The Hittinger Lab

Main Content

Publications

(&equal contributions, @corresponding author)

66. Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A. 2020. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nat Commun 11: 6096. Nature Communications PubMed  
65. Shen XX, Steenwyk JL, LaBella AL, Opulente D, Zhou X, Kominek J, Li Y, Groenewald M, Hittinger CT, Rokas A. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. FEMS Yeast Res. 2020 Nov 4: 6(45): eabd0079. doi: 10.1126/sciadv.abd0079. PNAS PubMed  
64. Stoneman H, Wrobel R, Place M, Graham M, Krause D, De Chiara M, Liti G, Schacherer J, Landick R, Gasch A, Sato T, Hittinger CT. CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations. G3. 2020 Nov 5: 10(11): 4287-4294. G3 PubMed  
63. Peris D, Alexander WG, Fisher KJ, Moriarty RV, Basuino MG, Ubbelohde EJ, Wrobel RL, Hittinger CT. Synthetic hybrids of six yeast species. Nat Commun. 2020 Apr 29: 11(1):2085. Nature Communications PubMed
62. Dharampal PS, Diaz-Garcia L, Haase MAB, Zalapa J, Currie CR, Hittinger CT, Steffan SA. 2020. Microbial diversity associated with the pollen stores of captive-bred bumble bee colonies. Insects 11: 250. InsectsPubMed
61. Langdon QK, Peris D, Eizaguirre JI, Opulente DA, Buh KV, Sylvester K, Jarzyna M, Rodríguez ME, Lopes CA, Libkind D@, Hittinger CT@. 2020. Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lagerbrewing hybrids. PLoS Genet 16: e1008680. PLOS Genetics PubMed  
60. Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Goncalves P, Sampaio JP, Libkind D, Hittinger CT. 2019. Fermentation innovation through complex hybridization of wild and domesticated yeasts. Nat Ecol Evol epub: https://doi: 10.1038/s41559-019-0998-8. Nat Ecol Evolution PubMed  
59. Labella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. 2019. Variation and selection on codon usage bias across an entire subphylum. PLoS Genet epub: https://doi.org/10.1371/journal.pgen.1008304. PLOS Genetics PubMed  
58. Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH. 2019. Multiple reinventions of mating-type switching during budding yeast evolution. Curr Biol 29: 2555-62. Current Biology PubMed  
57. Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT@, Rokas A@. 2019. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biol 17: e3000255. PLOS Genetics PubMed
56. Opulente DA, Langdon QK, Buh KV, Haase MAB, Sylvester K, Moriarty RV, Jarzyna M, Considine SL, Schneider RM, Hittinger CT@. 2019. Pathogenic budding yeasts isolated outside of clinical settings. FEMS Yeast Res 19: foz032. FEMS PubMed  
55. Baker EP, Hittinger CT@. 2019. Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function. PLoS Genetics. 15(4):e1007786 PLOS Genetics PubMed  
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: https://doi.org/10.1016/j.cell.2019.01.034. 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: https://doi.org/10.1101/333815. 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  
42. 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 PubMed  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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  

Reviews and Commentary

R13. Libkind D, Čadež N, Opulente DA, Langdon QK, Rosa CA, Sampaio JP, Gonçalves P, Hittinger CT, Lachance MA. 2020. Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences. FEMS Yeast Res epub: https://doi.org/10.1093/femsyr/foaa042. Science PubMed  
R12. Timothy Y James, Jason E Stajich, Chris Todd Hittinger, Antonis Rokas. 2020. Toward a Fully Resolved Fungal Tree of Life. Annu Rev Microbiol. Science PubMed  
R11. Libkind D, Peris D, Cubillos FA, Steenwyk JL, Opulente DA, Langdon QK, Rokas A, Hittinger CT. 2020. Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Res 20: foaa008. Science PubMed  
R10. Hittinger CT@. 2020. Evaluation of Kuroda et al.: insight into yeast isobutanol tolerance with advances still needed. Cell Syst 10: 124. CellSystems PubMed  
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.
Cover by CT Hittinger
Science PubMed
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