramón Botella,Alan M. Jones Open Biology 3(3): 1-23 doi: 10.1098/rsob.120186 |
Who is controlling whom within ectomycorrhiza symbiosis: insights from genomic and functional analysesClaire Veneault-Fourrey, Jonathan M. Plett and Francis Martin Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2, Chapter 47 pp. 501-512 doi: 10.1002/9781118297674.ch47 |
Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments.Stéphane Hacquard,Emilie Tisserant,Annick Brun,Valérie Legué,Francis Martin,Annegret Kohler Environmental Microbiology 15(6): 1853-1869 |
Evolutionary analyses of non-family genes in plantsChu-Yu Ye, Ting Li, Hengfu Yin, David J. Weston, Gerald A. Tuskan, Timothy J. Tschaplinski and Xiaohan Yang The Plant Journal 73(5): 788-797 |
Genome Anchored QTLs for Biomass Production in Hybrid Populus Grown Under Contrasting EnvironmentsWellington Muchero, Mitchell M Sewell, Priya Ranjan, Lee E Gunter, Timothy J Tschaplinski, Tongming Yin, Gerald A Tuskan PLoS ONE 8(1): e54468. doi:10.1371/journal.pone.0054468 — |
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communitiesShakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. Enivronmental Microbiology (2013), 15(6): 1882-1899 |
Inside arbuscular mycorrhizal roots-Molecular probes to understand the symbiosisDaniel Ruzicka,Srikar Chamala,Felipe H. Barrios-Masias,Francis Martin,Sally Smith,Louse E. Jackson,W. Brad Barbazuk,Daniel P. Schachtman The Plant Genome 6(2): 1-13 doi: 10.3835/plantgenome2012.06.0007 |
Publications – 2012 |
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Ten years of genomics for ectomycorrhizal fungi: what have we achieved and where are we headed?Francis Martin and Gregory Bonito Edible Ectomycorrhizal Mushrooms: Curretn Knowledge and Future Perspectives |
Temperature-Dependent Shade Avoidance Involves the Receptor-Like Kinase ERECTADhavel Patel, Manojit Basu, Scott Hayes,Imre Majláth,Flora M. Hetherington,Timothy J. Tschaplinski,Keara A. Franklin Plant Journal (2013) 73(6): 950-992 |
Involvement of auxin pathways in modulating root architecture during beneficial plant- microorganism interactionsPoornima Sukumar,Valérie Legué,Alice Vayssières,Francis Martin,Gerald A. Tuskan,Udaya C. Kalluri Plant, Cell and Environment 2012, doi: 10.1111/pce.12036 |
Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generatorMeng Lian, C. Patrick Collier, Mitchel J. Doktycz and Scott T. Retterer Biomicrofluidics 6(4), 044118: 1-12 |
The AINTEGUMENTA LIKE1 homeotic transcription factor PtAIL1 controls the formation of adventitious root primordia in Poplar.Adeline Rigal, Yordan S. Yordanov, Irene Perrone, Anna Karlberg, Emilie Tisserant, Catherine Bellini, Victor B. Busov, Francis Martin, Annegret Kohler, Rishi Bhalerao,Valérie Legué Plant Physiology 160(4): 1996-2006 |
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological nicheEmmanuelle Morin,Annegret Kohler,Adam R. Baker,Marie Foulongne-Oriol,Vincent Lombard,Laszlo G. Nagy,Robin A. Ohm,Aleksandrina Patyshakuliyeva,Annick Brun,Andrea L. Aerts,Andrew M. Bailey,Christophe Billette,Pedro M. Coutinho,Greg Deaking,Harshavardhan Doddapaneni,Dimitrios Floudas,Jane Grimwood,Kristina Hildén,Ursula Kües,Kurt M. LaButti,Alla Lapidus,Erika A. Lindquist,Susan M. Lucas,Claude Murat,Robert W. Riley,Asaf A. Salamov,Jeremy Schmutz,Venkataramanan Subramanian,Han A.B. Wösten,Jianping Xu,Daniel C. Eastwood,Gary D. Foster,Anton S.M. Sonnenberg,Dan Cullen,Ronald P. de Vries,Taina Lundell,David S. Hibbett,Bernard Henrissat,Kerry S. Burton,Richard W. Kerrigan,Michael P. Challen,Igor V. Grigoriev,Francis Martin PNAS USA 109(43): 17501-17506 Correction: 110(10) 4146-4148 |
