Core Y1000+ Project Papers
Opulente DA&, LaBella AL&, Harrison MC&&, Wolters JF&&, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A@, Hittinger CT@. 2024. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 384: eadj4503.
Groenewald M@, Hittinger CT, Bensch K, Opulente DA, Shen XX, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Ĉadež N, Péter G, Sampaio JP, Lachance MA, Yurkov AM, Daniel HM, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A. 2023. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Stud Mycol 105: 1-22.
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.
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.
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 6: 3927-39.
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 35: 100-9.
Select Y1000+ Project Discoveries
Harrison MC, Ubbelohde EJ, LaBella AL, Opulente DA, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT@, Rokas@. 2024. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proc Natl Acad Sci USA 121: e2315314121.
Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A, Hittinger CT@. 2024. Functional and evolutionary integration of a fungal gene with a bacterial operon. Mol Biol Evol 41: msae045.
David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A@. 2024. Saccharomycotina yeasts defy long-standing macroecological patterns. Proc Natl Acad Sci USA 121: e2316031121.
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT@. 2023. Mitochondrial genome diversity across the subphylum Saccharomycotina. Front Microbiol 14: 1268944.
Nalabothu RL&, Fisher KJ&@, LaBella AL, Meyer TA, Opulente DA, Wolters JF, Rokas A, Hittinger CT@. 2023. Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts. Mol Biol Evol 40: msad111.
Steenwyk JL, Phillips MA, Yang F, Date SS, Graham TR, Berman J, Hittinger CT, Rokas A. 2022. An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. Sci Adv 8: eabn0105.
LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A@. 2021. Signatures of optimal codon usage in metabolic genes inform budding yeast ecology. PLoS Biol 19: e3001185.
Haase MAB&, Kominek J&, Opulente DA, Shen XX, LaBella AL, Zhou X, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A@, Hittinger CT@. 2021. Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss. Genetics 217: iyaa012.
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. Sci Adv. 6: eabd0079.
Labella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A@. 2019. Variation and selection on codon usage bias across an entire subphylum. PLoS Genet 15: e1008304.
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.
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 176: 1356-66.
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.
Select Y1000+ Collaborator Publications
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 20: foaa042.
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.
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.
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.
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 113: 9882-7.

For a full list of publications, please see Hittinger Lab, Groenewald Lab, and Rokas Lab websites