Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast

Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence in COX1 affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.This work was supported by the NIH (grant GM080669) to J.C.F. Additional support to C.T.H. was provided by the USDA National Institute of Food and Agriculture (Hatch project 1003258), the National Science Foundation (DEB-1253634), and the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-SC0018409 and DE-FC02-07ER64494 to T. J. Donohue). C.T.H. is a Pew Scholar in the Biomedical Sciences and a Vilas Faculty Early Career Investigator, supported by the Pew Charitable Trusts and the Vilas Trust Estate, respectively. D.P. is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 747775).Peer reviewe

Mitochondrial DNA and temperature tolerance in lager yeasts

A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces, species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and industrial hybrids (Saccharomyces cerevisiae × Saccharomyces eubayanus or Saccharomyces pastorianus), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world’s most commonly fermented beverage.This work was supported by the USDA National Institute of Food and Agriculture (Hatch project no. 1003258), the NSF (grant no. DEB-1253634), and in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science; nos. DE-SC0018409 and DE-FC02-07ER64494). E.P.B. was supported by a Louis and Elsa Thomsen Wisconsin Distinguished Graduate Fellowship. C.T.H. is a Pew Scholar in the Biomedical Sciences and a Vilas Faculty Early Career Investigator, supported by the Pew Charitable Trusts and the Vilas Trust Estate. D.P. is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 747775). J.C.F. was supported by the NIH (no. GM080669)Peer Reviewe

Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production

Additional file 15. Summary of whole genome sequencing statistics

Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in ploidy and nutrient utilisation potential amongst wine isolates

The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations, such as those used for the production of biofuel and wine, where it outlasts and, under some conditions, outcompetes the major industrial yeast Saccharomyces cerevisiae. In order to investigate the level of inter-strain variation that is present within this economically important species, the genomes of four diverse D. bruxellensis isolates were compared. While each of the four strains was shown to contain a core diploid genome, which is clearly sufficient for survival, two of the four isolates have a third haploid complement of chromosomes. The sequences of these additional haploid genomes were both highly divergent from those comprising the diploid core and divergent between the two triploid strains. Similar to examples in the Saccharomyces spp. clade, where some allotriploids have arisen on the basis of enhanced ability to survive a range of environmental conditions, it is likely these strains are products of two independent hybridisation events that may have involved multiple species or distinct sub-species of Dekkera. Interestingly these triploid strains represent the vast majority (92%) of isolates from across the Australian wine industry, suggesting that the additional set of chromosomes may confer a selective advantage in winery environments that has resulted in these hybrid strains all-but replacing their diploid counterparts in Australian winery settings. In addition to the apparent inter-specific hybridisation events, chromosomal aberrations such as strain-specific insertions and deletions and loss-of-heterozygosity by gene conversion were also commonplace. While these events are likely to have affected many phenotypes across these strains, we have been able to link a specific deletion to the inability to utilise nitrate by some strains of D. bruxellensis, a phenotype that may have direct impacts in the ability for these strains to compete with S. cerevisiae.Anthony R. Borneman, Ryan Zeppel, Paul J. Chambers, Chris D. Curti

Genomic analysis and D-xylose fermentation of three novel Spathaspora

Three novel D-xylose-fermenting yeast species of Spathaspora clade were recovered from rotting wood in regions of the Atlantic Rainforest ecosystem in Brazil. Differentiation of new species was based on analyses of the gene encoding the D1/D2 sequences of large subunit of rRNA and on 642 conserved, single-copy, orthologous genes from genome sequence assemblies from the newly described species and 15 closely-related Debaryomycetaceae/Metschnikowiaceae species. Spathaspora girioi sp. nov. produced unconjugated asci with a single elongated ascospore with curved ends; ascospore formation was not observed for the other two species. The three novel species ferment D-xylose with different efficiencies. Spathaspora hagerdaliae sp. nov. and Sp. girioi sp. nov. showed xylose reductase (XR) activity strictly dependent on NADPH, whereas Sp. gorwiae sp. nov. had XR activity that used both NADH and NADPH as co-factors. The genes that encode enzymes involved in D-xylose metabolism (XR, xylitol dehydrogenase and xylulokinase) were also identified for these novel species. The type strains are Sp. girioi sp. nov. UFMG-CM-Y302(T) (=CBS 13476), Sp. hagerdaliae f.a., sp. nov. UFMG-CM-Y303(T) (=CBS 13475) and Sp. gorwiae f.a., sp. nov. UFMG-CM-Y312(T) (=CBS 13472).</p

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

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.Fil: Shen, Xing-Xing. Vanderbilt University; Estados UnidosFil: Opulente, Dana A.. University of Wisconsin; Estados UnidosFil: Kominek, Jacek. University of Wisconsin; Estados UnidosFil: Zhou, Xiaofan. Vanderbilt University; Estados Unidos. South China Agricultural University; ChinaFil: Steenwyk, Jacob L.. Vanderbilt University; Estados UnidosFil: Buh, Kelly V.. University of Wisconsin; Estados UnidosFil: Haase, Max A.B.. University of Wisconsin; Estados Unidos. University of New York. School of Medicine; Estados UnidosFil: Wisecaver, Jennifer H.. Purdue University; Estados Unidos. Vanderbilt University; Estados UnidosFil: Wang, Mingshuang. Vanderbilt University; Estados UnidosFil: Doering, Drew T.. University of Wisconsin; Estados UnidosFil: Boudouris, James T.. University of Wisconsin; Estados UnidosFil: Schneider, Rachel M.. University of Wisconsin; Estados UnidosFil: Langdon, Quinn K.. University of Wisconsin; Estados UnidosFil: Ohkuma, Moriya. Riken BioResource Research Center. Japan Collection of Microorganisms; JapónFil: Endoh, Rikiya. Riken BioResource Research Center. Japan Collection of Microorganisms; JapónFil: Takashima, Masako. Riken BioResource Research Center. Japan Collection of Microorganisms; JapónFil: Manabe, Ri-ichiroh. Riken Center for Integrative Medical Sciences; Japón. Riken Center For Life Science Technologies; JapónFil: Čadež, Neža. University of Ljubljana; EsloveniaFil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Rosa, Carlos A.. Universidade Federal de Minas Gerais; BrasilFil: DeVirgilio, Jeremy. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados UnidosFil: Hulfachor, Amanda Beth. University of Wisconsin; Estados UnidosFil: Groenewald, Marizeth. Westerdijk Fungal Biodiversity Institute; Países BajosFil: Kurtzman, Cletus P.. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados UnidosFil: Hittinger, Chris Todd. University of Wisconsin; Estados UnidosFil: Rokas, Antonis. Vanderbilt University; Estados Unido