Different trajectories of polyploidization shape the genomic landscape of the<i>Brettanomyces bruxellensis</i>yeast species

Eberlein, Chris; Saada, Omar Abou; Friedrich, Anne; Albertin, Warren; Schacherer, Joseph

doi:10.1101/2021.02.11.430840

Cited by 3 publications

(12 citation statements)

References 73 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Hybridization is a process common to the life history of many organisms and rapidly generates genomic diversity (14,79,80). Even though new hybrids tend to exhibit a low spore fertility, natural hybridizations have played an essential role in the diversification and evolution of the genome of many fungal, plant, and animal species.…”

Section: Discussionmentioning

confidence: 99%

“…The diploid organisms (or those with a higher ploidy) are usually heterozygous for many of these genetic variants across the genome. Nevertheless, a large number of studies have pointed out that regions of the genome can frequently become homozygous for these polymorphisms during mitotic divisions (7)(8)(9)(10)(11)(12)(13)(14)(15). These loss of heterozygosity (LOH) events result from the transfer of information from one homologous chromosome to the other, primarily a consequence of mitotic recombination, among other mechanisms (16).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

Dutta

Dutreux

Schacherer

2021

eLife

Self Cite

View full text Add to dashboard Cite

The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss-of-heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1 to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, i.e., tracts extending to the end of the chromosome (n = 3,168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

Dutta

Dutreux

Schacherer

2021

eLife

Self Cite

View full text Add to dashboard Cite

show abstract

“…This large population study allowed the identification of different genetic subpopulations within B. bruxellensis, which were subsequently validated and refined by whole genome sequencing approaches (Eberlein et al, 2021;Gounot et al, 2020;Serra Colomer, Chailyan, et al, 2020;Table S1). At least six subgroups can now be considered, either diploid (two groups) or triploid (four groups; Figure 1b).…”

Section: Population Structure Of Brettanomyces Bruxellensismentioning

confidence: 99%

“…Over the past decade, several de novo assemblies have been published with increasing quality (Table 1), in particular thanks to the combination of long-read sequencing (e.g., Oxford Nanopore sequencing) with short-read sequencing (Fournier et al, 2017). Such high quality assemblies were used as reference genomes for population genomic surveys (Eberlein et al, 2021;Gounot et al, 2020;Serra Colomer, Chailyan, et al, 2020). These population studies revealed that the pangenome is composed of 5,409 ORFs (open reading frames) with 5,106 core and 303 accessory ORFs within the species.…”

Section: Genomic Landscape Of Brettanomyces Bruxellensismentioning

confidence: 99%

“…Brettanomyces bruxellensis subpopulations are represented by different colours and named from previous reports (Avramova, Cibrario, et al, 2018;Gounot et al, 2020). The tree was built from whole genome Illumina short-read sequencing of 71 B. bruxellensis isolates aligned to the reference genome B. bruxellensis (Fournier et al, 2017) and 24,313 genetic variants evenly distributed across the genome (Eberlein et al, 2021). The ploidy level of each population was schematized, two chromosomes represent diploid groups, three chromosomes represent triploids ones.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast

et al. 2022

View full text Add to dashboard Cite

Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto-and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing low-nutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast's phenotypic landscape.

show abstract

Whole-genome sequencing and phenotyping reveal specific adaptations ofLachancea thermotoleransto the winemaking environment

Vicente,

Friedrich,

Schacherer

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures.Lachancea thermotolerans, a yeast related to the fermentative process and one of the current trends in wine technology research, has undergone an anthropization process that has led to a strong differentiation both from a genomic and phenomic perspective. Using whole-genome sequencing, we have investigated the genomic diversity of 145L. thermotoleransstrains, identifying six well-defined groups primarily delineated by their ecological origin and exhibiting high levels of genetic diversity. Anthropized strains showed lower genetic diversity due to the purifying selection imposed by the winemaking environment. Strong evidence of anthropization and adaptation to the wine environment through modification of gene content was also found. Differences in genes involved in the assimilation of alternative carbon and nitrogen sources, such as theMAL1andDAL5genes, which confer greater fitness in the winemaking environment, were observed. Additionally, we found that phenotypic traits considered domestication hallmarks are present in anthropized strains. Among these, increased fitness in the presence of ethanol and sulphites, assimilation of non-fermentable carbon sources such as glycerol, and lower levels of residual fructose under fermentative conditions highlight. We hypothesize that lactic acid production by wine-related strains is an anthropization signature consequence of the adaption of early Crabtree-positive yeasts to the fermentative environment. Overall, the results of this work provide valuable insight into the anthropization process inL. thermotoleransand demonstrate how fermentation environments give rise to similar adaptations in different yeast species.

show abstract

Different trajectories of polyploidization shape the genomic landscape of theBrettanomyces bruxellensisyeast species

Cited by 3 publications

References 73 publications

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast

Whole-genome sequencing and phenotyping reveal specific adaptations ofLachancea thermotoleransto the winemaking environment

Contact Info

Product

Resources

About