New North American truffles (Tuber spp.) and their ectomycorrhizal associationsGuevara G, Bonito G, Trappe JM, Cázares E, Williams G, Healy RA, Schadt CW, and Vilgalys R Mycologia 2013 105:194-209 |
Highly Efficient Isolation of Populus Mesophyll Protoplasts and Its Application in Transient Expression AssaysJianjun Guo,Jennifer L. Morrell-Falvey,Jessy L. Labbé,Wellington Muchero,Udaya C. Kalluri,Gerald A. Tuskan,Jin-Gui Chen PLoS ONE 7(9): e44908. |
Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoidesSteven D. Brown, Sagar M. Utturkar, Dawn M. Klingeman, Courtney M. Johnson, Stanton L. Martin, Miriam L. Land, Tse-Yuan S. Lu, Christopher W. Schadt, Mitchel J. Doktycz and Dale A. Pelletier J. Bacteriol. November 2012 vol. 194 no. 21 5991-5993 |
Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genesAbhijit A. Karve,Sara S. Jawdy,Lee E. Gunter,Sara M. Allen,Xiaohan Yang,Gerald A. Tuskan,Stan D. Wullschleger,David J. Weston New Phytologist Volume 196, Issue 3, pages 726-737, November 2012 |
De-constructing a mutualist: How the molecular blueprints of model symbiotic fungi are changing our understanding of mutualism.Jonathan M Plett, Annegret Kohler and Francis Martin Fungal Associations 2nd edition; The Mycota Volume IX pp. 93-117 doi: 10.1007/978-3-642-30826-0_6 |
Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolorJessy Labbé,Claude Murat,Emmanuelle Morin,Gerald A. Tuskan,Franoçois Le Tacon,Francis Martin PLoS ONE 7(8): e40197 |
Gene and translation initiation site prediction in metagenomic sequencesDoug Hyatt, Philip F. LoCascio, Loren J. Hauser, and Edward C. Uberbacher Bioinformatics (2012) 28 (17): 2223-2230. doi: 10.1093/bioinformatics/bts429 |
Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis and fitnessDavid Weston, Dale A. Pelletier, Jennifer L. Morrell-Falvey, Timothy J. Tschaplinski, Sara S. Jawdy, Tse-Yuan Lu, Sara M. Allen, Sarah J. Melton, Madhavi Z. Martin, Christoper W. Schadt, Abhijit A. Karve, Jin-Gui Chen, Xiaohan Yang, Mitchel J. Doktycz and Gerald A. Tuskan Molecular Plant-Microbe Interactions 25(6): 765-778 |
Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcAMichael R. Leuze, Tatiana V. Karpinets, Mustafa H. Syed, Alexander S. Beliaev and Edward C. Uberbacher Gene Regulation and Systems Biology 2012: (6) 93-107 |
Analyzing large biological datasets with association networksTatiana V. Karpinets, Byung H. Park, Edward C. Uberbacher Nucleic Acids Research. 2012 September; 40(17): 1-8 |
Communication Between Plant, Ectomycorrhizal Fungi and Helper BacteriaAurélie Deveau,Jonathan M. Plett,Valérie Legué,Pascale Frey-Klett, and Francis Martin Biocommunication of Fungi 2012, pp 229-247 |
