The Hittinger Lab


(&equal contributions, @corresponding author)

54. Kominek J&, Doering DT&, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT@. 2019. Eukaryotic acquisition of a bacterial operon. Cell epub:
  PNAS PubMed    
53. Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT@. 2019. Mitochondrial DNA and temperature tolerance in lager yeasts. Sci Adv 5: eaav1869.
  PNAS PubMed    
52. Li XC, Peris D, Hittinger CT, Sia EA, Fay JC. 2019. Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast. Sci Adv 5: eaav1848.
  PNAS PubMed    
51. Čadež N, Bellora N, Ulloa R, Hittinger CT, Libkind D. 2019. Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PLoS One 14: e0210792.
  PNAS PubMed    
50. Shen XX&, Opulente DA&, Kominek J&, Zhou X&, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT@, Rokas A@. 2018. Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175: 1533-45.
  PNAS PubMed    
49. Krause DJ, Kominek J, Opulente DA, Shen XX, Zhou X, Langdon QK, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT@. Functional and evolutionary characterization of a secondary metabolite gene cluster in
budding yeasts. Proc Natl Acad Sci USA 115: 11030-11035.
  PNAS PubMed    
48. Langdon QK, Peris D, Kyle B, Hittinger CT@. sppIDer: a species identification tool to investigate hybrid genomes with high-throughput sequencing. Mol Biol Evol in press doi:
  BMC Genomics PubMed    
47. Eizaguirre JI, Peris D, Rodríguez ME, Lopes CA, De Los Ríos P, Hittinger CT, Libkind D. Phylogeography of the wild Lager‐brewing ancestor (Saccharomyces eubayanus) in Patagonia. Environ Microbiol epub doi: 10.1111/1462-2920.14375.
  BMC Genomics PubMed    
46. Higgins DA, Young MK, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK. 2018. Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 210: 219-234.
  BMC Genomics PubMed    
45. Kuang MC, Kominek J, Alexander WG, Cheng JF, Wrobel RL, Hittinger CT. 2018. Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution. Mol Biol Evol epub.
  BMC Genomics PubMed    
44. Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH. 2018. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun 9: 1887.
  NatureCommunications PubMed    
43. Gonçalves C, Wisecaver JH, Kominek J, Oom MS, Leandro MJ, Shen XX, Opulente DA, Zhou X, Peris D, Kurtzman CP, Hittinger CT, Rokas A, Gonçalves P. 2018. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage. eLife 7: e33034.
  BMC Genomics PubMed    

Opulente DA, Rollinson EJ, Bernick-Roehr C, Hulfachor AB, Rokas A, Kurtzman CP, Hittinger CT@. 2018. Factors driving metabolic diversity in the budding yeast subphylum. BMC Biol 16: 26.

