Publications

Sweany RR, Breunig M, Opoku J, Clay K, Spatafora JW, Drott MT, Baldwin TT, Fountain JC. 2022. Why do plant pathogenic fungi produce mycotoxins? Potential roles for mycotoxins in the plant ecosystem. Phytopathology 112:2044-2051. https://doi.org/10.1094/PHYTO-02-22-0053-SYM
Tehan RM, Blount RR, Goold RL, Mattos DR, Spatafora NR, Tabima JF, Gazis R, Wang C, Ishmael JE, Spatafora JW, McPhail KL. 2022. Tolypocladamid H and the proposed tolypocladmide NRPS in Tolypocladium species. Journal of Natural Products 85: 1363–1373.
Chang Y, Wang Y, Mondo S, Ahrendt S, Andreopoulos W, Barry K, Beard J, Benny GL, Blankenship S, Bonito G, Cuoma C, Desiro A, Gervers KA, Hundley H, Kuo A, LaButti K, Lang BF, Lipzen A, O’Donnell K, Pangilinan J, Reynolds N, Sandor L, Smith MW, Tsang A, Grigoriev IV, Stajich JE, and Spatafora JW. 2022. Fungi are what they secrete: evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies. iScience 25 (8): 104840. https://doi.org/10.1016/j.isci.2022.104840.
Amses, K et al3. 2022. Phylogenomic analysis of zoosporic taxa suggests diploid-dominant life cycles characterized the early evolution of Fungi. PNAS 119 (36): e2116841119 https://doi.org/10.1073/pnas.2116841119.
Gervers KA, Thomas DC, Roy BA, Spatafora JW, Busby PE. 2022. Crown closure affects endophytic leaf mycobiome compositional dynamics over time in Pseudotsuga menziesii var. menziesii. Fungal Ecology 57-58: 101155.
Wu G, Miyauchi S, Morin E, Kuo A, Drula E, Varga T, Kohler A, Feng B, Cao Y, LaButti K, Ng V, Min B, Park H, Choi I-G, Plett J, Magnuson J, Spatafora JW, Nagy LG, Henrissat B, Grigoriev IV, Yang Z-L, Xu J, Martin FM. 2022. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales. New Phytologist 233: 1383-1400. https://doi.org/10.1111/nph.17858.
Hagestad OC, Hou L, Andersen JH, Hansen E, Altermark B, Li C, Kuhnert E, Crous PW, Spatafora JW, Grigoriev IV, Jackson SA, Cox R, Dobson ADW, Rämä T. 2021. Genomic characterization of three marine fungi, including a description of a new Emericellopsis species with signatures of a generalist lifestyle and marine biomass degradation. IMA Fungus 12, 21. https://doi.org/10.1186/s43008-021-00072-0
Hage H, Miyauchi S, Virágh M, Drula E, Min B, Chaduli D, Navarro D, Favel A, Norest M, Lesage-Meessen L, Bálint B, Merényi Z, de Eugenio L, Morin E, Martínez AT, Baldrian P, Štursová M, Martínez MJ, Novotny C, Magnuson JK, Spatafora JW, Maurice S, Pangilinan J, Andreopoulos W, LaButti K, Hundley H, Na H, Kuo A, Barry K, Lipzen A, Henrissat B, Riley R, Ahrendt S, Nagy LG, Grigoriev IV, Martin F, Rosso M-N. 2021. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay. Environ. Microbiol. 21: doi:10.1111/1462-2920.15423.
Li Y, Steenwyk JL, Chang Y, Grigoriev IV, James TY, Stajich JE, Spatafora JW, Groenewald M, Hittinger CT, Shen X-X, Rokas A. 2021. A genome-scale phylogeny of the kingdom Fungi: insights into early evolution, radiations, and the relationship between taxonomy and phylogeny. Current Biology 31: https://doi.org/10.1016/j.cub.2021.01.074.
Chang Y, Rochon DA, Sekimoto S, Wang Y, Chovatia M, Sandor L, Salamov A, Grigoriev IV, Stajich JE, Spatafora JW. 2021. Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi. Scientific Reports 11: https://doi.org/10.1038/s41598-021-82607-4
Tabima JF, Trautman IA, Chang Y, Mondo S, Kuo A, Salamov A, Grigoriev IV, Stajich JE, Spatafora JW. 2020. Phylogenomic analyses of non-Dikarya fungi support horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestional symbiont, Basidiobolus. G3: Genes, Genomes, Genetics 10: 3417-3433. doi: https://doi.org/10.1534/g3.120.401516
Shingo Miyauchi, Enikő Kiss, Alan Kuo, Elodie Drula, Annegret Kohler, Marisol Sanchez-Garcia, Bill Andreopoulos, Kerrie W. Barry, Gregory Bonito, Marc Buée, Akiko Carver, Cindy Chen, Nicolas Cichocki, Alicia Clum, David Culley, Pedro W. Crous, Laure Fauchery, Mariangela Girlanda, Richard D. Hayes, Zsófia Kéri, Kurt LaButti, Anna Lipzen, Vincent Lombard, Jon Magnuson, François Maillard, Emmanuelle Morin, Claude Murat, Matt Nolan, Robin Ohm, Jasmyn Pangilinan, Maira Pereira, Silvia Perotto, Martina Peter, Robert Riley, Yaron Sitrit, Benjamin Stielow, Gergely Szöllősi, Lucia Zifcakova, Martina Stursova, Joseph W. Spatafora, Leho Tedersoo, Lu-Min Vaario, Akiyoshi Yamada, Mi Yan, Pengfei Wang, Jianping Xu, Tom Bruns, Petr Baldrian, Rytas Vilgalys, Bernard Henrissat, Igor V. Grigoriev, David Hibbett, László G. Nagy, Francis M. Martin. 2020. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nature Communications 11, 5125. https://doi.org/10.1038/s41467-020-18795-w
Myers JM, Bonds AE, Clemon RA, Thapa NA, Simmon DR, Carter-House D, Ortanez J, Liu P, Miralles-Durán, Desirò A, Longcore JE, Bonito G, Stajich JE, Spatafora JW, Chang Y, Corrochano LM, Gryganskyi A, Grigoriev IV, James TY. 2020. Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses. mBIO 11:e02027-20. https://doi.org/10.1128/mBio.02027-20.
Gluck-Thaler E, Haridas S, Binder M, Grigoriev IV, Crous PW, Spatafora JW3,4, Bushley KE, Slot JC. 2020. Shared linkage reveals new dimensions of chemodiversity in the largest class of fungi. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msaa122
Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, Castanera R, Culley DE, Daum C, Ezra D, González, Henrisaat B, Kou A, Liang C, Lipzen A, Lutzoni F, Magnuson J, Mondo SJ, Nolan M, Ohm RA, Pangilinan J, Park H-J, Ramírez, Alfar M, Sun H, Tritt A, Yoshinaga Y, Zwiers L-H, Turgeon BG, Goodwin SB, Spatafora JW, Crous PW, Grigoriev IV. 2020. 101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens. Studies in Mycology 96: 141-153.