System-wide Studies of N-Lysine Acetylation in Rhodopseudomonas palustris Reveal Substrate Specificity of Protein AcetyltransferasesHeidi A. Crosby, Dale A. Pelletier, Gregory B. Hurst, and Jorge C. Escalante-Semerena The Journal of Biological Chemistry, 287, 15590-15601. |
Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoidesSteve Brown, Tse-Yuan Lu, Sagar Utturkar, Chris Schadt, Mitch Doktycz, Dale Pelletier Journal of Bacteriology 2012, 194(9): 2383-2384 DOI: 10.1128/JB.00198-12 |
The importance of individuals: intraspecific diversity of mycorrhizal plants and fungi in ecosystems. -Tansley review-David Johnson, Francis Martin, John W.G. Cairney and Ian C. Anderson New Phytologist 194(3): 614-628 |
Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolorJonathan M. Plett, Julien Gibon, Annegret Kohler, Kecia Duffy, Patrik J. Hoegger, Rajesh Velagapudi, James Han,Ursula Kües,Igor V. Grigoriev,Francis Martin Fungal Genetics and Biology Volume 49, Issue 3, March 2012, Pages 199-209 |
Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpaNag A, Karpinets TV, Chang CH, Bar-Peled M. Database (Oxford). 2012; 2012: bas013. |
Signaling in ectomycorrhizal symbiosisJudith Felten,Francis Martin,Valérie Legué Signaling and Communication in Plant Symbiosis Signaling and Communication in Plants Volume 10, 2012, pp 123-142 |
Molecular Interactions in Mycorrhizal DevelopmentJonathan M. Plett and Francis Martin Biocomplexity of Plant-Fungal Interactions (ed D. Southworth), chapter 2. doi: 10.1002/9781118314364. |
Poplar root exudates contain compounds that induce the expression of MiSSP7 in Laccaria bicolorJonathan M. Plett and Francis Martin Plant Signaling & Behavior 7(1): 12-15 |
The M. truncatula SUNN gene is expressed in vascular tissue, similarly to RDN1, consistent with the role of these nodulation regulation genes in long distance signalingElise Schnabel, Abhijit Karve, Tessema Kassaw, Arijit Mukherjee, Xin Zhou, Tim Hall and Julia Frugoli Plant Signaling and Behavior 7(1): 4-6 |
Publications – 2011 |
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Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap VelosZhou Li, Rachel M. Adams, Karuna Chourey, Gregory Blake Hurst, Robert L. Hettich, and Chongle Pan Journal of Proteome Research 2012, 11 (3), pp 1582-1590 |
The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiontE. Tisserant, A. Kohler, P. Dozolme-Seddas, R. Balestrini, K. Benabdellah, A. Colard, D. Croll, C. Da Silva, S.K. Gomez, R. Koul, N. Ferrol, V. Fiorilli, D. Formey, Ph. Franken, N. Helber, M. Hijri, L. Lanfranco, E. Lindquist, Y. Liu, M. Malbreil, E. Morin, J. Poulain, H. Shapiro, D. van Tuinen, A. Waschke,C. Azcón-Aguilar,G. Bécard,P. Bonfante,M.J. Harrison,H. Küster,P. Lammers,U. Paszkowski,N. Requena,S.A. Rensing,C. Roux,I.R. Sanders,Y. Shachar-Hill,G. Tuskan,J.P.W. Young,V. Gianinazzi-Pearson,F. Martin New Phytologist Volume 193(3), pages 755-769 |
Measuring Dissociation Rate Constants of Protein Complexes Through Subunit Exchanges: Experimental Design and Theoretical ModelingChongle Pan PLoS ONE 6 (12): e28827 |
Secretome of the Free-living Mycelium from the Ectomycorrhizal Basidiomycete Laccaria bicolorDelphine Vincent, Annegret Kohler, Stephane Claverol, Emilie Solier, Johann Joets, Julien Gibon, Marc-Henri Lebrun, Christophe Plomion, and Francis Martin Journal of Proteome Research 11(1), 157-171 |
