CAHNRS > Department of Plant Pathology > Jana U’Ren

Jana U’Ren

  1. Assistant Professor (Compressed Appt.)
Email Addressjana.uren@wsu.edu
LocationClark Hall

Biography

Research Specialty and Interests

The U’Ren lab studies the biodiversity, biogeography, evolutionary origins, and ecological roles of fungal endophytes using a combination of traditional culture-based microbiology, functional assays, and next-generation ‘omics tools. We are interested in characterizing the biotic and abiotic factors shaping the assembly of fungal endophyte communities that associate with diverse lineages of land plants, how endophyte community structure and diversity impact natural and agro-ecosystem functions, and the evolutionary dynamics of endophyte evolution in the context of closely related pathogens and saprotrophs.

Specific projects include:

Comparative and population genomics of fungi in the Xylariaceae s.l.

Global, large-scale surveys of phylogenetically diverse plants and lichens (where endophytes live in association with the algal photobiont) have revealed a particularly high richness of endophytes in the fungal family Xylariaceae (Sordariomycetes, Pezizomycotina, Ascomycota) in boreal, temperate, subtropical, and tropical forests. In addition to their ecological roles in living leaves, many endophyte species also are found in decomposing leaves, wood, bark, fruits, or flowers, thus suggesting abilities to degrade lignocellulose. In collaboration with the DOE Joint Genome Institute (Grant , we are addressing the evolution of plant-endophyte symbioses, the diversity of fungal secondary metabolites, and lignocellulose degradation in the Xylariaceae. Results of this work have been published in New Phytologist.

Dimensions of Endophyte Biodiversity in the boreal biome

In collaboration with Drs. Betsy Arnold (University of Arizona), François Lutzoni, Jolanta Miadlikowska (Duke University), and Ignazio Carbone (NC State University), have conducted global field surveys of phylogenetically diverse plants and lichens across the boreal biome to examine the diversity, biogeography, host associations, and climate sensitivity of fungal endophytes using both culture-based and culture-free methods. We have found that boreal endophyte communities are highly diverse, with the highest diversity occurring in non-vascular plants and lichens. At a global scale, endophyte community composition is structured by host lineage rather than geographic distance, and communities are characterized by a large fraction of both host and site-specific species. At a landscape scale, endophyte communities in the same hosts are influenced more strongly by climate than geographic distance or other abiotic factors.  However, endophytes in three different host genera (Picea, Pleurozium, and Cladonia) respond to the climate in different ways. Results from our work have been published in Nature Ecology and Evolution and Current Biology. This work was funded by the NSF-funded Dimensions of Endophyte Diversity.

Leveraging historical collections and new surveys to characterize foundational shifts in vital symbioses in the threatened Arctic

Using the same sampling and molecular methods, we are extending this work to examine endophytes in the same host plants and lichens across the threatened terrestrial Arctic, which is greatly imperiled by rapid climate change. The goal of this project is to track the temporal and spatial shifts of endophytic symbionts, which will help develop a better understanding of how fungal symbionts of iconic plants and lichens in the Arctic will respond as the climate shifts. This project involves extensive field surveys across all Arctic subzones (led by Arnold, Lutzoni, Miadlikowska), well as sampling of endophytes from plant and lichen herbarium specimens collected from the same geographic locations over the past 50+ years (led by Arnold, U’Ren), and biodiversity modeling conducted by Dr. Barnabas Daru (Co-PI, Standford University). This project is funded by NSF, DEB – Systematics and Biodiversity Science (Award No. 2031925)

Advancing Carbonyl Sulfide (OCS) as an Independent Atmospheric Tracer for Global Photosynthesis through Quantification of Microbial-mediated Sources and Sinks in Soils

In this collaborative project, the U’Ren lab is partnering with Drs. Laura Meredith (PI, University of Arizona), Roísín Commane (Co-I, Columbia University), Ian Baker (Co-I, Colorado State University), and Aleya Kaushik (NOAA) to characterize fluxes of Carbonyl Sulfide (OCS)—an atmospheric trace gas with potential to constrain estimates of global photosynthesis—in Boreal and Arctic sites in Alaska as these ecosystems are critical to the global carbon cycle. The over-arching goal of this project is to generate a better understanding of microbial-driven OCS fluxes to improve soil OCS representation in land-atmosphere models such as SiB4. To do so, we are using a interdisciplinary approach that includes field and laboratory OCS measurements, fungal genomics/transcriptomics, as well as culture-based and culture-free characterization of fungal communities in plants and soils. This project is funded by the NSF AGS Atmospheric Chemistry (Award No. 1933280).