Park H, Min B, Jang Y, Kim J, Lipzen A, Sharma A, Andreopoulos B, Johnson J, Riley R, Spatafora JW, Henrissat B, Kim KH, Grigoriev IV, Kim J-J, Choi I-G. 2019. Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613. Applied microbiology and biotechnology 103: 8145-8155.
Guarnaccia V, Gehrmann T, Silva-Junior GJ, Fourie PH, Harida S, Vu D, Spatafora J, Martin FM, Robert V, Grigoriev IV, Groenewald JZ, Crous PS. 2019. Phyllosticta citricarpa and sister species of global importance to Citrus. Molecular Plant Pathology DOI: 10.1111/mpp.12861.
Uehling J, Entler M, Meredith H, Millet L, Timm C, Aufrecht J, Bonito G, Engle N, Labbé J, Doktycz M, Retterer S, Spatafora J, Stajich J, Tschaplinski T, Vilgalys R. 2019. Microfluidics and metabolomics reveal symbiotic bacterial-fungal interactions between Mortierella elongata and Burkholderia include metabolite exchange. Frontiers Microbiology 10: 2163 DOI:10.3389/fmicb.2019.02163
Davis WJ, Chang Y, Amses K, Stajich JE, Benny G, Smith M, Spatafora JW, Grigoriev I, Carter-House D, James TY. 2019. Genome-scale phylogenetics analyses reveals a monophyletic Zoopagales (Zoopagomycota, Fungi) with predacious taxa evolving from mycoparasite ancestors. Molecular Phylogenetic and Evolution 133: 152-163.
Olarte RA, Menke J, Zhang Y, Sullivan S, Slot J, Huang YJ, Badalamenti JP, Quandt CA, Spatafora JW, and Bushley KE. 2019. Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum. BMC Genomics 20: 120.
Mujic AB, Zheng N, Kim K, Spatafora JW, Castellano MA, Smith ME. 2019. The Cedrus-associated truffle Trappeindia himalayensis is a morphologically unique and phylogenetically divergent species of Rhizopogon. Mycologia 111: 225–234.
Chang Y, Desiro A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev I, Martin F, Stajich J, Smith M, Bonito G, Spatafora JW. 2019. Phylogenomics of Endogonaceae and evolution of mycorrhizae within Mucoromycota. New Phytologist 122: 511-525.
Mujic AB, Huang B, Chen M-J, Wang P-H, Gernandt D, Hosaka K, Spatafora JW. 2019. Out of Western North America: evolution of the Rhizopogon-Pseudotsuga symbiosis inferred by genome-scale sequence typing. Fungal Ecology 39: 12-25.
Murat C, Payen T, Noel B, Kou A, Chen J, Kohler A, Krizsán K, Morin E, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Clum A, Dockter RB, Fauchery L, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Belfiori B, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Want M, Žifčáková L, Wipf D, Zambonelli A, Paolocci f, Nowrousian M, Ottonello S, Baldrina P, Spatafora JW, Henrissat B, Nagy L, Aury J-M, Wincker P, Grigoriev IV, Bonfante P, Martin FM. 2018. Genomics of Pezizomycetes reveal molecular basis of truffle lifestyle. Nature Evolution and Ecology. doi:10.1038/s41559-018-0710-4
Yang X, Feng P, Yin Y, Chen B, Bushley K, Spatafora JW, Wang C. Cyclosporin biosynthesis in Tolypocladium inflatum benefits fungal adaptation to the environment. 2018. mBio 9:e01211-18. https://doi.org/10.1128/mBio .01211-18.
Knapp DG, Némeht, BK, Hainaut M, Henrissat B, Johnson J, Kuo A, Lim JHP, Lipzen A, Nolan M, Ohm RA, Tamás L, Grigoriev IV, Spatafora JW, Nagy LG, Kovács GM. 2018. Comparative genomics reveals functional diversity in dark septate endophytic fungi of semiarid grasslands. Scientific Reports 8, Article number: 6321.
Kijpornyongpan T, Mondo S, Barry K, Sandor L, Lee J, Lipzen A, Pangilinan J, LaButti K, Hainaut M, Henrissat B, Grigoriev IV, Spatafora JW, Aime MC. 2018. Broad genomic sampling reveals a smut pathogenic ancestry of the fungal clade Ustilaginomycotina. Molec. Biol. Evol. 35: 1840-1854. doi:10.1093/molbev/msy072.
Mongkolsamrit S, Noisripoom W, Thanakitpipattana D, Wutikhun T, Spatafora JW, Luangsa-ard J. 2018. Disentangling cryptic species with isarioid morphs in Cordycipitaceae. Mycologia 110:1, 230-257, DOI: 10.1080/00275514.2018.1446651.
Quandt CA, Patterson W, Spatafora JW. 2018. Harnessing the power of phylogenomics to disentangle the directionality and signatures of interkingdom host jumping in the parasitic fungal genus Tolypocladium. Mycologia 110:1, 104-117, DOI: 10.1080/00275514.2018.1442618.
Lopez D, Ribeiro S, Label P, Fumanal B, Venisse J-S, Kohler A, de Oliveira RR, Labutti K, Lipzen A, Lail K, Bauer D, Ohm RA, Barry KW, Spatafora JW, Grigoriev IV, Martin FM, Pujade-Renaud V. 2018. Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors. Frontiers in Microbiology 9:276. https://doi.org/10.3389/fmicb.2018.00276
Martino E, Morin E, Grelet G-A, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo R, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja H-R, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S. 2018. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. New Phytologist 217: 1213–1229.
Kepler RM, Luangsa-ard JJ, Hywel-Jones NL, Quandt CA, Sung G-H, Rehner SA, Aime MC, Henkel TW, Sanjuan T, Zare R, Chen M, Rossman AY, Spatafora JW, Shrestha B. 2017. A phylogenetic-based nomenclature for Cordycipitaceae (Hypocreales). IMA Fungus 8: 335-353.
Spatafora JW, Aime CA, Grigoriev IV, Martin F, Stajich JE, Blackwell M. The Fungal Tree of Life: from molecular systematics to genome-scale phylogenies. 2017. Microbiology Spectrum 5(5): FUNK-0053-2016. doi:10.1128/microbiolspec.FUNK-0053-2016.
