The DOI matches its Crossref record; 112 of the 112 references it cites were found in a registry or an index.
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
Open accessAbstract
Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“In a previous study, the genomes of 343 yeast/fungi species combined with comprehensive genome annotations were publicly available 63 .”
From Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction (2022) · cites this paper as [63]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
Kumar, S., Stecher, G., & Tamura, K. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw054 · Cited by 43,923
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 26,312
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,145
Flagged first, then by citations
Cited by
Sorted by citations
Items 301–400 of 628
Wu, W., Cui, C., Zhu, Y., Chen, J., Zhuang, Q., Wang, Y., Liu, Z., Gao, H., Ou, G.-Z., Liu, C., et al. (2026) · Cell Research · doi:10.1038/s41422-026-01220-0 · Cited by 9
Self-citationLiang, J., Tang, H., Snyder, L. F., Youngstrom, C. E., & He, B. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011748 · Cited by 9
Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon
Sun, L., David, K. T., Wolters, J. F., Karlen, S. D., Gonçalves, C., Opulente, D. A., LaBella, A. L., Groenewald, M., Zhou, X., Shen, X., et al. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae045 · Cited by 7
Self-citationMota, M. N., Palma, M., & Sá‐Correia, I. (2024) · AMB Express · doi:10.1186/s13568-024-01754-9 · Cited by 7
Hybrid adaptation is hampered by Haldane’s sieve
Bautista, C., Gagnon-Arsenault, I., Utrobina, M., Fijarczyk, A., Bendixsen, D. P., Stelkens, R., & Landry, C. R. (2024) · Nature Communications · doi:10.1038/s41467-024-54105-4 · Cited by 7
Cyberlindnera sylvatica sp. nov., a yeast species isolated from forest habitats
Brysch‐Herzberg, M., Dlauchy, D., Seidel, M., & Péter, G. (2021) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004477 · Cited by 7
Regulation of alcohol oxidase gene expression in methylotrophic yeast Ogataea minuta
Yoko‐o, T., Komatsuzaki, A., Yoshihara, E., Zhao, S. Q., Umemura, M., Gao, X., & Chiba, Y. (2021) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2021.08.001 · Cited by 7
Solieri, L., Cassanelli, S., Huff, F., Barroso, L., Branduardi, P., Louis, E. J., & Morrissey, J. P. (2021) · FEMS Yeast Research · doi:10.1093/femsyr/foab058 · Cited by 7
Chai, C.-Y., Gao, W., Li, Y., Yan, Z., & Hui, F.-L. (2022) · MycoKeys · doi:10.3897/mycokeys.89.81119 · Cited by 7
Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms
Wadler, C. S., Wolters, J. F., Fortney, N. W., Throckmorton, K., Zhang, Y., Miller, C. R., Schneider, R. M., Wendt-Pienkowski, E., Currie, C. R., Donohue, T. J., et al. (2022) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-022-02168-0 · Cited by 7
Self-citationSystematics, Diversity and Ecology of the Genus Yarrowia and the Methanol-Assimilating Yeasts
Péter, G., Nagy, E. S., & Dlauchy, D. (2019) · Springer eBooks · doi:10.1007/978-3-030-21110-3_9 · Cited by 7
Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540
Tiukova, I., Jiang, H., Dainat, J., Hoeppner, M. P., Lantz, H., Piškur, J., Sandgren, M. O. J., Nielsen, J., Gu, Z., & Passoth, V. (2019) · Microorganisms · doi:10.3390/microorganisms7110489 · Cited by 8
Benning, F. M. C., Bell, T. A., Nguyen, T. H., Syau, D., Connell, L. B., Liao, Y., Keating, M. P., Coughlin, M., Nordstrom, A. E. H., Ericsson, M., et al. (2025) · Protein Science · doi:10.1002/pro.70207 · Cited by 7
Whole-Genome Sequences of Two Kazachstania barnettii Strains Isolated from Anthropic Environments
Devillers, H., Sarilar, V., Grondin, C., Sterck, L., Segond, D., Jacques, N., Sicard, D., Casarégola, S., & Tinsley, C. R. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac007 · Cited by 6
Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov.
