Publication list

 

Publications - 2017

Ancestral Alliances: Plant mutualistic symbioses with fungi and bacteria

Francis 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 signals

Amy 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 trees

Jessica 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 symbiosis

Jonathan 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 differentiation

Jeanne 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
Growth

Yuan 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 Fungi

Anaïs 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 Symbiosis

Joske 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 Topology

Deborah 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 cysteinexigens

Jessie 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 genomes

F. 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

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer

Qian 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 microbiome

Gregory 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

A New Method for Qualitative Multiscale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy

Cora Miquel Guennoc,Christophe Rose,Frédéric Guinnet,Igor Miquel,Jessy Labbé,Aurélie Deveau
Journal of Visualized Experiments

Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial System

Zhou 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,

Signaling pathways driving the development of ectomycorrhizal symbiosis

Yohann Daguerre,Jonathan M. Plett,Claire Veneault-Fourrey
Molecular Mycorrhizal Symbiosis
DOI: 10.1002/9781118951446.ch9

Harnessing mycorrhizal genomics for biological insights

Francis Martin
Molecular Mycorrhizal Symbiosis, ed. Francis Martin

The evolution of the mycorrhizal lifestyles - a genomic perspective

Annegret Kohler,Francis Martin
Molecular Mycorrhizal Symbiosis
Ed. Francis Martin

Mycorrhiza helper bacteria

Aurélie Deveau,Jessy Labbé
Molecular Mycorrhizal Symbiosis
Ed. Francis Martin

Molecular Mycorrhizal Symbiosis

Francis Martin

Fungal and plant gene expression in the Tulasnella calospora–Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas

Valeria 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 Evolution

Lázló 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 elasticity

Sahar 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 symbioses

Francis 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 physiology

Jeremiah 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
Populus

Udaya 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 geophilum

Martina 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 Populus

Yongil 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 analysis

Sagar 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 glycines

Jingyu 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 conditions

Aurélie 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 system

Collin 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 colonization

Amber 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 microarray

Fabiano 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 genomics

A.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 Populus

Kaijie 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

The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis

Xiaoping 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 Proteins

Clement 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 Rhizosphere

Dawn 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 bacteria

Collin 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 ancestors

Firoz 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 compartment

Collin 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 biology

Jonathan 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 biogeochemistry

Jennifer 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 microbiome

C. 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 plants

Jin-Gui Chen
Plant Signaling and Behavior 10(8):

Sequence data for Clostridium autoehanogenum using three generations of sequencing technologies

Sagar 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 defenses

Jonathan 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 sequencing

Miriam 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 mutualists

Annegret 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 mycorrhizas

Ian 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 communities

Cheryl 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

Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem function

David 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 microbiome

Stéphane Hacquard,Christopher W. Schadt
New Phytologist, doi: 10.1111/nph.13133

Expanding genomics of mycorrhizal symbiosis

Alan Kuo, Annegret Kohler, Francis M. Martin, and Igor V. Grigoriev
Frontiers in Microbiology. doi: 10.3389/fmicb.2014.00582

Quality scores for 32,000 genomes

Miriam 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 Populus

Jessy 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 establishment

Claire 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 erythrophthalmus

Kevin 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 Metabolomics

Yinfeng Wang,Guruprasad Kora,Benjamin P Bowen,Chongle Pan
Analytical Chemistry
DOI: 10.1021/ac5014783

Characterization of MORE AXILLARY GROWTH Genes in Populus

Olaf 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 yeasts

László 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 plants

Gregory 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 them

Jessy 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 sequences

Sagar 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 genes

Jonathan 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 Clostridia

Steven 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 Plants

Tatiana 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 Arabidopsis

Zhou 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 bicolor

Timothy 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 BBc6R8

A. 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 roots

Jonthan 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

Single cell swimming dynamics of Listeria monocytogenes using a nanoporous microfluidic platform

Evan Wright, Suresh Neethirajan, Ketih Warriner, Scott Retterer and Bernadeta Srijanto
Lab Chip, 2014 14(5): 938-46

The Mycorrhizal Symbiosis Genomics

Francis Martin and Annegret Kohler
The Ecological Genomics of Fungi December 2013

The Ecological Genomics of Fungi

Francis Martin
The Ecological Genomics of Fungi December 2013

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

Emilie 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'amour

Marc-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 populi

Posy 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 bisporus

Aleksandrina 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 Fungi

Claude 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 capture

Ryan 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 3742–3748
DOI: 10.1021/bm4011358

Extreme diversification of the mating type-high mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus

Rohan 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 function

Claire 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 microbiome

Amy 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 proteomics

Yingfeng 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 Plants

Olaf 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 kingdom

Daisuke 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 analyses

Claire 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 plants

Chu-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 Environments

Wellington 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 communities

Shakya 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 symbiosis

Daniel 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

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 ERECTA

Dhavel 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 interactions

Poornima 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 generator

Meng 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 niche

Emmanuelle 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 associations

Guevara 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 Assays

Jianjun 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 deltoides

Steven 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 genes

Abhijit 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 bicolor

Jessy 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 sequences

Doug 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 fitness

David 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 ArcA

Michael 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 networks

Tatiana V. Karpinets, Byung H. Park, Edward C. Uberbacher
Nucleic Acids Research. 2012 September; 40(17): 1-8

Communication Between Plant, Ectomycorrhizal
Fungi and Helper Bacteria

Aurélie 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 Acetyltransferases

Heidi 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 deltoides

Steve 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 bicolor

Jonathan 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 trichocarpa

Nag A, Karpinets TV, Chang CH, Bar-Peled M.
Database (Oxford). 2012; 2012: bas013.

Signaling in ectomycorrhizal symbiosis

Judith 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 Development

Jonathan 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 bicolor

Jonathan 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 signaling

Elise Schnabel, Abhijit Karve, Tessema Kassaw, Arijit Mukherjee, Xin Zhou, Tim Hall and Julia Frugoli
Plant Signaling and Behavior 7(1): 4-6

 


 

Publications - 2011

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

Zhou 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 symbiont

E. 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 Modeling

Chongle Pan
PLoS ONE 6 (12): e28827

Secretome of the Free-living Mycelium from the Ectomycorrhizal Basidiomycete Laccaria bicolor

Delphine 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 Symbiosis

Jonathan M. Plett and Francis Martin
Effectors in Plant-Microbe Interactions 2011, pages 295-326

Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

Florence 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 Microscopy

David 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 max

David 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 trichocarpa

Verónica 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 future

Jianjun 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 Development

Jonathan 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 Symbiosis

Jonathan 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 life

F. 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 approaches

Xiaohan 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 markers

Jessy 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

Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar

Olga 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 database

Byung 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 regions

Tatiana 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.