Mantooth K, Hadziabdic D, Boggess S, Windham M, Miller S, Cai G, Spatafora J, Zhang N, Staton M, Ownley B, Trigiano R. 2017. Confirmation of independent introductions of an exotic plant pathogen of Cornus species, Discula destructiva, on the east and west coasts of North America and subsequent population bottlenecks. PLOS ONE 12(7): e0180345. https://doi.org/10.1371/journal.pone.0180345
Supaphon P, Phongpaichit S, Sakayaroj J, Rukachaisirikul V, Spatafora JW. 2017. Phylogenetic community structure of fungal endophytes in seagrass species. Botanica Marina 60: 489-501. doi:10.1515/bot-2016-0089.
Rossman AY, Allen WC, Castlebury LA, Spatafora J, Romero AI, Verkley G. 2017. (2517–2519) Proposals to conserve the names Balansia claviceps against Ephelis mexicana, Claviceps paspali against Ustilagopsis deliquescens, and Tolypocladium inflatum against Cordyceps subsessilis (Ascomycota, Sordariomycetes, Hypocreales). Taxon 66: 749-750.
Mondo SJ, Dannebaum RO, Kuo RC, Louie K, LaButti K, Haridas A, Kuo A, Salamov A, Ahrendt SR, Bewick AJ, Lau R, Bowen B, Lipzen A, Sullivan W, Andreopoulos WB, Clum A, Lindquist E, Daum C, Northen TR, Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O’Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. 2017. Widespread Adenine N6-methylation of Active Genes in Fungi. Nature Genetics 49: 964–968; doi:10.1038/ng.3859
Mujic AB, Kuo A, Tritt A, Lipzen A, Chen C, Johnson J, Sharm A, Barry K, Grigoriev IV, Spatafora JW. 2017. Comparative genomics of the ectomycorrhizal sister species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) reveals a divergence of the mating type B locus. G3: Genes, Genomes, Genetics 7:1775-1789; https://doi.org/10.1534/g3.117.039396.
Marsberg A, Kemler M, Jami F, Nagel JH, Postma-Smidt A, Naidoo S, Wingfield MJ, Crous PW, Spatafora JW, Slippers B. 2016. Botryosphaeria dothidea: A latent pathogen of global importance to woody plant health. Molecular Plant Pathology doi:10.1111/mpp.12495.
Miettinen O, Riley R, Barry K, Cullen D, de Vries RP, Hainaut M, Hatakka A, Henrissat B, Hildén K, Kuo R, LaButti K, Lipzen A, Mäkelä MR, Sandor L, Spatafora JW, Grigoriev IV, Hibbett DS. 2016. Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2. Genome Announcements 4:e00976-16. doi:10.1128/genomeA.00976-16
Peter M, Kohler A, Ohm RA, Kuo A, Krützmann J, Morin E, Arend M, Barry KW, Binder M, Choi C, Clum A, Copeland A, Grisel N, Haridas S, Kipfer T, LaButti K, Lindquist E, Lipzen A, Maire R, Meier B, Mihaltcheva S, Molinier V, Murat C, Pöggeler Stefanie, Quandt CA, Sperisen C, Tritt A, Tisserant E, Crous PW, Henrissat B, Nehls U, Egli S, Spatafora JW, Grigoriev IV, Martin FM. 2016. Comparative and functional genomics support a role in host plant drought tolerance by the dominant ectomycorrhizal fungus Cenococcum geophilum. Nature Communications 7:12662 | DOI: 10.1038/ncomms12662.
Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O’Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. 2016. Zygomycete Genealogy of Life (ZyGoLife): a phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108: 1028–1046. DOI: 10.3852/16-042.
David A, Haridas S, LaButti K, Lim J, Lipzen A, Wang M, Barry K, Grigoriev I, Spatafora JW, May G. 2016. Draft genome sequence of Microdochium bolleyi, a dark-septate fungal endophyte of beachgrass. Genome Announcements 4:e00270–16, doi:10.1128/genomeA.00270-16.
Walker AK, Frasz SL, Siefert KA, Miller JD, Mondo SJ, LaButti K, Lipzen A, Dockter RB, Kennedy MC, Grigoriev IV, Spatafora JW. 2016. Full Genome of Phialocephala scopiformis DAOMC 229536, a Fungal Endophyte of Spruce Producing the Potent Anti-Insectan Compound Rugulosin. Genome Announcements 4(1):e01768-15.
Quandt CA, Di Y, Elser J, Jasiwal P and Spatafora JW. 2016. A truffle parasite responds to ancestral insect and current fungal hosts by differential expression of genes involved in host recognition, attachment and degradation. G3: Genes, Genomes, Genetics (early release).
Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Junyan A, Hesse C, Spatafora JW, Henrisaat B, Hainaut M, Grigoriev IV and Hibbett DS. 2016. The genome of Xylona heveae provides a window into fungal enophytism. Fungal Biology 120: 26-42.
Spatafora JW, Quandt CA, Kepler RM, Sung G-H, Shrestha B, Hywel-Jones NL and Luangsa-ard JJ. 2015. New 1F1N species combinations in Ophiocordycipitaceae (Hypocreales). IMA Fungus 6(2): 357–362 (2015).
Mujic AG, Durall DM, Spatafora JW and P Kennedy. 2015. Ecological determinants of ectomycorrhizal fungal niche breadth: vertical soil heterogeneity is necessary for competitive coexistence between Rhizopogon vinicolor and Rhizopogon vesiculosus. New Phytologist 209: 1174–1183. doi: 10.1111/nph.13677.
Sanjuan TI, Franco-Molano AE, Kepler RM, Spatafora JW, Tabima J, Vasco AM and S Restrepo. 2015. Five new species of entomopathogenic fungi from the Amazon in the genus Ophiocordyceps. Fungal Biology 119: 901-916.
Spatafora JW, Bushley KE. 2015. Phylogenomics and evolution of secondary metabolism in plant-associated fungi. Current Opinions in Plant Biology 26: 37-44. http://dx.doi.org/10.1016/j.pbi.2015.05.030.
Quandt CA, Bushley KE and JW Spatafora. 2015. The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal Peptaibiotics. BMC Genomics 16: 553.

Min B, Park H, Jang Y, Kim J-J, Kim KH, Pangilinan J, Lipzen A, Riley R, Grigoriev IV, Spatafora JW and I-G Choi. 2015. Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremidiation. Journal of Biotechnology 211: 42-43.
Chang Y, Wang S, Sekimoto S, Aerts A, Choi C, Clum A, LaButti K, Lindquist E, Ngan CY, Ohm R, Grigoriev I, Spatafora JW and M Berbee. 2015. Phylogenomic analyses suggest that early fungi evolved digesting cell walls of land plants and their algal ancestors. Genome Biology and Evolution 7(6): 1590–1601. doi:10.1093/gbe/evv090.
Quandt CA, Kohler A, Hesse C, Sharpton T, Martin F and JW Spatafora. 2015. Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria rich microbiome. Environmental Microbiology. doi:10.1111/1462-2920.12840.