Education

  • PhD Plant Pathology, Minor Ecology and Evolutionary Biology, School of Plant Sciences, The University of Arizona, Tucson, AZ
  • BA Biological Science, emphasis Ecology and Evolution, University of Missouri-Columbia, Columbia, MO

Professional Experience

  • 2023-current, Assistant Professor, Department of Plant Pathology, Washington State University
  • 2017-2023, Assistant Professor, Department of Biosystems Engineering and BIO5 Institute, The University of Arizona
  • 2015-2017, Postdoctoral Research Associate, Department of Agricultural and Biosystems Engineering, The University of Arizona
  • 2011-2015, Postdoctoral Research Associate, School of Plant Sciences, The University of Arizona

Awards, Honors, and Memberships

  • 2022, Kavli Frontiers of Science Fellow, National Academy of Science
  • 2008, R.P. Korf Mentor Student Travel Award, Mycological Society of America
  • 2008, Clark T. Rogerson Student Research Award, Mycological Society of America
  • 2015-present, American Society for Microbiology (ASM)
  • 2007-present, Mycological Society of America (MSA)

Publications

  • J.M. U’Ren, S. Oita, F. Lutzoni, J. Miadlikowska, B. Ball, I. Carbone, G. May, N.B. Zimmerman, D. Valle, V. Trouet, A.E. Arnold. 2024. Environmental drivers and cryptic biodiversity hotspots define endophytes in earth’s largest terrestrial biome. Current Biology https://doi.org/10.1016/j.cub.2024.01.063
  • M.N. Nickerson, L.P. Moore, J.M. U’Ren. 2023. Impact of polyphenolic compounds on the in vitro growth of oak-associated endophytic and saprotrophic fungi. Fungal Ecology, 62: 101226. https://doi.org/10.1016/j.funeco.2023.101226
  • Fauchery, M. Koriabine, L.P. Moore, Y, Yoshinaga, K. Barry, A. Kohler, J.M. U’Ren. 2023. Tissue Cultivation, Preparation, and Extraction of High Molecular Weight DNA for Single-Molecule Genome Sequencing of Plant-Associated Fungi. In. Methods in Molecular Biology. Eds. F. Martin & S. Uroz. Volume 2605, pgs. 79-102. 10.1007/978-1-0716-2871-3_5
  • J.P. Shaffer, et al. 2022. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nature Microbiology. https://doi.org/10.1038/s41564-022-01266-x.
  • M.E.E. Franco, J.H. Wisecaver, A.E. Arnold, Y-M. Ju, J.C. Slot, S. Ahrendt, L.P. Moore, K.E. Eastman, K. Scott, Z. Konkel, JGI Team, E. Drula, B. Henrissat, H-M. Hsieh, K. Youens-Clark, F. Lutzoni, J. Miadlikowska, D.C. Eastwood, R.C. Hamelin, I.V. Grigoriev, J.M. U’Ren. 2022. Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. New Phytologist. 233: 1317–1330. https://doi.org/10.1111/nph.17873
  • A.J. Ponsero, B.H. Hurwitz, N. Magain, J. Miadlikowska, F. Lutzoni, J.M. U’Ren. 2021. Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism. ISME Communications 1:56. https://doi.org/10.1038/s43705-021-00060-w
  • J.M. U’Ren, N.B. Zimmerman. 2021. Oaks provide new perspective on seed microbiome assembly. New Phytologist, 230: 1293–1295 (Invited Commentary). https://doi.org/10.1111/nph.17305
  • A.E. Arnold, A.H. Harrington, Y-L. Huang, J.M. U’Ren, N.C. Massimo, V. Knight-Connoni, P. Inderbitzin. 2021. Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov., three new species of endophytes with distinctive morphology and functional traits. International Journal of Systematic and Evolutionary Microbiology 71:005003. https://doi.org/10.1099/ijsem.0.005003
