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Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
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Preprints
Lee SK, West C, Opulente DA, Harrison MC, Wolters JF, Shen XX, Zhou X, Groenewald M, Hittinger CT, Rokas A, LaBella AL. Genomic factors limiting the diversity of Saccharomycotina plant pathogens. bioRxiv. 2025:2025-02. https://www.biorxiv.org/content/10.1101/2025.02.27.640420v1.full
Feng, B., Li, Y., Liu, H., Steenwyk, J.L., David, K.T., Tian, X., Xu, B., Goncalves, C., Opulente, D.A., LaBella, A.L. and Harrison, M.C., 2024. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. bioRxiv, pp.2024-06. https://doi.org/10.1101/2024.06.05.597512
David KT, Schraiber JG, Crandall JG, Labella AL, Opulente DA, Harrison MC, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT. Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade. bioRxiv. 2024 Jul 23.
2024
Zavala, B., Dineen, L., Fisher, K.J., Opulente, D.A., Harrison, M.C., Wolters, J.F., Shen, X.X., Zhou, X., Groenewald, M., Hittinger, C.T., Rokas, A.R, LaBella A.L, 2024. Genomic factors shaping codon usage across the Saccharomycotina subphylum. G3: Genes, Genomes, Genetics. 2024 Aug 30:jkae207. https://doi.org/10.1093/g3journal/jkae207
Harrison, M.C., Opulente, D.A., Wolters, J.F., Shen, X.X., Zhou, X., Groenewald, M., Hittinger, C.T., Rokas, A., LaBella, A.L. Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework. Yeast. 2024 Jul 16. https://doi.org/10.1002/yea.3981
Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cactus-associated yeasts. PLoS biology. 2024 Sep 23;22(9):e3002832. https://doi.org/10.1371/journal.pbio.3002832
Opulente DA*, LaBella AL*, Harrison MC, Wolters JF, Liu C, Li Y... Rokas AR^, Hittinger CT^. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science. 2024 Apr 26;384(6694):eadj4503. *Co-First, ^Co-Corresponding. https://doi.org/10.1126/science.adj4503
Harrison MC, Ubbelohde EJ, LaBella AL, Opulente DA, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proceedings of the National Academy of Sciences. 2024 Apr 30;121(18):e2315314121. https://doi.org/10.1073/pnas.2315314121
Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A. Functional and evolutionary integration of a fungal gene with a bacterial operon. Molecular Biology and Evolution. 2024 Apr;41(4):msae045. https://doi.org/10.1093/molbev/msae045
David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy long-standing macroecological patterns. Proceedings of the National Academy of Sciences. 2024 Mar 5;121(10):e2316031121. https://doi.org/10.1073/pnas.2316031121
David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy long-standing macroecological patterns. Proceedings of the National Academy of Sciences. 2024 Mar 5;121(10):e2316031121. https://doi.org/10.1073/pnas.2316031121
2023
P. Solé-Navais, et al (including A.L. LaBella) (2022) Genetic effects on the timing of parturition and links to fetal birth weight. Nature genetics. 2023 Apr 3:1-9. https://doi.org/10.1038/s41588-023-01343-9
Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen XX, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology. 2023 Mar. https://doi.org/10.3114/sim.2023.105.01
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial genome diversity across the subphylum Saccharomycotina. Frontiers in Microbiology. 2023;14.
R.L. Nalabothu, K.J, Fisher, A.L. LaBella, T.A. Meyer, D.A. Opulente, J.F. Wolters, A. Rokas, C.T. Hittinger. Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts. Molecular Biology and Evolution. 2023 May 8:msad111. https://doi.org/10.1093/molbev/msad111
Abraham A, LaBella AL, Benton ML, Rokas A, Capra JA. GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics. 2023 Jan 1;39(1):btad037. https://doi.org/10.1093/bioinformatics/btad037
2022
A. Abraham*, A.L. LaBella*, J.A. Capra, A. Rokas. Mosaic patterns of selection in genomic regions associated with diverse human traits. PLoS Genetics. 2022 Nov 7;18(11):e1010494. *Co-First Authors https://doi.org/10.1371/journal.pgen.1010494
M. Hugaboom, E.A. Hatmaker, A.L. LaBella, A. Rokas. Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi. (2022) G3 Genes|Genomes|Genetics, jkac285 https://doi.org/10.1093/g3journal/jkac285