Nagy, LG, Ohm RA, Kovács GM, Floudas D, Riley R, Gácser A, Sipiczki M, Davis JM, Doty SL, de Hoog GS, Lang BF, Spatafora JW, Martin FB, Grigoriev IV and DS Hibbett. 2014. Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nature Communications 5: 4471. DOI: 10.1038/ncomms5471.
Toome M. Kuo A, Henrissat B, Lipzen A, Tritt A, Yoshinaga Y, Zane M, Barry K, Grigoriev I, Spatafora JW and MC Aime. 2014. Draft genome sequence of a rare smut relative, Tilletaria anomala UBC 951. Genome Announcements 2(3):e00539-14. doi:10.1128/genomeA.00539-14.
Quandt CA, Kepler RM, Gams W, Araújo JPM, Ban S, Evans HC, Hughes D, Humber R, Hywel-Jones N, Li Z, Luangsa-ard JJ, Rehner SA, Sanjuan T, Sato H, Shrestha B, Sung G-H, Yao Y-J, Zare R and JW Spatafora. 2014. Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium. IMA Fungus 5: 121-134.
Myburg, A.A., Grattapaglia, D., Tuskan, G.A. and 76 other authors. 2014. The genome of Eucalyptus grandis – a global tree for fiber and energy. Nature 510: 356-362.
Rämä, T., Nordén, J., Davey, M.L., Mathiassen, G.H., Spatafora, J.W. and H. Kauserud. Fungi ahoy! Diversity on marine wooden substrates in the high North. Fungal Ecology 8: 46-58.
Sanjuan, T., Tabima, J., Restrepo, S., Læssøe, T., Spatafora, J.W. and A.E. Franco-Molano. Entomopathogens of Amazonian stick insects and locuts are members of the Beauveria species complex (Cordyceps sensu stricto). Mycologia 106: 260-275.
Toome, M., Ohm, R.A., Riley, R.W., James, T.Y., Lazarus, K.L., Henrisaat, B., Albu, S., Boyd, A., Chow, J., Clum, A., Heller, G., Lipzen, A., Nolan, M., Sandor, L., Zvenigorodsky, N., Grigoriev, I.V., Spatafora, J.W. and M.C. Aime. 2014. Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae. New Phytologist 202: 554-564.
Mujic. A.B., Hosaka, K. and J.W. Spatafora. 2014. Rhizopogon togasawarensis sp. nov., the first report of Rhizopogon associated with an Asian species of Pseudotsuga. Mycologia 106: 105-112.
Hibbett, D.S., Stajich, J.E., and J.W. Spatafora. 2013. Towards Genome-Enabled Mycology. Mycologia 105: 1339-1349.
Bushley, K.E., Li, Y., Wang, W.-J., WaRamng, X.-L., Jiao, L., Spatafora, J.W. and Y.-J. Yao. 2013. Isolation of the MAT1-1 mating type idiomorph and evidence for selfing in the Chinese medicinal fungus Ophiocordyceps sinensis. Fungal Biology 117: 599-610.
Kepler, R.M., Ban, S., Nakagiri, A., Bischoff, J., Hywel-Jones, N. and J.W. Spatafora. 2013. Phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: an application of one fungus one name. Fungal Biology 117: 611-622.
Dunham, S., Mujic, A.B., Spatafora, J.W. and A. Kretzer. 2013. Within-population genetic structure differs between two sympatric sister-species of ectomycorrhizal fungi, Rhizopogon vinicolor and R. vesiculosus. Mycologia 105: 814-826.
Bushley, K.E., Rajani. R., Jasiwal, P., Cumbie, J.S., Nonogaki, M., Boyd, A.E., Owensby, C.A., Knaus, B.J., Elser, J., Miller, D., Di, Y., McPhail, K.L. and J.W. Spatafora. 2013. The Genome of Tolypocladium inflatum: Evolution, Organization and Expression of the Cyclosporin Biosynthetic Gene Cluster. PLoS Genet 9(6): e1003496. doi:10.1371/journal.pgen.1003496
Manning, V.A., Pandelova, I., Dhillon, B., Wilhelm, L.J., Goodwin, S.B., Berlin, A.M., Figueroa, M., Freitag, M., Hane, J.K., Henrissat, B., Holman, W.H., Kodira, C.D., Martin, J., Oliver, R.P., Robbertse, B., Schackwitz, W., Schwartz, D.C., Spatafora, J.W., Turgeon, B.G., Yandava, C., Young, S., Zhou, S., Zeng, Q., Grigoriev, I.V., Birren, B.W., Ma, L.-J., and L. M. Ciuffetti. 2013. Comparative Genomics of a Pathogenic Fungus Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence. G3: Genes, Genomes, Genetics 3: doi: 10.1534/g3.112.004044
Ohm, R.A., Bradshaw, R.E., Condon, B.J., Feau, N., Henrissat, B., Horwitz, B.A., Schoch, C.L., Turgeon, B.G., Aerts, A., Barry, K., Copeland, A., Dhillon, B., Glaser, F., Grimwood, J., Hesse, C.N., Kosti, I., LaButti, K., Lindquist, E., Lowry, S., Lucas, S., Otillar, R., Salamov, A.A., Schmutz, J., Sun, H., Ciuffetti, L., Hamelin, R.C., Kema, G., Lawrence, C., Spatafora, J.W., de Wit, P.J.G.M., Zhong, S., Goodwin, S.B., and I.V. Grigoriev. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. 2012. PLoS Pathogens 8(12): e1003037. doi:10.1371/journal.ppat.1003037.
Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martínez, A.T., Ortillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Forest, B., Gaskell, J., Glotzer, D., Górecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N. Kersten, P., Khajamohiddin, S., Kohler, A., Kues, U., Kumar, T.K.A., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nolan, M., Ohm, R.A., Patyshakuliyeva, A., Rokas, A., Ruiz-Dueñas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St. John, F., Stenlid, J., Sun, H., Sun, S., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V. and D. S. Hibbett. 2012. The Paleozoic origin of enzymatic mechanisms for lignin decomposition reconstructed using 31 fungal genomes. Science 336: 1715-1719.
Kepler, R.M., Sung, G.-H., Harada, Y., Tanaka, K., Tanaka, E., Hososya, T., Bischoff, J.F. and J.W. Spatafora. 2012. Host jumping onto close relatives and across kingdoms by Tyrannicordyceps fratricida gen. nov. and Ustilaginoidea. American Journal of Botany 99: 552-561.
Spatafora J.W., Owensby C.A., Douhan G.W., Boehm E.W.A. and C.L. Schoch. 2012. Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes). Mycologia 104: 758–765 .
Kumar, T.K.A., Healy, R., Spatafora, J.W., Blackwell, M. and D.J. McLaughlin. 2012. Orbilia ultrastructure and the phylogeny of Pezizomycotina. Mycologia 104: 462-476.
Padamsee, M., Kumar, T.K.A., Riley, R., Binder, M., Boyd, A., Calvo, A.M.; Furukawa, K., Hesse, C., Hohmann, S., James, T.Y., LaButti, K., Lapidus, A., Lindquist, E., Lucas, S., Miller, M., Shantappa, S., Grigoriev, I.V., Hibbett, D.S., McLaughlin, D.J., Spatafora, J.W. and M.C Aime. 2012. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Biology and Genetics 49: 217-226.
Kepler, R. M., Sung, G.-H., Ban., S., Nakagiri, A., Chen, M.-J., Huang, B., Li, Z., and J.W. Spatafora. 2012. New Teleomorph Combinations in the entomopathogenic genus Metacordyceps. Mycologia 104: 182-197.
Searle, C.L., Biga, L.M., Spatafora, J.W. and A.R. Blaustein. 2011. Evidence for a dilution effect in an emerging amphibian pathogen, Batrachochytrium dendrobatidis. Proc. Natl. Acad. USA 108: 16322–16326.
Grigoriev, I.V., Cullen, D., Hibbett, D., Goodwin, S.B., Jeffries, T.W., Kubiek, C.P., Kuske, C., Magnuson, J., Martin, F., Spatafora, J.W., Tsang, A. and S. Baker. 2011. Fueling the Future with Fungal Genomics. Mycology 2 (3): 192-209.
Thrash, J.C., Boyd, A., Huggett, M.J., Grote, J., Carini, P., Yoder, R.J., Robbertse, B., Spatafora, J.W., Rappé, M.S., and S.J. Giovannoni. 2011. Phylogenetic evidence for a common ancestor of mitochondria and the SAR11 clade. Scientific Reports. 1: doi:10.1038/srep00013.
Rhind, N., Chen, Z., Yassour, M., Thompson, D.A., Haas, B.J., Habib, N., Wapinski, I., Roy, S., Lin, M.F., Heiman, D.I., Young, S.K., Furuya, K., Guo, Y., Pidoux, A., Chen, H.M., Robbertse, B., Goldberg, J.M., Aoki, K., Bayne, E.H., Berlin, A.M., Desjardins, C.A., Dobbs, E., Dukaj, L., Fan, L., FitzGerald, M.G., French, C., Gujja, S., Hansen, K., Keifenheim, D., Levin, J.Z., Mosher, R.A., Müller, C.A., Pfiffner, J., Priest, M., Russ, C., Smialowska, A., Swoboda, P., Sykes, S.M., Vaughn, M., Vengrova, S., Yoder, R., Zeng, Q., Allshire, R., Baulcombe, D., Birren, B.W., Brown, W., Ekwall, K., Kellis, M., Leatherwood, J., Levin, H., Margalit, H., Martienssen, R., Nieduszynski, C.A., Spatafora, J.W., Friedman, N., Dalgaard, J.Z., Baumann, P., Niki, H., Regev, A. and C. Nusbaum. 2011. Comparative Functional Genomics of Fission Yeasts. Science 332: 930-936.
Martin, F., Cullen, D., Hibbett, D., Pisabarro, A., Spatafora, J.W., Baker, S. E. and I.V. Grigoriev. 2011. Sequencing the Fungal Tree of Life. New Phytologist 190: 818-821.
Robbertse, Barbara; Yoder, Ryan J.; Boyd, Alex; Reeves, John; Spatafora, Joseph W. 2011. Hal: an Automated Pipeline for Phylogenetic Analyses of Genomic Data [Internet]. Version 63. PLoS Currents: Tree of Life. 2011 Jan 4 [revised 2011 Feb 7]. Available from: http://knol.google.com/k/barbara-robbertse/hal-an-automated-pipeline-for/360ntevzg9rsn/1.
Rouxel, T., Grandaubert, J., Hane, J.K., Hoede, C., van de Wouw, A.P., Couloux, A., Dominguez, V., Anthouard, V., Bally, P., Bourras, S., Cozijnsen, A.J., Ciuffetti, L.M., Degrave, A., Dilmaghani, A., Duret, L., Fudal, I., Goodwin, S.B., Gout, L., Glaser, N., Linglin, J., Kema, G.H.J., Lapalu, N., Lawrence, C.B., May, K., Meyer, M., Ollivier, B., Poulain, J., Schoch, C.L., Simon, A., Spatafora, J.W., Stachowiak, A., Turgeon, B.G., Tyler, B.M., Vincent, D., Weissenbach, J., Amselem, J., Quesneville, H., Oliver, R.P., Wincker, P., Balesdent, M.-H., Howlett, B.J. 2011. The compartmentalized genome of Leptosphaeria maculans: diversification of effectors within RIP-affected genomic regions. Nature Communications 2:202. DOI: 10.1038/ncomms1189.
Kepler, R.M., Kaitsu, Y., Tanaka, E., Shimano, S. and J.W. Spatafora. 2011. Ophiocordyceps pulvinata sp. nov., a pathogen of ants with a reduced stroma. Mycoscience 52: 39-47.
Sharanowski, B.J., Robbertse, B., Walker, J.,Voss, S.R., Yoder, R.,, Spatafora, J.W. and M. J. Sharkey. 2010. Expressed sequence tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta). Molecular Phylogenetics and Evolution 57: 101-112.
Giachini, A.J., Hosaka, K., Nouhra, E., Spatafora, J.W., and J.M. Trappe. 2010. Phylogenetic relationships of the Gomphales based on nuc-25S-rDNA, mit-12S-rDNA, and mit-atp6-DNA combined sequences. Fungal Biology 114: 224-234.
Boehm, E.W.A., Mugambi, G.K., Miller, A.N., Huhndorf, S.M., Marincowitz, S., Spatafora, J.W. and C.L. Schoch. 2009 [2010]. A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species. Studies in Mycology 64: 49-84.
Suetrong, S., Schoch, C.L., Spatafora, J.W., Kohlmeyer, J., Volkmann-Kohlmeyer, B. Sakayaroj, J., Phongpaichit, S., Kazuaki, T., Hirayama, K. and E.B. Gareth Jones. 2009 [2010]. Molecular systematics of the marine Dothideomycetes. Studies in Mycology 64: 155-174.
Schoch, C.L., Crous, P.W., Groenewald, J.Z., Boehm, E.W.A., Burgess, T.I., De Gruyter, J., De Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S.M., Hyde, K.D., Jones, E.B.G., Kohlmeyer, E.B.G., Kruys, Å., Lücking, R., Lumbsch, H.T., Marvanová, L., Mbatchou, J.S., McVay, A.H., Miller, A.N., Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C A., Phillips, A.J.L., Phongpaichit, S., Pointing, S.B., Pujade-Renaud, V., Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, B., Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., Zhang, Y. and J.W. Spatafora. 2009 [2010]. A class-wide phylogenetic assessment of Dothideomycetes. Studies in Mycology 64: 1-15.