  • A.E. Arnold, A.H. Harrington, J.M. U’Ren, S. Oita, P. Inderbitzin. 2021. Two new endophytic species enrich the Coniochaeta endophytica/C. prunicola clade: Coniochaeta lutea sp. nov. and C. palaoa sp. nov. Plant and Fungal Systematics 66: 66–78. https://doi.org/10.35535/pfsyst-2021-0006
  • Qu, E.M.K. Wijeratne, B.P. Bashyal, J. Xu, Y-M. Xu, M.X. Liu, M.C. Inácio, A.E. Arnold, J.M. U’Ren, A.A.L. Gunatilaka. 2021. Strobiloscyphones A–F, 6-Isopentylsphaeropsidones and other metabolites from Strobiloscypha sp. AZ0266, a leaf-associated fungus of Douglas fir. Journal of Natural Products 84: 2575–2586. https://doi.org/10.1021/acs.jnatprod.1c00662
  • Oita, A. Ibáñez, F. Lutzoni, J. Miadlikowsk, J. Geml, L.A. Lewis, E.F.Y. Hom, I. Carbone, J.M. U’Ren, A.E. Arnold. 2021. Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale. Communications Biology 4: 313. https://doi.org/10.1038/s42003-021-01826-7
  • Oita, J. Carey, I. Kline, A. Ibáñez, N. Yang, E.F.Y. Hom, I. Carbone, J. M. U’Ren, A.E. Arnold. 2021. Methodological approaches frame insights into endophyte richness and community composition. Microbial Ecology 82: 21–34. https://doi.org/10.1007/s00248-020-01654-y
  • Selbmann, Z. Benkő, C. Coleine, S. de Hoog, C. Donati, I. Druzhinina, T. Emri, C.L. Ettinger, A.S. Gladfelter, A.A. Gorbushina, I.V. Grigoriev, M. Grube, N. Gunde-Cimerman, Z. Á. Karányi, B. Kocsis, T. Kubressoian, I. Miklós, M. Miskei, L. Muggia, T. Northen, M. Novak-Babič, C. Pennacchio, W.P. Pfliegler, I. Pòcsi, V. Prigione, M. Riquelme, N. Segata, J. Schumacher, E. Shelest, K. Sterflinger, D. Tesei, J.M U’Ren, G.C. Varese, X. Vázquez-Campos, V.A. Vicente, E.M. Souza, P. Zalar, A.K. Walker, J.E. Stajich. 2020. Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES. Life 10: 362. https://doi.org/10.3390/life10120362
  • Y.M. Xu, A.E. Arnold, J.M. U’Ren, L.J. Xuan, W.Q. Wang, A.A.L. Gunatilaka. 2020. Teratopyrones A–C, Dimeric Naphtho-γ-Pyrones and other metabolites from Teratosphaeria sp. AK1128, a fungal endophyte of Equisetum arvense. Molecules 25: 5058; https://doi.org/10.3390/molecules25215058.
  • Apprill, C. Miller, J. M. U’Ren, M. S. Leslie, L. Weber, R. Baird, J. Robbins, S. Landry, M. Niemeyer, G. Waring, A. Bogolomoni. 2020. Host phylogeny shapes marine mammal skin microbiomes. Royal Society Open Science. https://doi.org/10.1098/rsos.192046
  • J.M. U’Ren, F. Lutzoni, J. Miadlikowska, N.B. Zimmerman, I. Carbone, G. May, A.E. Arnold. 2019. Host availability drives distributions of fungal endophytes in the imperiled boreal realm, Nature Ecology and Evolution 3: 1430–1437. https://doi.org/10.1038/s41559-019-0975-2
  • Dietzel, D. Valle, N. Fierer, J.M. U’Ren, A. Barberán. 2019. Geographical distribution of fungal plant pathogens in dust across the United States. Frontiers in Ecology and Evolution https://doi.org/10.3389/fevo.2019.00304
  • Carbone, J.B. White, J. Miadlikowska, A.E. Arnold, M.A. Miller, N. Magain, J.M. U’Ren, F. Lutzoni. 2019. T-BAS Version 2.1: Tree-Based Alignment Selector toolkit for evolutionary placement of DNA sequences and viewing alignments and specimen metadata on curated and custom trees. Microbiology Resource Announcements, https://doi.org/10.1128/MRA.00328-19
  • H. Harrington, M. del Olmo-Ruiz, J.M. U’Ren, K. Garcia, D.C. Sandberg, Y.L. Huang, M.T. Hoffman, A.E. Arnold. 2019. Coniochaeta endophytica sp. nov., a foliar endophyte associated with healthy photosynthetic tissue of Platycladus orientalis (Cupressaceae). Plant and Fungal Systematics 64: 65–79.  https://doi.org/10.2478/pfs-2019-0008