  BMC Genomics PubMed    
41. Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, Coon JJ, Lafontaine I. 2018. A molecular portrait of de novo genes in yeasts. Mol Biol Evol 35: 631-645.
  BMC Genomics PubMed    
40. Zhou X, Shen XX, Hittinger CT, Rokas A. 2018. Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Mol Biol Evol 35: 486-503.
  BMC Genomics PubMed    
39. Morais CG, Batista TM, Kominek J, Borelli BM, Furtado C, Moreira RG, Franco GR, Rosa LH, Fonseca C, Hittinger CT, Lachance MA, Rosa CA. 2017 Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade. Int J Syst Evol Microbiol 67: 3798–805.
  BMC Genomics PubMed    
38. Steffan SA, Dharampal PS, Diaz-Garcia L, Currie CR, Zalapa J, Hittinger CT. 2017. Empirical, metagenomic, and computational techniques illuminate the mechanisms by which fungicides compromise bee health. J Vis Exp 128: e54631.
  BMC Genomics PubMed    
37. Haase MAB, Kominek J, Langdon QK, Kurtzman CP, Hittinger CT@. 2017. Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species Candida tenuis. FEMS Yeast Res epub.
  BMC Genomics PubMed    
36. Shen XX, Hittinger CT, Rokas A. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat Ecol Evol 1: 0126.
  BMC Genomics      
35. Peris D, Moriarty RV, Alexander WG, Baker E, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK, Hittinger CT. 2017. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels March 27; 10:78.
  BMC Genomics PubMed    
34. Shen XX, Zhou X, Kominek J, Kurtzman CP@, Hittinger CT@, Rokas A@. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3: 070235.
  G3 PubMed    
33. Bellora N, Moliné M, David-Palma M, Coelho MA, Hittinger CT, Sampaio JP, Gonçalves P, Libkind D. 2016. Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. BMC Genomics 17: 901.
  BMC Genomics PubMed    
32. Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. 2015. in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies. G3: 028134.
  G3 PubMed    
31. Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Narasimhan RA, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Piotrowski JS, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R. 2016. Directed evolution reveals unexected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae. PLoS Genet 12: e1006372.
  PLOS Genetics PubMed    
30. Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. 2016. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. Elife. 2016 Sep 30; 5. e19027.
  Elife PubMed    
29. Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, MeierKolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW. Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci USA epub: 201603941.
  PNAS PubMed    
28. Peris D, Langdon Q, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D, Hittinger CT@. Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus. PLoS Genet. 2016 Jul 6; 12(7): e1006155.
  PLOS Genetics PubMed    
27. Wisecaver JH, Alexander WG, King SB, Hittinger CT, Rokas A. 2016. Dynamic evolution of nitric oxide detoxifying flavohemoglobins, a family of single-protein metabolic modules in bacteria and eukaryotes. Mol Biol Evol. 2016 Aug; 33(8):1979-87.
  MBE PubMed    
26. Lopes MR&, Morais CG& , Kominek J, Cadete RM, Soares MA, Uetanabaro APT, Fonseca C, Lachance MA, Hittinger CT, Rosa CA. Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae f. a., sp. nov., and Spathaspora gorwiae f. a., sp. nov. FEMS Yeast Res 16: fow044.
  FEMS Yeast Research PubMed    
25. McIlwain SJ, Peris D, Sardi M, Moskvin OV, Zhan F, Myers K, Riley NM, Buzzell A, Parreiras L, Ong IM, Landick R, Coon JJ, Gasch AP, Sato TK, Hittinger CT@. 2016. Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research. G3 (Bethesda) 2016 June 1;6:(6) 1757-66.
  G3 PubMed    
24. Alexander WG, Wisecaver JH, Rokas A, Hittinger CT@. 2016. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc Natl Acad Sci USA. 2016 Apr 12; 113(15):4116-21.
  PNAS PubMed    
23. Alexander WG, Peris D, Pfannenstiel BT, Opulente DA, Kuang M, Hittinger CT(@). 2016. Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces. Fungal Genet Biol. 2016 Apr; 89: 10-7.
  Fungal Genetics and Biology PubMed Press Coverage  
22. Leducq JB, Nielly-Thibault L, Charron G, Eberlein C, Verta JP, Samani P, Sylvester K, Hittinger CT, Bell G, Landry CR. 2016. Speciation driven by hybridization and chromosomal plasticity in a wild yeast. Nat Microbiol 1: 15003.
  Nature Microbiology PubMed    
21. Baker EC, Wang B, Bellora N, Peris D, Hulfachor A, Koshalek J, Adams M, Libkind D, Hittinger CT(@). 2015. The genome sequence of Saccharomyces eubayanus and the domestication of lager-brewing yeasts. Molecular Biology and Evolution. 2015 Nov; 32:2818-31.
  MBE PubMed Press Coverage  
20. Coelho MA, Almeida JMGCF, Hittinger CT, Gonçalves P. 2015. Draft genome sequence of Sporidiobolus salmonicolor CBS 6832, a red-pigmented basidiomycetous yeast. Genome Announc 3: e00444-15.
  Genome A PubMed    
19. Sylvester K, Wang QM, James B, Mendez R, Hulfachor AB, Hittinger CT(@). 2015. Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species. FEMS Yeast Res 15:fov002.
  FEMS Yeast Research PubMed Press Coverage  
18. Alexander WG, Doering DT, Hittinger CT(@). 2014. High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces. Genetics 2014 Nov; 198(3):859-66.
  Genetics PubMed Press Coverage  
17. Almeida P, Gonçalves C, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarede I, Albertin W, Durrens P, Sherman DJ, Marullo P, Hittinger CT, Gonçalves P, Sampaio JP. 2014. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun 2;5:4044.
  NatureCommunications PubMed    
16. Peris D, Sylvester K, Libkind D, Gonçalves P, Sampaio JP, Alexander WG, Hittinger CT(@). 2014. Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Molecular Ecology 23:2031-2045.
  Molecular Ecology PubMed Press Coverage  
15. Leducq JB, Charron G, Samani P, Dubé AK, Sylvester K, James B, Almeida P, Sampaio JP, Hittinger CT, Bell G, Landry CR. 2014. Local climatic adaptation in a widespread microorganism. Proc Biol Sci 281: 20132472.
  Proc Biol Sci PubMed    
14. Libkind D (&), Hittinger CT (&), Valério E, Gonçalves C, Dover J, Johnston M, Gonçalves P, Sampaio JP. 2011. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proceedings of the National Academy of Sciences of the USA 108:14539-44.
  PNAS PubMed Press Coverage Data Link
13. Scannell DR (&), Zill OA (&@), Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT (@). 2011. The awesome power of yeast evolutionary genetics: New genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3: Genes | Genomes | Genetics 1: 11-25.
  G3 PubMed Press Coverage Data Link
12. Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A. 2010. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-58.
  Nature PubMed Press Coverage Data Link
11. Hittinger CT, Johnston M, Tossberg JT, Rokas A. 2010. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proceedings of the National Academy of Sciences of the USA 107 (4): 1476-1481.
  PNAS PubMed Press Coverage Data Link
10. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. 2009. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Molecular Biology and Evolution 26 (12): 2731-2744.
  MBE PubMed    
9. Hittinger CT, Carroll SB. 2008. Evolution of an insect-specific GROUCHO interaction motif in the ENGRAILED selector protein. Evolution and Development 10 (5): 537-545.
  Evolution & Development PubMed    
8. Hittinger CT (@), Carroll SB (@). 2007. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449 (7163): 677-681.
  Nature PubMed Press Coverage Faculty of 10008.0
7. Tour E, Hittinger CT, McGinnis W. 2005. Evolutionarily conserved domains required for activation and repression functions of the Drosophila Ultrabithorax protein. Development 132 (23): 5271-5281.
  Development PubMed    
6. Hittinger CT, Stern DL, Carroll SB. 2005. Pleiotropic functions of a conserved insect-specific Hox peptide motif. Development 132 (23): 5261-5270.
  Development PubMed Press Coverage Faculty of 10006.0
5. Hittinger CT, Rokas A, Carroll SB. 2004. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proceedings of the National Academy of Sciences of the USA 101 (39): 14144-14149.
  PNAS PubMed Press Coverage  
4. Palangat M, Hittinger CT, Landick R. 2004. Downstream DNA selectively affects a paused conformation of human RNA polymerase II. Journal of Molecular Biology 341 (2): 429-442.
  JMB PubMed    
3. King N, Hittinger CT, Carroll SB. 2003. Evolution of key cell signaling and adhesion protein families predates animal origins. Science 301 (5631): 361-363.
  Science PubMed   Faculty of 10004.8
2. Guettler S, Jackson EN, Lucchese SA, Honaas L, Green A, Hittinger CT, Tian Y, Lilly WW, and Gathman AC. 2003. ESTs from the basidiomycete Schizophyllum commune grown on nitrogen-replete and nitrogen-limited media. Fungal Genetics and Biology 39 (2): 191-198.
  Fungal Genetics and Biology PubMed    
1. Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. 2002. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proceedings of the National Academy of Sciences of the USA 99 (15): 9650-9655.
  PNAS PubMed   Faculty of 10003.0