Zhang, Y., Schoch, C.L., Fournier, J., Crous, P.W., de Gruyter, J., Woudenberg, J.H.C., Hirayama, K., Tanaka, K., Pointing, S.B., Spatafora, J.W. and K.D. Hyde. 2009 [2010]. Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation. Studies in Mycology 64: 85-102.
McLaughlin, D.J., Hibbett, D.S., Lutzoni, F., Spatafora, J.W. and R. Vilgalys. 2009. The Search for the Fungal Tree of Life. Trends in Microbiology 17: 488-497.
Stajich, J.E., Berbee, M.L., Blackwell, M., Hibbett, D.S., James, T.Y., Spatafora, J.W. and J. W. Taylor. 2009. Primer: The Fungi. Current Biology 19: R840-R845.
Schoch, C.L., Sung, G.-H., López-Giráldez, F., Townsend, J.P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P.B., Kauff, F., Wang, Z., Andrie, R., Trippe, K., Ciuffetti, L., Amtoft, A., Fraker, E., Hodkinson, B.P., Bonito, G., Lutzoni, F., Groenewald, J.Z., Arzanlou, M., de Hoog, S., Crous, P.W., Hewitt, D., Pfister, D.H., Peterson, K., Gryzenhout, M., Wingfield, M.J., Aptroot, A., Suh, S.-O., Blackwell, M., Hillis, D.M., Griffith, G., Castlebury, L., Rossman, A., Lumbsch, H.T., Lücking, R., Diederich, P., Ertz, D., Geiser, D., Hosaka, K., Inderbitzin, P., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Mostert, L., O’Donnell, K., Rogers, J., Shoemaker, R., Sugiyama, J., Summerbell, R., Untereiner, W., Johnston, P., Stenroos, S., Zuccaro, A., Dyer, P., Crittenden, P., Trappe, J.M. and J.W. Spatafora. 2009. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology 58: 224-239.
Schoch, C.L., Wang, Z., Townsend, J.P. and J.W. Spatafora. 2009. Geoglossomycetes cl. nov., Geoglossales ord. nov and Taxa above Class Rank in the Ascomycota Tree of Life. Persoonia 22: 129-138.
Mongkolsamrit, S., Luangsa-ard, J.J., Spatafora, J.W., Sung, G.-H., and N.L. Hywel-Jones. 2009. A combined ITS rDNA and β-tubulin phylogeny of Thai species of Hypocrella with non-fragmenting ascospores. Mycol. Res. 113: 684-699.
Boehm, E.W.A., Schoch, C.L. and J.W. Spatafora. On the evolution of the Hysteriaceae and Mytilinidiaceae (Pleosporomycetidae, Dothideomycetes, Ascomycota) using four nuclear genes. 2009. Mycological Research 113: 461-479.
Johnson, D.M., Sung, G.-H., Hywel-Jones, N.L., Luangsa-ard, J.J., Bischoff, J.F., Kepler, R.M. and J.W. Spatafora. 2009. Systematics and evolution of the genus Torrubiella (Hypocreales, Ascomycota). Mycological Research 113: 279-289.
Sung, G.-H., Poinar, G.O., and J.W. Spatafora. 2008. The oldest fossil evidence of animal parasitism by fungi supports a Cretaceous diversification of fungal-arthropod symbioses. Molec. Phylogen. Evol. 49: 495-502.
Hosaka, K., Castellano, M.A., and J.W. Spatafora. Biogeography of the Hysterangiales (Phallomycetidae, Basidiomycota). 2008. Mycological Research 112: 448-462.
Zuccaro, A., Schoch, C.L., Spatafora, J.W., Kohlmeyer, J., Draeger, S., and J.I. Mitchell. 2008. Detection and identification of predominant fungi associated with the brown seaweed Fucus serratus, using different environmental analysis. Applied and Environmental Microbiology 74: 931-941.
Andrie, R.M., Schoch, C.L., Hedges, R., Spatafora, J.W. and L.M. Ciufetti. 2008. Homologs of ToxB, a host-selective toxin gene from Pyrenophora tritici-repentis, are present in the genome of sister-species Pyrenophora bromi and other members of the Ascomycota. Fungal Genetics and Biology 45: 363-377.
Hane, J.K., Lowe, R.G.T., Solomon, P.S., Tan, K.-C., Schoch, C.L., Spatafora, J.W., Crous, P.W., Kodira, C., Birren, B.W., Torriani, S.F.F., McDonald, B.A. and R. P. Oliver. 2007. Dothideomycete-plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. The Plant Cell 19: 3347-3368.
Dunham, S., Larson, K.H., and J.W. Spatafora. 2007. Species richness and community composition of mat-forming ectomycorrhizal fungi in old- and second-growth Douglas-fir forests of the HJ Andrews Experimental Forest, Oregon, USA. Mycorrhiza 17: 633-645.
Sung, G.-H., J.-M. Sung, N.L. Hywel-Jones and J.W. Spatafora. 2007. A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution 44: 1204-1223.
Hibbett, D.S. Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T.Y., Kirk, P.M., Lucking, R., Lumbsch, H.T., Lutzoni, F.L., Matheny, P.B., McLaughlin, D.J., Powell, M.J., Redhead, S., Schoch, C.L., Spatafora, J.W., Stalpers, J.A., Vilgalys, R., Aime, M.C., Aptroot, A., Bauer, R., Begerow, D., Benny, G.L., Castlebury, L.A., Crous, P.W., Dai, Y.-C., Gams, W., Geiser, D.M., Griffith, G.W., Gueidan, C., Hawksworth, D.L., Hestmark, G., Hosaka, K., Humber, R.A., Hyde, K.D., Ironside, J.E., Koljag, U., Kurtzman, C.P., Larsson, K.-H., Lichtwardt, R., Longcore, J., Miadlikowska, J., Miller, A., Moncalvo, J.-M., Mozley-Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J.D., Roux, C., Ryvarden, L., Sampaio, J.P., Schußler, A., Sugiyama, J., Thorn, R.G., Tibell, L., Untereiner, W.A., Walker, C., Wang, Z., Weir, A., Weiss, M., White, M.M., Winka, K., Yao, Y.-J., and Zhang, N. 2007. A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547.
Sung, G.-H., Hywel-Jones, N.L., Sung, J.-M., Luangsa-ard, J.J., Shrestha, B. and J.W. Spatafora. 2007. Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Studies in Mycology 57: 5-59.
Spatafora, J.W., G.-H. Sung, N.L. Hywel-Jones, J.-M. Sung and J.F. White. 2007. Phylogenetic evidence for an animal pathogen origin of ergot and the grass endophytes. Molecular Ecology 16: 1701-1711.
Schoch, C.L., Sung, G.-H., Volkmann-Kohlmeyer, B., Kohlmeyer, J. and Spatafora, J.W. 2007. Novel marine fungal lineages in the Hypocreomycetidae. Mycological Research 111: 154-162.
Blackwell, M., D.S. Hibbett, J.W. Taylor, and J.W. Spatafora. 2006. Research Coordination Networks: A Phylogeny for Kingdom Fungi (Deep Hypha). Mycologia 98: 829-837.
Wang Z., Johnston P.R., Takamatsu S., Spatafora J.W. and Hibbett D.S. 2006. Phylogenetic classification of the Leotiomycetes based on rDNA data. Mycologia 98: 1067-1077.
Schoch, C.L., Shoemaker, R.A., Seifert, K.A., Hambleton, S., Spatafora, J.W., Crous, P.W. 2006. A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 1043-1054.
Hosaka, K., Bates, S.T., Beever, R.E., Castellano, M.A., Colgan, W. III, Domínguez, L.S., Nouhra, E.R., Geml, J., Giachini, A.J., Kenney, S.R., Simpson, N.B., Spatafora, J.W., and Trappe, J.M. 2006. Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders. Mycologia 98: 949-959.
Spatafora, J.W., Sung, G.-H.,, Johnson, D., Hesse, C., O’Rourke, B., Serdani, M., Spotts, R., Lutzoni, F., Hofstetter, V., Fraker, E., Gueidan, C., Miadlikowska, J., Reeb, V., Lumbsch, T., Lücking, R., Schmitt, I., Aptroot, A., Roux, C., Miller, A., Geiser, D., Hafellner, J., Hestmark, G., Arnold, A.E., Büdel, B., Rauhut, A., Hewitt, D., Untereiner, W., Cole, M.S., Scheidegger, C., Schultz, M., Sipman., H. and Schoch, C. 2006. A five-gene phylogenetic analysis of the Pezizomycotina. Mycologia 98: 1020-1030.
James, T.Y., Kauff, F., Schoch, C., Matheny, P.B., Hofstetter, V., Cox, C.J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H.T., Rauhut, A., Reeb, V., Arnold, A.E., Amtoft, A., Stajich, J.E., Hosaka, K., Sung, G.-H., Johnson, D., O’Rourke, B., Crockett, M., Binder, M., Curtis, J.M., Slot, J.C., Wang, Z., Wilson, A.W., Schußler, A., Longcore, J.E., O’Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P.M., Powell, M.J., Taylor, J.W., White, M.M., Griffith, G.W., Davies, D.R., Humber, R.A., Morton, J.B., Sugiyama, J., Rossman, A.Y., Rogers, J.D., Pfister, D.H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R.A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R.A., Serdani, M., Crous, P.W., Hughes, K.W., Matsuura, K., Langer, E., Langer, G., Untereiner, W.A., Lucking, R., Budel, B., Geiser, D.M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D.S., Lutzoni, F., McLaughlin, D.J., Spatafora, J.W. and Vilgalys, R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: 818-822.
Wang, Z., Binder, M., Schoch, C., Johnston, P.R., Spatafora, J.W., and Hibbett, D.S. 2006. Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny. Molecular Phylogenetics and Evolution 41: 295-312.
Robbertse, B., J. Reeves, C. Schoch, and J.W. Spatafora. 2006. A phylogenomic analysis of the Ascomycota. Fungal Genetics and Biology 43: 715-725.
Dunn, S.R., W.S. Phillips, J.W. Spatafora, D.R. Green and V.M. Weis. 2006. Highly conserved caspase and Bcl-2 homologues from the sea anemone Aiptasia pallida: Lower metazoans as models for the study of apoptosis evolution. Journal of Molecular Evolution 63: 95-107.
Schoch, C., J. Kohlmeyer, B. Volkmann-Kohlmeer, C.K.M. Tsui and J.W. Spatafora. 2006. Glomeroblus gelineus is a member of the Ostropales. Mycological Research 110: 257-263.
Kretzer, A.M., S. Dunham, R. Molina and J.W. Spatafora. 2005. Patterns of vegetative growth and gene flow in Rhizopogon vinicolor and R. vesiculosus (Boletales, Basidiomycota). Mol. Ecol. 14: 2259-2268.
Campbell, J., Volkmann-Kohlmeyer, B., Gräfenhan, Spatafora, J.W. and Kohlmeyer, J. 2005. A re-evaluation of Lulworthiales: relationships based on 18S and 28S rDNA. Mycol. Res. 109: 556-568.
Smith, J.E., McKay, D., Brenner, D., McIvers, J. and Spatafora J.W. 2005. Early impacts of forest restoration treatments on the ectomycorrhizal fungal community and fine root biomass in a mixed conifer forest. Journal of Applied Ecology 42: 526–535.
Fujimura, K.E., J.E. Smith, T.R. Horton, N.S. Weber, and J.W. Spatafora. 2005. Pezizalean mycorrhizas and sporocarps in ponderosa pine (Pinus ponderosa) after prescribed fires in eastern Oregon, USA. Mycorrhiza 15: 79-86.
Shrestha, B., Kim, H.-K., Sung, G.-H., Spatafora, J.W. and Sung, J.M. 2004. Bipolar heterothallism, a principal mating system of Cordyceps militaris in vitro. Biotechnology and Bioprocess Engineering 9: 440-446.
Smith, J.E., D. McKay, C.G. Niwa, W.G. Thies, G. Brenner, and J.W. Spatafora. 2004. Short-term effects of seasonal prescribed burning on the ectomycorrhizal fungal community and fine root biomass in ponderosa pine stands in the Blue Mountains of Oregon. Canad. Jour. For. Res. 34: 2477-2491.
Allen, E., X. Zhixin X., A.M. Gustafson, G.-H. Sung, J.W. Spatafora, and J.C. Carrington. 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics 36: 1282-1290.
Lutzoni, F., F. Kauff, C. J. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T. Y. James, E. Baloch, M. Grube, V. Reeb, V. Hofstetter, C. Schoch, A. E. Arnold, J. Miadlikowska, J.W. Spatafora, D. Johnson, S. Hambleton, M. Crockett, R. Shoemaker, G.-H. Sung, R. Lücking, T. Lumbsch, K. O’Donnell, M. Binder, P. Diederich, D. Ertz, C. Gueidan, K. Hansen, R. C. Harris, K. Hosaka, Y.-W. Lim, B. Matheny, H. Nishida, D. Pfister, J. Rogers, A. Rossman, I. Schmitt, H. Sipman, J. Stone, J. Sugiyama, R. Yahr, and R. Vilgalys. 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany 91: 1446–1480.
Castlebury, L.A., Rossman, A.Y., Sung, G.-H., Hyten, A.S., and J.W. Spatafora. 2004. Multigene phylogeny reveals new lineage for Stachybotrys chartarum, the indoor air fungus. Mycol. Research 108: 864-872.