  • M.J. Taylor, R.W. Mannan, J.M. U’Ren, N.P. Garber, R.E. Gallery, A.E. Arnold. 2019. Age-related variation in the oral microbiome of urban Cooper’s hawks (Accipiter cooperii). BMC Microbiology 19: 47. https://doi.org/10.1186/s12866-019-1413-y
  • Huang, Y.-L., E.A. Bowman, N.C. Massimo, N.P. Garber, J.M. U’Ren, D.C. Sandberg, A.E. Arnold. 2018. Using collections data to infer biogeographic, environmental, and host structure in communities of endophytic fungi. Mycologia, 110:1, 47–6. https://doi.org/10.1080/00275514.2018.1442078.
  • Padumadasa, C., Y.-M. Xu, E.M. Kithsiri Wijeratne, P. Espinosa, J.M. U’Ren, A.E. Arnold, A.A.L. Gunatilaka. 2018. Cytotoxic and non-cytotoxic metabolites from Teratosphaeria sp. FL2137, a fungus associated with Pinus clausa. Journal of Natural Products, J. Nat. Prod. 81: 616–624. https://doi.org/10.1021/acs.jnatprod.7b00838
  • B.L. Hurwitz, A. Ponsero, J. Thorton, Jr., J.M. U’Ren. 2018. Phage Hunters: computational strategies for finding phages in large-scale ‘omics datasets. Virus Research. 244: 110–115. https://doi.org/10.1016/j.virusres.2017.10.019
  • Sarmientoa, P-C. Zalamea, J.W. Dalling, A.S. Davis, S.M. Stump, J.M. U’Ren, A.E. Arnold. 2017. Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest. Proceedings of the National Academy of Sciences USA. 114: 11458–11463. https://doi.org/10.1093/bioinformatics/btw808
  • Schaffer, J.M. U’Ren, R.E. Gallery, D.A.. Baltrus, A.E. Arnold. 2017. An endohyphal bacterium (Chitinophaga, Bacteroidetes) Alters carbon source use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae). Frontiers in Microbiology 8:350.  https://doi.org/10.3389/fmicb.2017.00350
  • Carbone, J.B. White, J. Miadlikowska, A.E. Arnold, M.A. Miller, F. Kauff, C. Schoch, J.M. U’Ren, G. May & F. Lutzoni. 2017. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization, Bioinformatics 33: 1160–1168. https://doi.org/10.1093/bioinformatics/btw808
  • J.M. U’Ren & A.E. Arnold. 2016. Diversity, distributions, and host associations of fungal communities in living, senescent, and fallen leaves at five sites across North America, Peer J e2768.  https://doi.org/10.7717/peerj.2768
  • J.M. U’Ren, J. Miadlikowska, N. Zimmerman, J.E. Stajich, F. Lutzoni & A.E. Arnold. 2016. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution 98: 210–232. https://doi.org/10.1016/j.ympev.2016.02.010
  • B.L. Hurwitz & J.M. U’Ren. 2016. Viral metabolic reprogramming in marine ecosystems. Current Opinion in Microbiology 31: 161–168.  https://doi.org/10.1016/j.mib.2016.04.002
  • B.L. Hurwitz, J.M. U’Ren & K. Youens-Clark. 2016. Computational prospecting in the great viral unknown. FEMS Microbiology Reviews. http://dx.doi.org/10.1093/femsle/fnw077.
  • J.M. U’Ren, J.H. Wisecaver, A.L. Paek, B.L. Dunn & B.L. Hurwitz. 2015. Draft genome sequence of the ale-fermenting Saccharomyces cerevisiae strain GSY2239. Genome Announcements 3: 4. https://doi.org/10.1128/genomeA.00776-15
  • K.E.M. Wijeratne, G.M.K.B. Gunaherath, V.M. Chapla, J. Tillotson, F. de la Cruz, M. Kang, J.M. U’Ren, A.R. Araujo, A.E. Arnold, E. Chapman & AA.L. Gunatilaka. 2015. Oxaspirol B with p97 inhibitory activity and other oxaspirols from Lecythophora sp. FL1375 and FL1031, endolichenic fungal strains inhabiting Parmotrema tinctorum and Cladonia evansii. Journal of Natural Products 79:340–352. https://doi.org/10.1021/acs.jnatprod.5b00986