Y. Li, H. Liu, J. Steenwyk, A.L. LaBella, M.C. Harrison, M. Groenwald, X. Zhou, T. Zhao, C.T. Hittinger, A. Rokas. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology. 2022, Nov 4 https://doi.org/10.1016/j.cub.2022.10.025
A.C. Colabardini, N. Van Rhijn, A.L. LaBella, C. Valero, L. Dineen, A. Rokas, G.H. Goldman GH. Aspergillus fumigatus FhdA transcription factor is important for mitochondrial activity and codon usage regulation during the caspofungin paradoxical effect. Antimicrobial Agents and Chemotherapy. 2022 Sep 20;66(9):e00701-22. https://doi.org/10.1128/aac.00701-22
R. Markowitz, A. L. LaBella, M. Shi, A. Rokas; J. A. Capra, J, Ferguson, J. D. Mosley, S. R. Bordenstein (2022) Microbiome-associated human genetic variants impact phenome-wide disease risk. Proceedings of the National Academy of Sciences. 2022 Jun 28;119(26):e2200551119. https://doi.org/10.1073/pnas.2200551119
J.L. Steenwyk, T.J. Buida III, C. Gonçalves, D.C. Goltz, G. Morales, M. Mead, A.L. LaBella, C.M. Chavez, P. Gonçalves, J.E. Schmitz, M. Hadjifrangiskou, Y. Li, A. Rokas. (2022) BioKIT: A versatile toolkit for processing and analyzing diverse types of sequence data. Genetics. 2022 Jul;221(3):iyac079.https://doi.org/10.1101/2021.10.02.462868
MC Harrison, A. L. LaBella, C.T. Hittinger, A. Rokas. (2022) The Evolution of the GALactose Utilization Pathway in Budding Yeasts. Trends in Genetics: Sep 15 https://doi.org/10.1016/j.tig.2021.08.013
2021
J.L. Steenwyk, M.E. Mead, P. Alves de Castro, C. Valero, A. Ricardo de Lima Damásio, R.A.C. dos Santos, A.L. LaBella, Y. Li, S.L. Knowles, H.A. Raja, N.H. Oberlies, X. Zhou, O.A. Cornely, P. Koehler, F. Fuchs, G.H. Goldman, A. Rokas. (2021) Genomic and phenotypic analysis of coronavirus-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. Microbiology Spectrum, 9(1) https://doi.org/10.1128/Spectrum.00010-21
A.L. LaBella, D.A. Opulente, J.L. Steenwyk, C.T. Hittenger, A. Rokas. (2021) Signatures of optimal codon usage predict metabolic ecology in budding yeasts. PLOS Biology: 19 (4) https://doi.org/10.1371/journal.pbio.3001185
J.L. Steenwyk, T.J. Buida III, A.L. LaBella, Y. Li, X.X. Shen, A.R. Rokas. (2021) PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics: btab096 https://doi.org/10.1093/bioinformatics/btab096
M.L. Benton, A. Abraham, A.L. LaBella, P. Abbot, A. Rokas, J. Capra. (2021) The Influence of Evolutionary History on Human Health and Disease. Nature Reviews Genetics: 1-15 https://doi.org/10.1038/s41576-020-00305-9
M.A.B. Haase, J. Kominek, D. Opulente, X.X. Shen, A.L. LaBella, X. Zhou, J. DeVirgilio, A. Hulfachor, C.P. Kurtzman, A. Rokas, C.T. Hittinger (2021) Repeated horizontal transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss. Genetics: iyaa012 https://doi.org/10.1093/genetics/iyaa012
2020
A. Rokas, S. Mesiano, O. Tamam, A.L. LaBella, G. Zhang, L.J. Muglia. (2020) Developing a Theoretical Evolutionary Framework to Solve the Mystery of Parturition Initiation. eLife: 9: e58343 https://elifesciences.org/articles/58343
X.X. Shen, J.L. Steenwyk, A.L. LaBella, D.A. Opulente, X. Zhou, Y. Li, M. Groenwald, C.T. Hittinger, A. Rokas (2020) Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science Advances: 6: eabd0079 https://www.science.org/doi/full/10.1126/sciadv.abd0079
A.L. LaBella*, A. Abraham*, Y. Pichkar, S.L. Fong, G. Zhang, L. Muglia, P. Abbot, A. Rokas, J.A. Capra (2020) Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nature Communications: 11:3731 *co-first https://www.nature.com/articles/s41467-020-17258-6
2019
Z.A. Ely, J.M. Moon, G.R. Sliwoski, A.K. Sangha, X.X. Shen, A.L. LaBella, J. Meiler, J.A. Capra, A. Rokas. (2019) The impact of natural selection on the evolution and function of placentally expressed galectins. Genome Biology and Evolution: evz183 https://doi.org/10.1093/gbe/evz183
A.L. LaBella, D.A. Opulente, J.L. Steenwyk, C.T. Hittinger, A. Rokas. (2019) Variation and selection on codon usage bias across an entire subphylum. PLoS Genetics: 15(7): e1008304 https://doi.org/10.1371/journal.pgen.1008304
J. Steenwyk, D.A. Opulente, J. Kominek, X.X. Shen, X. Zhou, A.L. LaBella, N.P. Bradley, B.F. Eichman, N. Čadež, D. Libkind, J. DeVirgilio, A.B. Hulfachor, C.P. Kurtzman, C.T. Hittinger, A. Rokas. (2019) Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar yeasts. PLoS Biology: Volume 17, Issue 5 https://doi.org/10.1371/journal.pbio.3000255
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