Sung, G.-H. and J.W. Spatafora. 2004. Cordyceps cardinalis sp. nov., a new species of Cordyceps with a east Asian-eastern North American distribution. Mycologia 96: 658-666.
Kretzer, A.M., S. Duhnam, R. Molina, and J.W. Spatafora. 2004. Microsatellite markers reveal below ground clone structure in two species of Rhizopogon forming tuberculate ectomycorrhizae on Douglas-fir. New Phytologist 161: 313-320.
Christensen, T.M., Z. Vejlupkova, Y.K. Sharma, K.M. Arthur, J.W. Spatafora, C. Albright, R.B. Meeley, J.P. Duvick, R.S. Quatrano, J.E. Fowler. 2003. Conserved Subgroups and Developmental Regulation in the Monocot rop Gene Family. Plant Physiology 133: 1791-1808.
Kretzer, A.M., D. Luoma, R. Molina, and J.W. Spatafora. 2003. Rhizopogon vinicolor Smith is a complex of two non-interbreeding species: congruent evidence from internal transcribed spacer sequences and microsatellite loci. Mycologia 95: 479-486.
Currie, C.R., Wong, B., Stuart, A.E., Schultz, T.R., Rehner, S.A., Mueller, U.G., Sung, G.-H., Spatafora, J.W., and Straus, N.A. 2003. Ancient tripartite coevolution in the attine ant–microbe symbiosis. Science 299: 386-388.
Grubisha, L.C., J. Trappe, R. J. Molina, and J.W. Spatafora. 2002. Biology of the ectomycorrhizal genus, Rhizopogon. VI. Re-examination of infrageneric relationships inferred from phylogenetic analyses of ITS sequences. Mycologia 94: 607-619.
Duncan, R.A., R. Sullivan, S.C. Alderman, J.W. Spatafora, J.F. White. 2002. Claviceps purpurea var. spartinae var nov.: an ergot adapted to the aquatic environment. Mycotaxon 81: 11-25.
Gernandt, D.S., J.L. Platt, J.K. Stone, J.W. Spatafora, A. Holst-Jensen, R.C. Hamelin, and L.M. Kohn. 2001. Phylogenetics of Helotiales and Rhytismatales based on partial small subunit nuclear ribosomal DNA sequences. Mycologia 93: 915-933.
Humpert, A.J., E.L. Muench, A. Giachini, M.A. Castellano, and J.W. Spatafora. 2001. Molecular phylogenetics of Ramaria and related genera: evidence from nuclear large subunit and mitochondrial small subunit rDNA sequences. Mycologia 93: 465-477.
Sung, G.-H., J.W. Spatafora, R. Zare, K.T. Hodge, and W. Gams. 2001. A revision of Verticillium sect. Prostrata. II. Phylogenetic analyses of SSU and LSU nuclear rDNA sequences from anamorphs and teleomorphs of the Clavicipitaceae. Nova Hedwigia 72: 29-46.
Sullivan, R., M.S. Bergen, R. Patel, G.F. Bills, S.C. Alderman, J.W. Spatafora, and J.F. White, Jr. 2001. Neoclaviceps monostipa: features of an enigmatic clavicipitalean fungus and the phyletic status of the anamorphic genus Ephelis. Mycologia 93: 90-99.
Grubisha, L.C., J.M. Trappe, R. Molina, and J.W. Spatafora. 2001. Biology of the ectomycorrhizal genus, Rhizopogon V. Phylogenetic relationships in the Boletales: evidence from nuclear large subunit rDNA sequences. Mycologia 93: 82-89.
Kretzer, A.M., M. I. Bidartondo, L.C. Grubisha, J. W. Spatafora, T. M. Szaro, and T. D. Bruns. 2000b. Regional specialization of Sarcodes sanguinea (Ericaceae) on a single fungal symbiont from the Rhizopogon ellenae (Rhizopogonaceae) species complex. American Journal of Botany 87: 1778-1782.
Kretzer, A.M., R. Molina, and J.W. Spatafora. 2000a. Microsatellite markers for the ectomycorrhizal basidiomycete Rhizopogon vinicolor. Molecular Ecology 9: 1171-1173.
Kohlmeyer, J., J.W. Spatafora, and B. Volkmann-Kohlmeyer. 2000. Lulworthiales, a new order of marine Ascomycota. Mycologia 92: 453-458.
Platt, J. L. and J.W. Spatafora. 2000. Evolutionary relationships of nonsexual lichenized fungi; molecular phylogenetic hypotheses for the genera Siphula and Thamnolia from SSU and LSU rDNA analyses. Mycologia 92: 475-487.
Dahlman, M., E. Danell, and J.W. Spatafora. 2000. Molecular systematics of Craterellus: cladistic analysis of nuclear LSU rDNA sequence data. Mycological Research 104: 388-394.
Platt, J.L. and J.W. Spatafora. 1999. A re-examination of generic concepts of baeomycetoid lichens based on phylogenetic analyses of nuclear SSU and LSU ribosomal DNA. The Lichenologist 31: 409-418.
Ranghoo, V.M., Hyde, K.D., Liew, E.C.Y., and Spatafora, J.W. 1999. Family placement of Ascotaiwania and Ascolacicola based on DNA sequences from the large subunit rRNA gene. Fungal Diversity 2: 159-168.
Spatafora, J.W., B. Volkmann-Kohlmeyer, and J. Kohlmeyer. 1998. Independent terrestrial origins of the Halosphaeriales (marine Ascomycota). American Journal of Botany 85: 1569-1580.
Suh, S.-O., J.W. Spatafora, G.R.S. Ochiel, H. C. Evans, and M. Blackwell. 1998. Molecular phylogenetic study of a termite pathogen, Cordycepioideus bisporus. Mycologia 90: 611-617.
Spatafora, J.W. 1995. Ascomal evolution among filamentous ascomycetes: evidence from molecular data. Canadian Journal of Botany 73(Suppl. 1): 811-815.
Spatafora, J.W., T. G. Mitchell, and R. Vilgalys. 1995. Analysis of Genes Coding for Small subunit rRNA Sequences in Studying Phylogenetics of Dematiaceous fungal Pathogens. Journal of Clinical Microbiology 33: 1322-1326.
Spatafora, J.W. and M. Blackwell. 1994a. The polyphyletic origins of ophiostomatoid fungi. Mycological Research 98: 1-9.
Spatafora, J.W. and M. Blackwell. 1993. Molecular systematics of unitunicate perithecial ascomycetes: The Clavicipitales-Hypocreales connection. Mycologia 85: 912-922.
Kaltenboeck, B. K., J.W. Spatafora, X. Zhang, K. Kousoulas, M. Blackwell, and J. Stortz. 1992. Efficient production of single-stranded DNA as long as 2 kb for sequencing of PCR-amplified DNA. Biotechniques 12: 164-171.