NSF Dimensions Press Releases
Publications
Main Projects:
- Hittinger C.T., et al. (2015) Genomics and the making of yeast biodiversity. Dec 2015; 35:100-9.
- Lopes M.R., et al. (2016) Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora haerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov. Jun 2016; 16(4). pii fow044.
- Riley R., et al. (2016). Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci USA. 30 Aug 2016; 113(35):9882-7.
- Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT@, Rokas A@. 2016. in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies. G3 (Bethesda) 6: 3655-62.
- Shen XX, Zhou X, Kominek J, Kurtzman CP@, Hittinger CT@, Rokas A@. 2016. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 (Bethesda) 6: 3927-39.
- 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 17: fox019.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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, Cadez 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.
- 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.
- Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Cadez 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.
- 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.
- 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.
- 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. Science Advances. 2020 Nov 4: 6(45): eabd0079. doi: 10.1126/sciadv.abd0079.
- 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.
Related Projects:
- Rokas, A. (2016). Systematics in the age of genomics. In "Next Generation Systematics", Olson P. D., J. Hughes, & J. A. Cotton (Eds.), Cambridge University Press, pp. 219-228.
- Rokas, A., & P. S. Soltis, Eds. (2015). Special issue on Genomes and Evolution. Curr. Opin. Genet. Dev., volume 35: 1-126.
- Rokas A., Soltis P. S. (2015) Editorial overview: Genomes and evolution: "Seq-ing" answers in life's genomes. Dec 2015; 35:iv-vi.
- Coelho M. A., Almeida J. M., Hittinger C. T., Goncalves P. (2015) Draft Genome Sequence of Sporidiobolus salmonicolor CBS 6832, a Red-Pigmented Basidiomycetous Yeast. 21 May 2016;3(3). pii: 300444-15.
- Alexander W. G., Peris D., Pfannenstiel B. T., Opulente D. A., Kuang M., Hittinger C. T. (2016) Effient engineering of marker-free synthetic allotetraploids of Saccharomyces. Apr 2016; 89:10-7.
- Alexander W. G., Wiscaver J. H., Rokas A., Hittinger C. T. (2016) Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. 12 Apr 2016; 113(15):4116-21.
- Kobert K., Salichos L., Rokas A., Stamatakis A. (2016) Computing the Internode Certainty and Related Measures from Partial Genet Trees. Jun 2016; 33(6):1606-17.
- Wisecaver J.H., Alexander W.G., King S.B., Hittinger C.T., Rokas A. (2016) Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes. Aug 2016;33(8):1979-87.
- Shen X.X., Salichos L., Rokas A. (2016) A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. 2 Sep 2016; 8(8):2565-80.
- Kuang M.C., Hutchins P.D., Russell J.D., Coon J.J., Hittinger C.T. (2016) Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. 30 Sep 2016; 5 pii: 319027.
- 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 10: 78.
- 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.
- 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.
- 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.
- 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.
- 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.
- Cadez 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.
- 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.
- 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.
- 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.
- Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A. 2020. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nat Commun 11: 6096.
