Publications

2019

  1. Bewick AJ, Hofmeister BT, Powers RA, Mondo SJ, Grigoriev IV, James TY, Stajich JE, Schmitz RJ. Diversity of cytosine methylation across the fungal tree of life. Nat Ecol Evol. 2019; 3(3):479-490. doi: 10.1038/s41559-019-0810-9.
  2. Davis WJ, Amses KR, James ES, James TY. A new 18S rRNA phylogeny of uncultured predacious fungi (Zoopagales). Mycologia. 2019; 111(2):291-298. doi: 10.1080/00275514.2018
  3. Davis WJ, Amses KR, Benny GL, Carter-House D, Chang Y, Grigoriev I, Smith ME, Spatafora JW, Stajich JE, James TY. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).  Mol Phylogenet Evol. 2019; 133:152-163. doi: 10.1016/j.ympev.2019.01.006
  4. Reynolds NK, Benny GL, Ho HM, Hou YH, Crous PW, Smith ME. Phylogenetic and morphological analyses of the mycoparasitic genus Piptocephalis. Mycologia. 2019;  doi: 10.1080/00275514.2018.1538439.
  5. Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, Del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J Eukaryot Microbiol. 2019; 66(1):4-119. doi: 10.1111/jeu.12691.
  6. Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. New Phytol. 2019 222(1):511-525. doi: 10.1111/nph.15613

2018

  1. Benny GL, Smith ME. Notes on Syncephalis (Zoopgales, Zoopagomycota) from the Farlow Herbarium with the description of a new species, Syncephalis aethiopica. Mycologia. 2018; 110(1):192-200. doi: 10.1080/00275514.2018.1426960
  2. Chen EC, Mathieu S, Hoffrichter A, Sedzielewska-Toro K, Peart M, Pelin A, Ndikumana S, Ropars J, Dreissig S, Fuchs J, Brachmann A, Corradi N. Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi. Elife. 2018; 7. pii: e39813. doi: 10.7554/eLife.39813.
  3. Mathieu S, Cusant L, Roux C, Corradi N. Arbuscular mycorrhizal fungi: intraspecific diversity and pangenomes. New Phytol. 2018; 220(4):1129-1134. doi: 10.1111/nph.15275
  4. Ahrendt SR, Quandt CA, Ciobanu D, Clum A, Salamov A, Andreopoulos B, Cheng JF, Woyke T, Pelin A, Henrissat B, Reynolds NK, Benny GL, Smith ME, James TY, Grigoriev IV. Leveraging single-cell genomics to expand the fungal tree of life. Nat Microbiol. 2018; 3(12):1417-1428. doi: 10.1038/s41564-018-0261-0
  5. Arnesen JA, Małagocka J, Gryganskyi A, Grigoriev IV, Voigt K, Stajich JE, De Fine Licht HH. Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases. G3 Genes | Genetics | Genomics. 2018;8(10):3311-3319. doi: 10.1534/g3.118.200656.
  6. Gryganskyi AP, Golan J, Dolatabadi S, Mondo S, Robb S, Idnurm A, Muszewska A, Steczkiewicz K, Masonjones S, Liao HL, Gajdeczka MT, Anike F, Vuek A, Anishchenko IM, Voigt K, de Hoog GS, Smith ME, Heitman J, Vilgalys R, Stajich JE. Phylogenetic and Phylogenomic Definition of Rhizopus Species. G3 Genes | Genetics | Genomics. 2018; 8(6):2007-2018. doi: 10.1534/g3.118.200235.
  7. Wang Y, Stata M, Wang W, Stajich JE, White MM, Moncalvo JM. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis. mBio. 2018;9(3). pii: e00636-18. doi: 10.1128/mBio.00636-18.
  8. Desirò A, Hao Z, Liber JA, Benucci GMN, Lowry D, Roberson R, Bonito G. Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle. ISME J. 2018; Online. doi: 10.1038/s41396-018-0053-9.
  9. Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. New Phytologist 2018; Online. doi: 10.1111/nph.14989.
  10. Chuang S-C, Ho H-M, Tsai J-L, Reynolds N, Smith ME, Benny GL, Chien C-Y. Preliminary phylogeny of Coemansia (Kickxellales) with the description of four new species from Taiwan. Mycologia. 2018;109:5, 815-831doi: 10.1080/00275514.2017.1401892.
  11. Fisher KE, Romberger I, Lowry D, Shange P, Roberson RW. Hyphal tip growth and cytoplasmic characters of Conidiobolus coronatus (Zoopagomycota, Entomophthoromycotina)Mycologia. 2018 110(1):31-38. doi: 10.1080/00275514.2017.1403808.

