Over time, species evolve substantial phenotype differences. Yet, genetic analysis of these traits is limited by reproductive barriers to those phenotypes that distinguish closely related species. Here, we conduct a genome-wide non-complementation screen to identify genes that contribute to a major difference in thermal growth profile between two Saccharomyces species. S. cerevisiae is capable of growing at temperatures exceeding 40C, whereas S. uvarum cannot grow above 33C but outperforms S. cerevisiae at 4C. The screen revealed only a single nuclear-encoded gene with a modest contribution to heat tolerance, but a large effect of the species' mitochondrial DNA (mitotype). Furthermore, we found that, while the S. cerevisiae mitotype confers heat tolerance, the S. uvarum mitotype confers cold tolerance. Recombinant mitotypes indicate multiple genes contribute to thermal divergence. Mitochondrial allele replacements showed that divergence in the coding sequence of COX1 has a moderate effect on both heat and cold tolerance, but it does not explain the entire difference between the two mitochondrial genomes. Our results highlight a polygenic architecture for interspecific phenotypic divergence and point to the mitochondrial genome as an evolutionary hotspot for not only reproductive incompatibilities, but also thermal divergence in yeast.
24S. eubayanus, the wild, cold-tolerant parent of hybrid lager-brewing yeasts, has a 25 complex and understudied natural history. The exploration of this diversity can be used both to 26 develop new brewing applications and to enlighten our understanding of the dynamics of yeast 27 evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. 28 eubayanus strains, the largest collection to date. S. eubayanus has a multilayered population 29 structure, consisting of two major populations that are further structured into six subpopulations. 30Four of these subpopulations are found exclusively in the Patagonian region of South America; 31 one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is 32 specific to the Holarctic ecozone. S. eubayanus is most abundant and genetically diverse in 33 Patagonia, where some locations harbor more genetic diversity than is found outside of South 34America. All but one subpopulation shows isolation-by-distance, and gene flow between 35 subpopulations is low. However, there are strong signals of ancient and recent outcrossing, 36 including two admixed lineages, one that is sympatric with and one that is mostly isolated from 37 its parental populations. Despite S. eubayanus' extensive genetic diversity, it has relatively little 38 phenotypic diversity, and all subpopulations performed similarly under most conditions tested. 39Using our extensive biogeographical data, we constructed a robust model that predicted all 40 known and a handful of additional regions of the globe that are climatically suitable for S. 41 eubayanus, including Europe. We conclude that this industrially relevant species has rich wild 42 diversity with many factors contributing to its complex distribution and biology. 43 44 45 46
23Fructophily is a rare trait that consists in the preference for fructose over other carbon sources. 24Here we show that in a yeast lineage (the Wickerhamiella/Starmerella, W/S clade) formed by 25 fructophilic species thriving in the floral niche, the acquisition of fructophily is part of a wider 26 process of adaptation of central carbon metabolism to the high sugar environment. Coupling 27 comparative genomics with biochemical and genetic approaches, we show that the alcoholic 28 fermentation pathway was profoundly remodeled in the W/S clade, as genes required for 29 alcoholic fermentation were lost and subsequently re-acquired from bacteria through horizontal 30 gene transfer. We further show that the reinstated fermentative pathway is functional and that an 31 enzyme required for sucrose assimilation is also of bacterial origin, reinforcing the adaptive 32 nature of the genetic novelties identified in the W/S clade. This work shows how even central 33 carbon metabolism can be remodeled by a surge of HGT events.
New genes, with novel protein functions, can evolve “from scratch” out of intergenic sequences. These de novo genes can integrate the cell’s genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo genes in 15 yeast species from two genera whose phylogeny spans at least 100 million years of evolution. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We validated 82 candidates, by providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from non-coding to coding for 30 Saccharomyces de novo genes. We found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. We found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination would be a major driving force of de novo gene emergence in yeasts.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.