  • P.L. Chagnon, J.M. U’Ren, J. Miadlikowska, F. Lutzoni & A.E. Arnold. 2015. Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale. Oecologia https://doi.org/10.1007/s004442-015-3457-5.
  • Y-M. Xu, J. Mafezoli, M.C.F. de Oliveira, J.M. U’Ren, A.E. Arnold & A.A.L. Gunatilaka. 2015. Anteaglonialides A–F and Palmarumycins CE1–CE3 from Anteaglonium sp. FL0768, a fungal endophyte of the spikemoss Selaginella arenicola. Natural Product Communications 78: 2738–2747.
  • Wei H, Y.M. Xu, P. Espinosa-Artiles, M.X. Liu, J.G. Luo, J.M. U’Ren, A.E. Arnold & A.A.L. Gunatilaka. 2015. Sesquiterpenes and other constituents of Xylaria sp. NC1214, a fungal endophyte of the moss Hypnum sp. Phytochemistry 118: 102–8.
  • Y-L. Huang, M.M.N. Devan, J.M. U’Ren, S.H. Furr & A.E. Arnold. 2015. Pervasive effects of wildfire on foliar endophyte communities in montane forest trees. Microbial Ecology doi 10.1007/s00248-015-0664-x.
  • Y-M. Xu, B.P. Bashyal, M.X. Liu, P. Espinosa-Artiles, J.M. U’Ren, A.E. Arnold & A.A.L. Gunatilaka. 2015. Cytotoxic cytochalasins and other metabolites from Xylariaceae sp. FL0390, a fungal endophyte of Spanish moss. Natural Product Communications 10: 1655–1658.
  • N.C. Massimo, M.M.N. Devan, K.R. Arendt, M.H. Wilch, J.M. Riddle, S.H. Furr, C. Steen, J.M. U’Ren, D.C. Sandberg & A.E. Arnold. 2015. Fungal Endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts. Microbial Ecology 70: 61–76.
  • K-H. Chen, J. Miadlikowska, K. Molnár, A.E. Arnold, J.M. U’Ren, E. Gaya, C. Gueidan & F. Lutzoni. 2015. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales and a new order – Phaeomoniellales. Molecular Phylogenetics and Evolution 85: 117–130.
  • J.M. U’Ren, J.M. Riddle, J.T. Monacell, I. Carbone, J. Miadlikowska & A.E. Arnold. 2014. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Molecular Ecology Resources 14: 1032–1048.
  • J-G. Luo, X. Wang, Y-M. Xu, J.M. U’Ren, A.E. Arnold, L-Y. Kong & A.A.L. Gunatilaka. 2014. Delitschiapyrone A, a Pyrone–naphthalenone Adduct bearing a new pentacyclic ring system from the leaf-associated fungus Delitschia sp. FL1581. Organic Letters 6: 5944–5947.
  • Oono, F. Lutzoni, A.E. Arnold, L. Kaye, J.M. U’Ren, G. May & I. Carbone. 2014. Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species. American Journal of Botany 101: 1362–1374.
  • J.M. U’Ren, F. Lutzoni, J. Miadlikowska, A.D. Laetsch & A.E. Arnold. 2012. Host- and geographic structure of endophytic and endolichenic fungal communities at a continental scale. American Journal of Botany. 99: 898–914.
  • E.M.K. Wijeratne, B.P. Bashyal, M.X. Liu, D.D. Rocha, G.M. Kamal, B. Gunaherath, J.M. U’Ren, M.K. Gunatilaka, A.E. Arnold, L. Whitesell & A.A.L. Gunatilaka. 2012. Geopyxins A – E, ent-kaurane diterpenoids from endolichenic fungal strains, Geopyxis aff. majalis and Geopyxis sp. AZ0066: structure-activity relationships of geopyxins and their analogues. Journal of Natural Products. 75: 361–369.
  • X-N Wang, B.P. Bashyal, E.M.K. Wijeratne, J.M. U’Ren, M.X. Liu, M.K. Gunatilaka, A.E. Arnold & A.A.L. Gunatilaka. 2011. Smardaesidins A – G, new isopimarane and 20-nor-isopimarane diterpenoids from Smardaea sp., a fungal endophyte of the moss Ceratodon purpureus. Journal of Natural Products. 74: 2052–2061.