Opulente, D. A., Langdon, Q. K., Jarzyna, M., Buh, K. V., Haase, M. A. B., Groenewald, M., & Hittinger, C. T. (2023) · Yeast · doi:10.1002/yea.3905 · Cited by 6
Self-citationPeri, K. V. R., Yuan, L., Faria‐Oliveira, F., Persson, K. O., Alalam, H., Lisbeth Olsson, A., Larsbrink, J., Kerkhoven, E. J., & Geijer, C. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01135-24 · Cited by 7
Shazad, A., Tlais, A. Z. A., Gottardi, D., Filannino, P., Patrignani, F., Lanciotti, R., Gobbetti, M., & Cagno, R. D. (2025) · Current Research in Food Science · doi:10.1016/j.crfs.2025.101100 · Cited by 7
Hanson, S. J., Cinnéide, E. Ó., Salzberg, L. I., Wolfe, K. H., McGowan, J., Fitzpatrick, D. A., & Matlin, K. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab211 · Cited by 6
Schwarz, L. V., Valera, M. J., Delamare, A. P. L., Carrau, F., & Echeverrigaray, S. (2022) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2022.100129 · Cited by 6
A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species
Lu, H., Kerkhoven, E. J., & Nielsen, J. (2022) · Biomolecules · doi:10.3390/biom12111632 · Cited by 6
Evolution of the triplet BRCT domain
Mota, M. B. S., Woods, N. T., Carvalho, M. A., Monteiro, Á. N. A., & Mesquita, R. D. (2023) · DNA repair · doi:10.1016/j.dnarep.2023.103532 · Cited by 6
The evolution of anaerobic growth in Saccharomycotina yeasts
Krause, D. J. (2023) · Yeast · doi:10.1002/yea.3890 · Cited by 7
Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event
Evans-Yamamoto, D., Dubé, A. K., Saha, G., Plante, S., Bradley, D. T. C., Gagnon‐Arsenault, I., & Landry, C. R. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad246 · Cited by 6
Molecular approaches improving our understanding of Brettanomyces physiology
Varela, C., & Borneman, A. R. (2022) · FEMS Yeast Research · doi:10.1093/femsyr/foac028 · Cited by 6
Srikant, S., Gaudet, R., & Murray, A. W. (2023) · Current Biology · doi:10.1016/j.cub.2023.08.039 · Cited by 7
Aguirre‐López, B., Escalera‐Fanjul, X., Hersch-González, J., Rojas‐Ortega, E., El‐Hafidi, M., Lezama, M., González, J., Bianchi, M. M., López, G., Márquez, D., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01843 · Cited by 6
Walker, J. F., Shen, X., Rokas, A., Smith, S. A., & Moyroud, E. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.20.049999 · Cited by 5
Self-citationThe Influence of Model Violation on Phylogenetic Inference: A Simulation StudyPreprint
Naser-Khdour, S., Minh, B. Q., & Lanfear, R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.22.461455 · Cited by 6
A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergencesPreprint
Liu, H., Steenwyk, J. L., Zhou, X., Schultz, D. T., Kocot, K. M., Shen, X., Rokas, A., & Li, Y. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.20.556338 · Cited by 6
Self-citationGenomic evolution and patterns of horizontal gene transfer in Papilio
Wang, J., Wu, Y., Zhu, L., Guo, K., Gao, S., & Dong, Y. (2024) · Genomics · doi:10.1016/j.ygeno.2024.110956 · Cited by 5
Footprints of Human Migration in the Population Structure of Wild Baker's Yeast
Peña, J. J., da Costa, E. S. F., Ward, A. K., & Bensasson, D. (2025) · Molecular Ecology · doi:10.1111/mec.17669 · Cited by 5
Spaans, M., Winkler, L. S., van den Broek, M. A., & Daran, J.-M. G. (2025) · Food Microbiology · doi:10.1016/j.fm.2025.104903 · Cited by 5
Vu, D., de Vries, M., van den Ende, B. G., Houbraken, J. A. M. P., Nilsson, R. H., Brankovics, B., Hernández‐Restrepo, M., Groenewald, J. Z., Crous, P. W., Hagen, F., et al. (2025) · Molecular Ecology Resources · doi:10.1111/1755-0998.70082 · Cited by 5
Self-citationImpact of GC content on de novo gene birth
Roginski, P., Papadopoulos, C., Herman, S., Baumann, A., Grislain, A., & Lopes, A. (2026) · Nature Communications · doi:10.1038/s41467-025-68022-7 · Cited by 5
Discovery of additional ancient genome duplications in yeasts
David, K. T., Horianopoulos, L. C., Gonçalves, C., Steenwyk, J. L., Pontes, A., Gonçalves, P., Hittinger, C. T., Pennell, M., & Rokas, A. (2026) · Current Biology · doi:10.1016/j.cub.2025.12.053 · Cited by 5
Self-citationAncient co-option of LTR retrotransposons as yeast centromeres
Haase, M. A. B., Lazar‐Stefanita, L., Baudry, L., Wudzinska, A. M., Zhou, X., Rokas, A., Hittinger, C. T., Pfander, B., Musacchio, A., & Boeke, J. D. (2026) · Nature · doi:10.1038/s41586-025-10092-0 · Cited by 5
Self-citationGenome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626
Palma, M., Mondo, S. J., Pereira, M. B., Vieira, É., Grigoriev, I. V., & Sá‐Correia, I. (2022) · Journal of Fungi · doi:10.3390/jof8030254 · Cited by 6
PhyloForge : Unifying Micro‐ and Macroevolution With Comprehensive Genomic Signals
Wang, Y., Dong, W., Liang, Y., Lin, W., Chen, J., Henry, R. J., & Chen, F. (2024) · Molecular Ecology Resources · doi:10.1111/1755-0998.14050 · Cited by 5
Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes
Mondo, S. J., He, G., Sharma, A., Ciobanu, D., Riley, R. W., Andreopoulos, W., Lipzen, A., Kuo, A., LaButti, K. M., Pangilinan, J. L., et al. (2025) · iScience · doi:10.1016/j.isci.2025.112472 · Cited by 5
Divergent patterns of selection on metabolite levels and gene expression
Kern, A., Yang, G. X., Khosla, N. M., Ang, R. M. L., Snyder, M. P., & Fraser, H. B. (2021) · BMC Ecology and Evolution · doi:10.1186/s12862-021-01915-5 · Cited by 5
Protein innovation through template switching in the Saccharomyces cerevisiae lineage
Abraham, M., & Hazkani‐Covo, E. (2021) · Scientific Reports · doi:10.1038/s41598-021-01736-y · Cited by 5
Magnusiomyces siamensis sp. nov., a yeast-like fungus isolated from food waste
Dudhat, J., Sakpuntoon, V., Angchuan, J., Kaewwichian, R., & Srisuk, N. (2022) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.005435 · Cited by 5
Genome doubling enabled the expansion of yeast vesicle traffic pathways
Purkanti, R., & Thattai, M. (2022) · Scientific Reports · doi:10.1038/s41598-022-15419-9 · Cited by 5
Espinoza‐Simón, E., Moreno‐Alvarez, P., Nieto-Zaragoza, E., Ricardez-García, C., Ríos‐Castro, E., Uribe‐Carvajal, S., & Torres‐Quiroz, F. (2022) · Fermentation · doi:10.3390/fermentation8100505 · Cited by 5
Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ
McPherson, K. S., Rizzo, A. A., Erlandsen, H., Chatterjee, N., Walker, G. C., & Korzhnev, D. M. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102859 · Cited by 5
Čadež, N., Boundy‐Mills, K., Botha, A., Качалкин, А. В., Dlauchy, D., & Péter, G. (2023) · Yeast · doi:10.1002/yea.3904 · Cited by 5
Self-citationSurprising effects of differential loss in genome evolution: the last-one-out
Bremer, N., Martin, W. F., & Steel, M. (2025) · FEMS Microbiology Letters · doi:10.1093/femsle/fnaf051 · Cited by 9
The teenage years of yeast population genomics — trace history, admixing and getting wilder
Tsai, I. J. (2022) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2022.101942 · Cited by 5
Salzberg, L. I., Martos, A. A. R., Lombardi, L., Jermiin, L. S., Blanco, A., Byrne, K. P., & Wolfe, K. H. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010525 · Cited by 5
Complex intron generation in the yeast genus Lipomyces
Ág, N., Kavalecz, N., Pénzes, F., Karaffa, L., Scazzocchio, C., Flipphi, M. J. A., & Fekete, E. (2020) · Scientific Reports · doi:10.1038/s41598-020-63239-6 · Cited by 5
Feature frequency profile-based phylogenies are inaccurate
Li, Y., David, K. T., Shen, X., Steenwyk, J. L., Halanych, K. M., & Rokas, A. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013143117 · Cited by 5
Self-citationZhou, S., Wu, Y., Zhao, Y., Zhang, Z., Jiang, L., Liu, L., Zhang, Y., Tang, J., & Yuan, Y. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.19.453002 · Cited by 5
Oss, S. B. V., Parikh, S. B., Coelho, N. C., Wacholder, A. C., Belashov, I. A., Zdancewicz, S., Michaca, M., Xu, J., Kang, Y. P., Ward, N. P., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.19.476918 · Cited by 5
A Novel Virus Discovered in the Yeast Pichia membranifaciensPreprint
Lee, M. D., Creagh, J. W., Fredericks, L. R., Crabtree, A., Patel, J. S., & Rowley, P. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.05.475065 · Cited by 5
Machine learning illuminates how diet influences the evolution of yeast galactose metabolismPreprint
Harrison, M., Ubbelohde, E. J., LaBella, A. L., Opulente, D. A., Wolters, J. F., Zhou, X., Shen, X., Groenewald, M., Hittinger, C. T., & Rokas, A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.20.549758 · Cited by 5
Self-citationLittle, J., Meyer, G., Grover, A., Francette, A. M., Partha, R., Arndt, K. M., Smith, M. R., Clark, N. L., & Chikina, M. D. (2025) · Genome Research · doi:10.1101/gr.280586.125 · Cited by 5
Gonçalves, C., Steenwyk, J. L., Rinker, D. C., Opulente, D. A., LaBella, A. L., Harrison, M.-C., Wolters, J. F., Zhou, X., Shen, X.-X., Covo, S., et al. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf285 · Cited by 4
Self-citationPark, S. O., Khondker, R. C., Blank, A. F., Dyatel, A., Frazer, C., Bennett, R. J., Reid, R. J. D., Rothstein, R. J., & Berchowitz, L. E. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003396 · Cited by 4
Horianopoulos, L. C., Rokas, A., & Hittinger, C. T. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00778-0 · Cited by 5
Self-citationPinto, J., & Stelkens, R. B. (2025) · Evolution · doi:10.1093/evolut/qpaf244 · Cited by 4
Nashed, S., Barbry, H. E., Benchouaia, M., Dijoux-Maréchal, A., Delaveau, T., Ruiz-Gutierrez, N., Gaulier, L., Tribouillard‐Tanvier, D., Chevreux, G., Crom, S. L., et al. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010848 · Cited by 4
García‐Acero, Á. M., Morais, C. G., Souza, G. F. L., Santos, A. R. O., Lachance, M., Velásquez-Lozano, M. E., & Rosa, C. A. (2024) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006273 · Cited by 4
Self-citationSignatures of Innovation and Selection in the Extremotolerant Yeast Kluyveromyces marxianus
Christensen, K. E., Deal, A., Wang, J.-T. J., Duarte, A., Edwards, J. L., Goodman, J. L. N., Ma, Z., Padilla, S. I., Szewczyk, E., Rha, C. H., et al. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag060 · Cited by 4
Isobutanol production by Candida glabrata – A potential organism for future fuel demands
Lakshmi, N. M., Binoop, M., Salini, C. N., Narisetty, V., Sindhu, R., Pandey, A., & Binod, P. (2021) · Fuel · doi:10.1016/j.fuel.2021.121634 · Cited by 4
Sharma, S., & Kumar, S. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac236 · Cited by 5
Santos, A. R. O., Barros, K. O., Batista, T. M., Souza, G. F. L., Alvarenga, F. B. M., Abegg, M. A., Sato, T. K., Hittinger, C. T., Lachance, M., & Rosa, C. A. (2023) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006125 · Cited by 4
Self-citationNatural trait variation across Saccharomycotina species
Wang, J.-T. J., Steenwyk, J. L., & Brem, R. B. (2024) · FEMS Yeast Research · doi:10.1093/femsyr/foae002 · Cited by 4
Self-citationZheng, B., Wang, G., Qu, Z., Hu, J., Bao, Z., & Wang, M. (2024) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2024.105177 · Cited by 4
Self-citationMixão, V., Saus, E., Hagen, F., Boekhout, T., Stevens, R. L., & Gabaldón, T. (2024) · Mycosphere · doi:10.5943/mycosphere/15/1/9 · Cited by 4
Lyu, Y., Shi, Y., Song, K., Zhou, J., Chen, H., Li, X., Yu, Y., & Lü, H. (2026) · Nature Communications · doi:10.1038/s41467-025-68164-8 · Cited by 4
Wang, M., & Ruan, R. (2020) · Genomics · doi:10.1016/j.ygeno.2020.09.025 · Cited by 4
Self-citationHeineike, B. M., & El‐Samad, H. (2021) · Frontiers in Fungal Biology · doi:10.3389/ffunb.2021.642336 · Cited by 4
Torulaspora jiuxiensis sp. nov., a novel yeast species isolated from rotting wood
Chu, S.-B., Hu, W.-T., & Hui, F.-L. (2022) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.005629 · Cited by 4
The chromosomal evolutionary lineage of the genus Zygosaccharomyces
Sato, A., & Ohnishi, Y. (2023) · FEMS Yeast Research · doi:10.1093/femsyr/foad017 · Cited by 4
Danielozyma pruni sp. nov., an asexual yeast species isolated from insect frass
Liu, S., Guo, Q.-C., An, Z.-R., & Hui, F.-L. (2023) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006124 · Cited by 4
Brejová, B., Hodorová, V., Mutalová, S., Cillingová, A., Tomáška, Ľ., Vinař, T., & Nosek, J. (2024) · DNA Research · doi:10.1093/dnares/dsae014 · Cited by 4
Takashi Nakase's last tweet: what is the current direction of microbial taxonomy research?
Takashima, M., Suh, S., Bai, F., & Sugita, T. (2019) · FEMS Yeast Research · doi:10.1093/femsyr/foz066 · Cited by 5
Self-citationEngineering of molybdenum-cofactor-dependent nitrate assimilation in Yarrowia lipolytica
Perli, T., Borodina, I., & Daran, J.-M. G. (2021) · FEMS Yeast Research · doi:10.1093/femsyr/foab050 · Cited by 5
Steenwyk, J. L., Phillips, M. A., Yang, F., Date, S. S., Graham, T. R., Berman, J. G., Hittinger, C. T., & Rokas, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.09.451830 · Cited by 3
Self-citationDiverse signatures of convergent evolution in cacti-associated yeastsPreprint
Gonçalves, C., Harrison, M., Steenwyk, J. L., Opulente, D. A., LaBella, A. L., Wolters, J. F., Zhou, X., Shen, X., Groenewald, M., Hittinger, C. T., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.14.557833 · Cited by 4
Self-citationWalunjkar, N., Lai, T. Y., Akhter, N., Miller, J. H., Bettinger, J. Q., Marcus, E., Phizicky, E. M., Ghaemmaghami, S., & Fay, J. C. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf137 · Cited by 3
Vandeputte, M., Diependaele, E., & Van Bogaert, I. N. A. (2025) · FEMS Yeast Research · doi:10.1093/femsyr/foaf048 · Cited by 4
Spermine and thermospermine synthases emerged multiple times during eukaryote evolution
Li, B., Liang, J., Baniasadi, H. R., Phillips, M. A., & Michael, A. J. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.111028 · Cited by 3
Yeasty memories, yeast genomes and beyond—from controversy to collaboration
Dujon, B., & Cooper, T. (2025) · FEMS Yeast Research · doi:10.1093/femsyr/foaf073 · Cited by 3
Gadar-Lopez, A. E., de Carvalho, A. C., Li, X., Rago, D., Ahonen, L. L., Gotfredsen, C. H., Lukassen, M. V., Cano‐Prieto, C., Chen, L., Jayachandran, S., et al. (2026) · Nature Chemical Biology · doi:10.1038/s41589-026-02282-2 · Cited by 3
Shi, T., Zeng, J., Zhou, J., Yu, Y., & Lü, H. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.865829 · Cited by 4
Schmitz, J. M., Wolters, J. F., Murray, N. H., Guerra, R. M., Bingman, C. A., Hittinger, C. T., & Pagliarini, D. J. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.102981 · Cited by 3
Self-citationPhylogenetic analyses reveal insights into interdomain horizontal gene transfer of microbial lipases
Medeiros, P., Canato, D., Braz, A. S. K., & Paulino, L. C. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108069 · Cited by 3
The relationship between cell density and cell count differs among Saccharomyces yeast species
Pinto, J., Tavakolian, N., Li, C., & Stelkens, R. B. (2024) · PubMed Central · doi:10.17912/micropub.biology.001215 · Cited by 3
Wang, P., Driscoll, W. W., & Travisano, M. (2024) · Communications Biology · doi:10.1038/s42003-024-06485-y · Cited by 3
Sun, Q.-L., Yuan, Z., Sun, Y., & Sun, L. (2024) · Microbiome · doi:10.1186/s40168-024-01960-4 · Cited by 3
Oda, A., Yasukawa, T., Tamura, M., Sano, A., Masuo, N., & Ohta, K. (2025) · Genes to Cells · doi:10.1111/gtc.70010 · Cited by 3
Cope, A. L., & Shah, P. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2419889122 · Cited by 3
Han, W., Xiao, L., Sun, H., Xiang, G. M., Jia, Q., Wang, H., Ji, B., Zhang, C., Kerkhoven, E. J., Nielsen, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-75549-w · Cited by 3
Centromeres in budding yeasts are conserved in chromosomal location but not in structure
Hession, C., Byrne, K. P., Wolfe, K. H., & Butler, G. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011814 · Cited by 3
Santa‐Brígida, R., Santos, A. R. O., Martins, M. B., Rosa, L. H., Lachance, M., & Rosa, C. A. (2023) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006035 · Cited by 3
Self-citationHigh nitrogen concentration causes G2/M arrest in Hanseniaspora vineae
Schwarz, L. V., Sandri, F. K., Scariot, F. J., Delamare, A. P. L., Valera, M. J., Carrau, F., & Echeverrigaray, S. (2023) · Yeast · doi:10.1002/yea.3911 · Cited by 3
Starmerella kisarazuensis f.a., sp. nov., a novel yeast isolated from Trifolium pratense flowers
Shibayama, K., Miyazaki, Y., Ikeda, M., Yamaguchi, K., Inaba, S., & Yamazaki, A. (2024) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006253 · Cited by 3
Zehetner, L., Széliová, D., Kraus, B., Bort, J. A. H., & Zanghellini, J. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012236 · Cited by 5
Iordache, S.-M., Iordache, A., Florea, A.-M., Caramizoiu, S., Pârvulescu, C. C., Baiasu, F., Neguț, I., & Bita, B. I. (2025) · C – Journal of Carbon Research · doi:10.3390/c11010009 · Cited by 3
Metadata
- Authors
- Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., Boudouris, J. T., Schneider, R. M., Langdon, Q. K., Ohkuma, M., Endoh, R., Takashima, M., Manabe, R.-I., Čadež, N., Libkind, D., Rosa, C. A., DeVirgilio, J., Hulfachor, A. B., Groenewald, M., Kurtzman, C. P., Hittinger, C. T., & Rokas, A.
- Affiliations
- Vanderbilt University (US)
- University of Wisconsin–Madison (US)
- South China Agricultural University (CN)
- RIKEN BioResource Research Center (JP)
- RIKEN Center for Integrative Medical Sciences (JP)
- University of Ljubljana (SI)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Universidade Federal de Minas Gerais (BR)
- Agricultural Research Service (US)
- Westerdijk Fungal Biodiversity Institute (NL)
- Corresponding author
- Hittinger, Chris Todd
- Rokas, Antonis
- ORCID
- Shen, Xing-Xing
- Opulente, Dana A.
- Kominek, Jacek
- Zhou, Xiaofan
- Steenwyk, Jacob L.
- Haase, Max A.B.
- Wisecaver, Jennifer H.
- Wang, Mingshuang
- Doering, Drew T.
- Langdon, Quinn K.
- Ohkuma, Moriya
- Takashima, Masako
- Manabe, Ri-ichiroh
- Čadež, Neža
- Libkind, Diego
- Rosa, Carlos A.
- DeVirgilio, Jeremy
- Hulfachor, Amanda Beth
- Groenewald, Marizeth
- Kurtzman, Cletus P.
- Hittinger, Chris Todd
- Rokas, Antonis
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-11
- Volume
- 175
- Issue
- 6
- Pages
- 1533-1545.e20
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6291210
- OpenAlex
- W2899763402
- Cited by
- 619
- References
- 112
- Citations by year
- 2026: 56 · 2025: 72 · 2024: 109 · 2023: 83 · 2022: 70 · 2021: 116 · 2020: 68 · 2019: 43 · 2018: 1
- FWCI
- 20.28
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- Funders
- National Science Foundation (DEB-1442113, DEB-1442148, IOS-1401682, DGE-1256259)
- DOE Great Lakes Bioenergy Research Center (DE-FC02-07ER64494, DE-SC0018409)
- Pew Charitable Trusts
- Vilas Trust Estate
- Guggenheim
- Vanderbilt
- National Key Project for Basic Research of China (2015CB150600)
- NHGRI (5T32HG002760)
- NIH (5T32GM007133)
- CONICET (PIP 392)
- FONCyT (PICT 2542)
- Universidad Nacional del Comahue (B199)
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Fundação de Amparo a Pesquisa do Estado de Minas Gerais
- Topics
- Life Sciences › Immunology and Microbiology › Microbiology › Yeasts and Rust Fungi Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Saccharomyces cerevisiae, Saccharomycotina, genome evolution, phylogeny, horizontal gene transfer, metabolic phenotypes, common ancestor, reductive evolution, gene loss
- MeSH terms
- Saccharomycetales, Phylogeny, Genome, Fungal, Evolution, Molecular, Gene Transfer, Horizontal
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
