Publications [lab trainees]



  1. Pratt CJ, Meili C, Jones AL, Jackson DK, England EE, Wang Y, Hartson S, Rogers J, Elshahed MS, Youssef NH. Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution. Preprint at bioRxiv. [full text]
  2. Gryganskyi AP, Golan J, Myszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith MM, Reynolds N, James TY, Grigoriev IV, Spatafora J, Stajich JE. 2023. Sequencing the genomes of the first terrestrial fungal lineages: what have we learned? Microorganisms 11: 1830. [full text]
  3. Meili C, Jones AL, Arreola A, Habel J, Pratt CJ, Hanafy RA, Wang Y, Yassin A, TagEIDein MA, Moon C, Janssen P, Shrestha M, Rajbhandari P, Nagler M, Vinzelj JM, Podmirseg SM, Stajich JE, Goetsch AL, Hayes J, Young D, Fliegerova K, Grilli DJ, Vodička R, Moniello G, Mattiello S, Kashef MT, Nagy YI, Edwards JA, Dagar SS, Foote AP, Youssef N, Elshahed M. 2023. Patterns and determinants of the global herbivorous Mycobiome. Nat. Commun. 14: 3798. [full text]
  4. Knudsen K, Kocourková J, Hodkovå E, Malíček J, Wang Y. 2023. Acarosporaceae of New Mexico: eight new species of Acarospora and Sarcogyne. West. N. Am. Nat. 83(1): 51–88.
  5. Chaudhary S, Wu Y, Strongman DB, Wang Y. 2023. CIGAF – a database and interactive platform for insect-associated trichomycete fungi. Database 2023: baad038. [full text]
  6. Wang Y, Chang Y, Ortanez J, Pena J, Carter-House D, Reynolds N, Smith M, Benny G, Mondo S, Salamov A, Lipzen A, Pangilinan J, Guo J, LaButti K, Andreopolous W, Tritt A, Keymanesh K, Yan M, Barry K, Grigoriev I, Spatafora J, Stajich J. 2023. Divergent evolution of early terrestrial fungi reveals the evolution of Mucormycosis pathogenicity factors. Genome Biol. Evol. 15(4): evad046. [full text]
  7. Hanafy RA, Wang Y, Stajich JE., Pratt C, Youssef NH, Elshahed MS. 2023. Phylogenomic analysis of the Neocallimastigomycota: Proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae. Int. J. Syst. Evol. Microbiol. 73: 005735. [pdf]
  8. 2022

  9. Strongman DB and Wang Y. 2022. Trichomycetes from freshwater and salt marsh mosquito larvae with a new species in the monotypic genus Legerioides. Botany 100: 857-867. [pdf]
  10. Chang Y, Wang Y, Mondo S, Ahrendt S, Andreopoulos W, Barry K, Beard J, Benny G, Blankenship S, Bonito G, Cuomo C, Desirò A, Gervers K, Hundley H, Kuo A, LaButti K, Lang BF, Lipzen A, O'Donnell K, Pangilinan J, Reynolds N, Sandor L, Smith M, Tsang A, Grigoriev I, Stajich J, Spatafora J. 2022. Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies. iScience 25, 104840. [pdf]
  11. Malar MC, Wang Y, Stajich JE, Kokkoris V, Villeneuve-Laroche M, Yildirir G, Corradi N. 2022. Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina. Microbial Genomics 8(4): 000810. [pdf]
  12. Sun J, Barrett H, Hall D, Kutarna S, Wu X, Wang Y, Peng H. 2022. Ecological role of 6OH-BDE47: is it a chemical offence molecule mediated by enoyl-ACP reductases? Environmental Science & Technology 56(1): 451–459. [text]
  13. 2021

  14. Knudsen K, Kocourková J, Hodkovå E, Malíček J, Wang Y. 2021. Acarosporaceae of the Chihuahuan Desert: four Magnusson species saved from synonymy and a new yellow species. The Bryologist 124(4): 533-551. [text]
  15. Knudsen K, Kocourková J, Hodkovå E, Adams JN, Wang Y. 2021. Three species of Trimmatothelopsis (Acarosporaceae) from Europe and North America. The Bryologist 124(2): 271-280. [text]
  16. Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. 2021. A genome-scale phylogeny of the kingdom Fungi. Current Biology 31 (8), 1653-1665. [pdf]
  17. ​Malar MC, Krüger M, Krüger C, Wang Y, Stajich JE, Keller J, Chen CH, Yildirir G, Villeneuve-Laroche M, Roux CR, Delaux PM, Corradi N. 2021. The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis. Current Biology 31 (7), 1570-1577. [pdf]
  18. ​Knudsen K, Kocourková J, Hodkovå E, Wang Y. 2021. Lichenological Notes 8: Acarospora fusca. Opuscula Philolichenum 20, 19-24. [pdf]
  19. Chang Y, Rochon D, Sekimoto S, Wang Y, Chovatia M, Sandor L, Salamov A, Grigoriev I, Stajich J, Spatafora J. 2021. Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi. Scientific Reports 11, 3217. [full-text]
  20. Dong N, Bandura J, Zhang Z-L, Wang Y, Labadie K, Noel B, Davison A, Koene JM, Sun H-S, Coutellec M-A, Feng Z-P. 2021. Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis. BMC Genomics 22, 18. [pdf]
  21. 2020

  22. Tabima JF, Trautman IA, Chang Y, Wang Y, Mondo SJ, Salamov A, Grigoriev IV, Stajich JE, Spatafora JW. 2020. Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus. G3: Genes|Genomes|Genetics 10 (9): 3417-3433. [pdf]
  23. Knudsen K, Adams JN, Kocourková J, Wang Y, Ortañez J, Stajich JE. 2020. The monophyletic Sarcogyne canadensis–wheeleri clade, a newly recognized group sister to the European Acarospora glaucocarpa group. The Bryologist 123(1): 11-30.[full-text]
  24. 2019

  25. Wang Y, White MM, and Moncalvo J-M. 2019. Diversification of the gut fungi (Harpellales) co-occurred with the origin of complete metamorphosis of their symbiotic insect hosts (lower Diptera). Mol Phylogenet Evol 139: 106550.[pdf]
  26. Wang Y, Youssef NH, Couger MB, Hanafy RA, Elshahed MS, Stajich JE. 2019. Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes. mSystems 4(4): e00247-19.[pdf]
  27. Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD, and Quest for Orthologs Consortium. 2019. Advances and Applications in the Quest for Orthologs. Mol Biol Evol 36: 2157–2164.[full-text]
  28. Murphy CM, Youssef NH, Hanafy RA, Couger MB, Stajich JE., Wang Y, Baker K, Dagar SS, Griffith GW, Farag IF, Callaghan TM, and Elshahed MS. 2019. Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage. Appl Environ Microbiol 85: e00988-19.[pdf]
  29. 2018 & earlier

  30. Wang Y, Stata M, Wang W, Stajich JE, White MM, and Moncalvo J-M. 2018. Comparative genomics reveals the core gene toolbox for the fungus-insect symbiosis. mBio 9(3): e00636-18.[pdf]
  31. Wang Y, White MM, Kvist S, Moncalvo JM. 2016. Genome-wide survey of gut fungi (Harpellales) reveals the first horizontally transferred ubiquitin gene from a mosquito host. Mol Biol Evol 33: 2544-2554.[pdf]
  32. Wang Y, White MM, Moncalvo JM. 2016. Draft Genome Sequence of Capniomyces stellatus, the obligate gut fungal symbiont of stonefly. Genome Announc 4(4): e00804-16.[pdf]
  33. Wang Y, Tretter ED, Johnson EM, Kandel P, Lichtwardt RW, Novak SJ, Smith JF, White MM. 2014. Using a five-gene phylogeny to test morphology-based hypotheses of Smittium and allies, endosymbiotic gut fungi (Harpellales) associated with arthropods. Mol Phylogenet Evol 79: 23–41.[pdf]
  34. Tretter ED, Johnson EM, Benny GL, Wang Y, Kandel P, White MM. 2014. An eight-gene molecular phylogeny of the Kickxellomycotina, including the first phylogenetic placement of Asellariales. Mycologia 106: 912-935.[pdf]
  35. Wang Y, Tretter ED, Lichtwardt RW and White MM. 2013. Overview of 75 years of Smittium research, establishing a new genus for Smittium culisetae, and prospects for future revisions of the “Smittium” clade. Mycologia 105: 90-111.[pdf]
  36. Tretter ED, Johnson EM, Wang Y, Kandel P, White MM. 2013. Examining new phylogenetic markers to uncover the evolutionary history of early-diverging fungi: comparing MCM7, TSR1 and rRNA genes for single- and multi-gene analyses of the Kickxellomycotina. Persoonia 30: 106–125.[pdf]
  37. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, (et al. with over 100 authors as Fungal Barcoding Consortium). 2012. The nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. P Natl Acad Sci USA 109(16):6241–6246.[pdf]
  38. Wang Y. 2008. Morphological and anatomical comparative studies on needles structure of 4 species in Pinaceae in Shanxi Province. Shanxi Forestry Science and Technology 2: 16–19.
  39. Wang Y, Zhang F. 2008. Study on the classification and ordination of wetland vegetations in Lianbo flooding plain of Fen river, Shanxi. Highlights of Sciencepaper Online 1(11): 1285–1291.