  • J.M. U’Ren, F. Lutzoni, J. Miadlikowska & A.E. Arnold. 2010. Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microbial Ecology 60: 340–353.
  • J.M. U’Ren. 2009. Is the hope for a cellulosic biofuel a lot of rot? Environmental Microbiology. 11: 2475–2476.
  • T.S. Simonson, R.T. Okinaka, B. Wang, W.R. Easterday, L. Huynh, J.M. U’Ren, M. Dukerich, S.R. Zanecki, L.J. Kenefic, J. Beaudry, et al. 2009. Bacillus anthracis in China and its relationship to worldwide lineages. BMC Microbiology 9: 71.
  • J.M. U’Ren, J.W. Dalling, R.E. Gallery, D.R. Maddison, E.C. Davis, C.M. Gibson & A.E. Arnold. 2009. Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analyzing environmental samples of fungi. Mycological Research 113: 432–449.
  • J.M. U’Ren, H. Hornstra, T. Pearson, J.M. Schupp, B. Leadem, S. Georgia, R.W. Sermswan & P. Keim. 2007. Fine scale genetic diversity among Burkholderia pseudomallei soil isolates in Northeast Thailand.  Journal of Applied and Environmental Microbiology 73: 6678–6681.
  • Pearson, J.M. U’Ren, J.M. Schupp, G. Allan, P.G. Foster, M.J. Mayo, D.Gal, J. Low Choy, R. Leadem Daugherty, S. Kachur, et al. 2007. VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia. Infection, Genetics and Evolution 7: 416–423.
  • N. Van Ert, W.R. Easterday, L.Y. Huynh, R.T Okinaka, M.E. Hugh Jones, J. Ravel, S.R. Zanecki, T. Pearson, T.S. Simonson, J.M. U’Ren, et al. 2007. Global genetic population structure of Bacillus anthracis. PLoS One 5:e461.
  • J.M. U’Ren, J.M. Schupp, T. Pearson, H. Hornstra, C.L. Clark Friedman, K.L. Smith, R.R. Leadem Daugherty, S.D. Rhoton, B. Leadem, S. Georgia, et al. 2007. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping.  BMC Microbiology 7: 23.
  • M.N. Van Ert, W.R. Easterday, T.S. Simonson, J.M. U’Ren, T. Pearson, L.J. Kenefic, J.D. Busch, L.Y. Huynh, M. Dukerich, C.B. Trim, et al. 2007. Strain-specific single nucleotide polymorphism assays for the Bacillus anthracis Ames strain. Journal of Clinical Microbiology 45: 47–53.
  • J.M. U’Ren, M.N. Van Ert, J.M. Schupp, W.R. Easterday, T. Simonson, R. Okinaka, T. Pearson & P. Keim. 2005. Use of a real-time PCR TaqMan assay for rapid identification and differentiation of Burkholderia pseudomallei and Burkholderia mallei. Journal of Clinical Microbiology 43: 5771–5774.
  • Pearson, J. Busch, J. Ravel, T. Read, S. Rhoton, J.M. U’Ren, T. Simonson, S. Kachur, R. Leadem, M. Cardon, et al. 2004. Phylogenetic discovery bias in Bacillus anthracis using single nucleotide polymorphisms from whole genome sequencing. Proceedings of the National Academy of Sciences USA 101: 13536–13541.
  • M.I. Tenaillon, J. U’Ren, O. Tenaillon & B.S. Gaut. 2004. Selection versus demography:  a multilocus investigation of the domestication process in maize. Molecular Biology and Evolution 21: 1214–1225.

Protocols

High throughput measurement of endophyte growth:

High throughput quantification of phenolic compounds:

Protocols for fungal DNA extraction for genotyping via PCR:

Protocols for fungal DNA extraction for genome sequencing:

Protocol for growing fungi on solid media for RNA or DNA extraction:

Protocols to extract total gDNA from plants for microbial studies:

Protocols for ITS/16S library preparation for Illumina Amplicon Sequencing: