The concept of niche generalists and specialists stands across the tree of life. Overall, generalists perform relatively well across many ecological niches, while specialists are experts in thriving in their own niche. Researchers from the Yeast Genomics Research Lab at UCIBIO-NOVA, participated in a study, recently published in the journal Science, where genomic, metabolic, and ecological datasets were generated for nearly every known yeast species, to shed light on the contribution of intrinsic (genome encoded) factors and extrinsic (ecological) factors in shaping niche breath.
Using evolutionary, machine learning, and network analyses, “we found that yeast metabolic niche breadth is largely shaped by intrinsic factors. Unexpectedly, no trade-offs were observed in being a carbon generalist, i.e., in being able to use a wide range of compounds as carbon sources. In fact, generalist yeasts grew faster than specialists on carbon sources that both are capable of assimilating”, said the authors.
The comprehensive compilation of genomic, metabolic, evolutionary, and ecological data encompassing the majority of recognized species within the 400-million-year-old yeast subphylum Saccharomycotina, as presented herein, along with the concurrent presence of various genetic models within the subphylum, constitutes an unparalleled asset and structure for establishing connections between genomic variability and phenotypic as well as ecological variability.
Figure: A comprehensive initiative capturing genomic, metabolic, and ecological diversity among 1154 yeasts of the fungal subphylum Saccharomycotina.
We built a robust phylogeny and generated extensive genomic, phenotypic, and ecological data. We identified carbon niche breadth variation and used machine leaning to identify several intrinsic factors that contribute to carbon generalism.
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Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
Dana A. Opulente, Abigail Leavitt Labella, Marie-cCaire Harrison, John F. Wolters, Chao Liu, Yonglin Li, Jacek Kominek, Jacob L. Steenwyk, Hayley R. Stoneman, Jenna Vandenavond, Caroline R. Miller, Quinn K. Langdon, Margarida Silva, Carla Gonçalves, Emily J. Ubbelohde, Yuanning Li, Kelly V. Buh, Martin Jarzyna, Max A. B. Haase, Carlos A. Rosa, Neža Čcadež, Diego Libkind, Jeremy H. Devirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, José Paulo Sampaio, Paula Gonçalves, Xiaofan Zhou, Xing-xing Shen, Marizeth Groenewald, Antonis Rokas, And Chris Todd Hittinger
SCIENCE, Vol 384, Issue 6694