R9. Lachance MA, Hittinger CT. 2018. Introducing 'ecoYeast': ecology and communities of yeasts. Yeast 35: 313.
  Science PubMed    
R8. Hittinger CT, Steele JL, Ryder DS. Diverse yeasts for diverse fermented beverages and foods. Curr Opin Biotechnol epub: doi:10.1016/j.copbio.2017.10.004.
  Science PubMed    
R7. Peris D, Pérez-Torrado R, Hittinger CT, Barrio E, Querol A. On the origins and industrial applications of Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids. Yeast epub: doi:10.1002/yea.3283.
  Science PubMed    
R6. Gibson B, Geertman JA, Hittinger CT, Krogerus K, Libkind D, Louis EJ, Magalhães F, Sampaio JP. New yeasts-new brews: modern approaches to brewing yeast design and development. 2017. FEMS Yeast Res 17: fox038.
  Science PubMed    
R5. Hittinger CT@, Rokas A, Bai FY, Boekhout T, Gonçalves P, Jeffries TW, Kominek J, Lachance MA, Libkind D, Rosa CA, Sampaio JP, Kurtzman CP. Genomics and the making of yeast biodiversity. Curr Opin Genet Dev, 2015 Dec;35:100-9.
  Science PubMed    
R4. Hittinger CT (@), 2013. Saccharomyces diversity and evolution: a budding model genus. Trends in Genetics 29 (5): 309-317.
  Science PubMed   Cover by CT HIttinger
R3. Hittinger CT (@), 2012. Endless rots most beautiful. Science 336 (6089): 1649-1650.
  Science PubMed    
R2. Hittinger CT (@), Hesselberth JR. 2010. Nucleosome patterning evolution: steady aim despite moving targets. Molecular Systems Biology 6: 376.
  Molecular Systems Biology PubMed    
R1. Rokas A, Hittinger CT. 2007. Transcriptional rewiring: the proof is in the eating.  Current Biology 17 (16): R626-R628.
  Current Biology PubMed    



Chris Todd Hittinger
Laboratory of Genetics
425-G Henry Mall
4340-4360 Genetics/Biotechnology Center
Madison, Wisconsin 53706-1580
United States

Contact the Lab: HittingerLab at genetics(dot) wisc(dot)edu UW Directory Link

©2008-2017 by Chris Todd Hittinger