Mutualistic Effectors: Architects of SymbiosisJonathan M. Plett and Francis Martin Effectors in Plant-Microbe Interactions 2011, pages 295-326 |
Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial EnvironmentsFlorence Wisniewski-Dyé, Kirill Borizak, Gurusahai Khalsa-Moyers, Gladys Alexandre, Leonid O. Sukharnikov, Kristin Wuichet, Gregory B. Hurst, W. Hayes McDonald, Jon S. Robertson, Valérie Barbe, Alexandra Calteau, Zoé Rouy, Sophie Mangenot, Claire Prignet-Combaret, Philippe Normand, Michaël Boyer, Patricia Siguier, Yves Dessaux, Claudine Elmerich, Guy Condemine, Ganisan Kirshnen, Ivan Kennedy, Andrew H. Paterson, Victor González, Patrick Mavingui, Igor B. Zhulin PLoS Genetics 7(12): e1002430 |
Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.Brendan P. Hodkinson, Neil R. Gottel, Christopher W. Schadt and François Lutzoni Environ Microbiol. 2012 Jan;14(1):147-61. doi: 10.1111/j.1462-2920.2011.02560.x. Epub 2011 Sep 12. |
Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.Neil R. Gottel, Hector F. Castro, Marily Kerley, Zamin Yang, Dale A. Pelletier, Mircea Podar, Tatiana Karpinets, Ed Uberbacher, Gerald A. Tuskan, Rytas Vilgalys, Mitchel J. Doktycz, and Christopher W. Schadt Appl Environ Microbiol. 2011 Sep;77(17):5934-44. doi: 10.1128/AEM.05255-11. Epub 2011 Jul 15. |
Innovative biological solutions to challenges in sustainable biofuels production.Xiaohan Yang, Ting Li, David Weston, Abhijit Karve, Lee E. Gunter, Poornima Sukumar, Anne Borland, Jin-Gui Chen, Stan D. Wullschleger,Jessy Labbé,Timothy J. Tschaplinski,Gerald A. Tuskan Biofuel Production-Recent development and Prospects.(eds. MADS Bernardens), pp. 375-414 |
Bacterial Immobilization for Imaging by Atomic Force MicroscopyDavid P. Allison, Claretta J. Sullivan, Ninell Pollas Mortensen, Scott T. Retterer, and Mitchel J. Doktycz J Vis Exp. 2011 Aug 10;(54). pii: 2880. doi: 10.3791/2880. |
Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine maxDavid J. Weston, Abhijit A. Karve, Lee E. Gunter, Sara S. Jawdy, Xiaohan Yang, Sara M. Allen and Stan D. Wullschleger. Plant, Cell & Environment Volume 34, Issue 9, pages 1488-1506, September 2011 |
Structure and Expression Profile of the Phosphate Pht1 Transporter Gene Family in Mycorrhizal Populus trichocarpaVerónica Loth-Pereda, Elena Orsini, Pierre-Emmanuel Courty, Frédéric Lota, Annegret Kohler, Loic Diss, Damien Blaudez, Michel Chalot, Uwe Nehls, Marcel Bucher, and Francis Martin Plant Physiology 156: 2141-2154 |
Abscisic acid receptors: past, present and futureJianjun Guo, Xiaohan Yang, David J. Weston and Jin-Gui Chen Journal of Integrative Plant Biology Volume 53, Issue 6, pages 469-479, June 2011 |
A Secreted Effector Protein of Laccaria bicolor is Required for Symbiosis DevelopmentJonathan M. Plett, Minna Kemppainen, Shiv D. Kale, Annegret Kohler, Valérie Legué, Annick Brun, Brett M. Tyler, Alejandro G. Pardo, and Francis Martin Current Biology 21 (14): 1197-203, doi:10.1016/j.cub.2011.05.033 |
Mutualistic interactions on a knife-edge between saprotrophy and pathogenesis.Claire Veneault-Fourrey and Francis Martin Curr Opin Plant Biol. 2011 Aug;14(4):444-50. doi: 10.1016/j.pbi.2011.03.022. Epub 2011 Apr 27. |