2017

  1. Truong C, Mujic AB, Healy R, Kuhar F, Furci G, Torres D, Niskanen T, Sandoval-Leiva PA, Fernández N, Escobar JM, Moretto A, Palfner G, Pfister D, Nourha E, Swenie R, Sánchez-García M, Matheny PB, Smith ME. How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity. New Phytologist. 2017; 214(3):913-919.  doi: 10.1111/nph.14509.
  2. Lazarus KL, Benny GL, Ho H-M, Smith ME. Phylogenetic systematics of Syncephalis (Zoopagales, Zoopagomycotina). Mycologia. 2017; 109(2):333-349. doi: 10.1080/00275514.2017.1307005 
  3. Desirò A, Rimington W, Jacob A, Vande Pol N, Smith M, Trappe J, Bidartondo M, Bonito G. Multigene phylogeny of Endogonales, an early diverging lineage of fungi associated with plants. IMA Fungus 2017; 8: 245-257. doi:10.5598/imafungus.2017.08.02.03
  4. Li Z, Yao Q, Dearth SP, Entler MR, Castro Gonzalez HF, Uehling JK, Vilgalys RJ, Hurst GB, Campagna SR, Labbé JL, Pan C. Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system. Environmental Microbiology. 2017; 19(3):1041–1053, doi:10.1111/1462-2920.13605.
  5. Uehling J, Deveau A, Paoletti M. Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems. PLoS Pathog. 2017; 13:e1006578, doi:10.1371/journal.ppat.1006578.
  6. Harper, C.J., Krings, M., Dotzler, N., Taylor, E.L. & Taylor, T.N. Deciphering interfungal relationships in the 410-million-yr-old Rhynie chert: Morphology and development of vesicle-colonizing microfungi. Geobios 2017; 50:9–22. doi: 10.1016/j.geobios.2016.11.003
  7. Krings, M. & Harper, C.J.  A mantled fungal reproductive unit from the Lower Devonian Windyfield chert, Scotland, with prominent spines and otherwise shaped projections extending out from the mantle. Neues Jahrbuch für Geologie und Paläontologie, Abhandlungen 2017; 285: 201–211. doi: 10.1127/0077-7749/2014/0423
  8. Krings, M., Harper, C.J., White, J.F., Barthel, M., Heinrichs, J., Taylor, E.L. & Taylor, T.N. Fungi in a Psaronius root mantle from the Rotliegend (Asselian, Lower Permian/Cisuralian) of Thuringia, Germany. Review of Palaeobotany and Palynology 2017; 239:14–30. doi: 10.1016/j.revpalbo.2016.12.004
  9. Beaudet D, Chen ECH, Mathieu S, Yildirir G, Ndikumana S, Dalpé Y, Séguin S, Farinelli L, Stajich JE, Corradi N. Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungiDNA Res. 2018; 25(2):217-227. doi: 10.1093/dnares/dsx051
  10. Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE, Blackwell M. The Fungal Tree of Life: from Molecular Systematics to Genome-Scale PhylogeniesMicrobiol Spectr. 2017;5(5). doi: 10.1128/microbiolspec.FUNK-0053-2016.
  11. Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O’Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. Widespread adenine N6-methylation of active genes in fungi. Nat Genet. 2017; 49(6):964-968. doi: 10.1038/ng.3859.
  12. Torres-Cruz TJ, Billingsley Tobias TL, Almatruk M, Hesse CN, Kuske CR, Desirò A, Benucci GMN, Bonito G, Stajich JE, Dunlap C, Arnold AE, Porras-Alfaro A. Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitatsMycologia. 2017;109(3):363-378. doi: 10.1080/00275514.2017.1364958
  13. Uehling J, Gryganskyi A, Hameed K, Tschaplinski T, Misztal PK, Wu S, Desirò A, Vande Pol N, Du Z, Zienkiewicz A, Zienkiewicz K, Morin E, Tisserant E, Splivallo R, Hainaut M, Henrissat B, Ohm R, Kuo A, Yan J, Lipzen A, Nolan M, LaButti K, Barry K, Goldstein AH, Labbé J, Schadt C, Tuskan G, Grigoriev I, Martin F, Vilgalys R, Bonito G. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigensEnviron Microbiol. 2017;9(8):2964-2983. doi: 10.1111/1462-2920.13669.
  14. Corradi N, Brachmann A. Fungal Mating in the Most Widespread Plant Symbionts? Trends Plant Sci. 2017;22(2):175-183. doi: 10.1016/j.tplants.2016.10.010.

2016

    1. Benny GL, Ho HM, Lazarus K, Smith ME. Five new species of the obligate mycoparasite Syncephalis (Zoopagales, Zoopagomycotina) from soil. Mycologica; 2017;108(6):1114-1129. doi: 10.3852/15-073.
    2. Wang Y, White MM, Moncalvo JM. Draft Genome Sequence of Capniomyces stellatus, the Obligate Gut Fungal Symbiont of Stonefly. Genome Announc. 2016;4(4). pii: e00761-16. doi: 10.1128/genomeA.00761-16.
    3. Stajich JE. Fungal Evolution: Mucor and Phycomyces See Double. Curr Biol. 2016; 26(16):R775-7. doi: 10.1016/j.cub.2016.06.049.
    4. 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. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016; 108(5):1028-1046. doi: 10.3852/16-042.
    5. Benny GL, Smith ME, Kirk PM, Tretter ED, White MM. Challenges and future perspectives in the systematics of Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina. In: Biology of Microfungi (D-W Li, ed.)  Springer Press.  2016; pgs. 65-126. doi: 10.1007/978-3-319-29137-6_5
    6. Wang Y, White MM, Kvist S, Moncalvo JM. Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host. Mol Biol Evol. 2016;33(10):2544-54. doi: 10.1093/molbev/msw126.
    7. Hajek AE, Gryganskyi A, Bittner T, Liebherr JK, Liebherr JH, Jensen AB, Moulton JK, Humber RA. Phylogenetic placement of two species known only from resting spores: Zoophthora independentia sp. nov. and Z. porteri comb nov. (Entomophthorales: Entomophthoraceae). J Invertebr Pathol. 2016;140:68-74. doi: 10.1016/j.jip.2016.09.002.
    8. Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, Marton T, Krüger M, Fuchs J, Brachmann A, Corradi N. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol. 2016;1(6):16033. doi: 10.1038/nmicrobiol.2016.33
    9. Fisher KE, Roberson RW. Hyphal tip cytoplasmic organization in four zygomycetous fungi. Mycologia. 2016; 108(3):533-42. doi: 10.3852/15-226.