Tapping Genomics to Unravel Ectomycorrhizal SymbiosisJonathan M Plett, Barbara Montanini, Annegret Kohler, Simon Ottonello and Francis Martin. Fungal Genomics: Methods and Protocols. Methods in Molecular Biology Series 722:249-281 |
Sequencing the fungal tree of lifeF. Martin, D. Cullen, D. HIbbett, A Pisabarro, J.W. Spatafora, S.E. Baker and I.V. Grigoriev New Phytologist 190: 818-821 |
Discovery and annotation of small proteins using genomics, proteomics, and computational approachesXiaohan Yang, Timothy J. Tschaplinski, Gregory B. Hurst, Sara Jawdy, Paul E. Abraham, Patricia K. Lankford, Rachel M. Adams, Manesh B. Shah, Robert L. Hettich, Erika Lindquist, Udaya C. Kalluri, Lee E. Gunter, Christa Pennacchio, and Gerald A. Tuskan Genome Res. 2011. 21: 634-641 |
Identification of quantitiative trait loci affecting ectomycorrhizal symbiosis in an interspecific F1 poplar cross and differentail expression of genes in ectomycorrhizas of the two parents: Populus deltoides and Populus trichocarpa.Jessy Labbé, Véronique Jorge, Annegret Kohler, Patrice Vion, Benoît Marçais, Catherine Bastien, Gerald A. Tuskan, Francis Martin, and François Le Tacon Tree Genetics & Genomes Volume 7, Issue 3 , pp 617-627 |
Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markersJessy Labbé, Claude Murat, Emmanuelle Morin, François Le Tacon, and Francis Martin Curr Genet. 2011 Apr;57(2):75-88. doi: 10.1007/s00294-010-0328-9. Epub 2010 Dec 4. |
Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes.Jonathan M. Plett and Francis Martin Trends Genet. 2011 Jan;27(1):14-22. doi: 10.1016/j.tig.2010.10.005. Epub 2010 Nov 27. |
Characterization of cell surface and extracellular matrix remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy.Amanda N. Edwards, Piro Siuti, Amber N. Bible, Gladys Alexandre, Scott T. Retterer, Mitchel J. Doktycz, and Jennifer L. Morrell-Falvey FEMS Microbiol Lett. 2011 Jan;314(2):131-9. doi: 10.1111/j.1574-6968.2010.02156.x. Epub 2010 Nov 24. |
Publications – 2010 |
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Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplarOlga Pechanova, Chuan-Yu Hsu, Joshua P. Adams, Tibor Pechan, Lindsay Vandervelde, Jenny Drnevich, Sara Jawdy, Ardeshir Adeli, Jeffrey C. Suttle, Amanda M. Lawrence, Timothy J. Tschaplinski, Armand Seguin and Cetin Yuceer BMC Genomics 2010, 11:674 doi:10.1186/1471-2164-11-674 |
CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy databaseByung H Park, Tatiana V Karpinets, Mustafa H Syed, Michael R Leuze, and Edward C Uberbacher Glycobiology (2010) 20 (12): 1574-1584 |
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regionsTatiana Karpinets, Margaret F. Romine, Denise D. Schmoyer, Guruprasad Kora, Mustafa H. Syed, Michael R. Leuze, Margrethe H. Serres, Byung H. Park, Nagiza F. Samatova, and Edward C. Uberbacher Database (Oxford). 2010 Jul 6;2010:baq012. doi: 10.1093/database/baq012. |
Biosynthesis and emission of insect-induced methyl salicylate and methyl benzoate from rice.Nan Zhao,Ju Guan,Jean-Luc Ferrer,Nancy Engle,Mawsheng Chern,Pamela Ronald,Timothy J. Tschaplinski,Feng Chen Plant Physiol Biochem. 2010 Apr;48(4):279-87. doi: 10.1016/j.plaphy.2010.01.023. Epub 2010 Feb 8. |
