Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species

Li, Xueying C.; Fay, Justin C.

doi:10.1093/gbe/evx072

Cited by 38 publications

(50 citation statements)

References 61 publications

(91 reference statements)

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“…A large portion of SNPs that showed significant associations to climate, and SNPs that showed high FST and LD between Italy and Sweden populations were enrichment among nonsynonymous/cis-regulatory variation at sites showing significant functional constraint. These results, further support an important role of cis-regulatory (Lasky, et al 2014;Siepel and Arbiza 2014;Li and Fay 2017;Sackton, et al 2019) and nonsynonymous variation (Nachman, et al 2003;Coop, et al 2009;Lasky, et al 2012;Huber, et al 2014;Svetec, et al 2016; in adaptation. Among the list of candidate genes underlying fitness QTL and showing significant evidence of local adaptation at functionally constraint sites, we identified FLDH.…”

Section: Discussionsupporting

confidence: 72%

In the presence of population structure: From genomics to candidate genes underlying local adaptation

Price

López

Platts

et al. 2019

Preprint

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Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. Mixed linear models that identify allele associations to environment, while controlling for genome-wide variation at other loci, have emerged as the method of choice when studying local adaptation.Despite their importance, it is unclear whether this approach performs better than identifying environmentally-associated SNPs without accounting for population structure. To examine this, we first use the mixed linear model GEMMA, and simple Spearman correlations, to identify SNPs showing significant associations to climate with and without accounting for population structure. Subsequently, using Italy and Sweden populations, we compare evidence of allele frequency differentiation (FST), linkage disequilibrium (LD ≈ 2 �� ), fitness variation, and functional constraint, underlying these SNPs. Using a lenient cut-off for significance, we find that SNPs identified by both approaches, and SNPs uniquely identified by Spearman correlations, were enriched at sites showing genomic evidence of local adaptation and function but were limited across Quantitative Trait Loci (QTL) explaining fitness variation. SNPs uniquely identified by GEMMA, showed no direct or indirect evidence of local adaptation, and no enrichment along putative functional sites. Finally, SNPs that showed significantly high FST and LD, were enriched along fitness QTL peaks and cis-regulatory/nonsynonymous sites showing significant functional constraint. Using these SNPs, we identify genes underlying fitness QTL, and genes linking flowering time to local adaptation. These include a negative regulator of abscisic-acid (FLDH) and flowering time genes PIF3, FIO1, and COL5.

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Section: Discussionsupporting

confidence: 72%

In the presence of population structure: From genomics to candidate genes underlying local adaptation

Price

López

Platts

et al. 2019

Preprint

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“…This is in line with initial comparisons of C. orthopsilosis genomes, which showed no preferential retention of any of the parental genomes in regions undergoing LOH (Pryszcz et al 2014). Previous studies in natural ( Epichloë ) and artificial ( S. cerevisiae x S. uvarum ) fungal hybrids have also reported no strong preferential over-expression of one of the parental sub-genomes (Cox et al 2014; X. C. Li and Fay 2017), which suggests this may be a general phenomenon in ascomycete fungal hybrids.…”

Section: Discussionmentioning

confidence: 80%

“…However, our understanding of the impact of hybridization at the transcriptomic level remains poorly characterized, with few studies performed on industrial or plant saprophyte hybrids (Metzger, Wittkopp, and Coolon 2017; Tirosh et al 2009; Cox et al 2014; X. C. Li and Fay 2017; Hovhannisyan et al 2020). To date no study of the transcriptomic aftermath of hybridization has been performed in hybrid human pathogens, limiting our insights on how hybridization leads to emergent traits, including virulence.…”

Section: Introductionmentioning

confidence: 99%

The transcriptional aftermath in two independently formed hybrids of the opportunistic pathogenCandida orthopsilosis

Hovhannisyan

Saus

Ksiezopolska

et al. 2020

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AbstractInterspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight on the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains, and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ~4% of the studied genes. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ~9.5% of the heterozygous genes in the hybrids. Some of these altered genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. Additionally, the number of shared genes with imbalanced expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids.ImportanceHow new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to a higher virulence is unclear. Here we show that hybrids selectively retain gene regulation plasticity inherited from the two parents, and that this plasticity affects genes involved in virulence.

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“…We first observed significant differences of plasticity between the ancestors, highlighting genetic variation for transcription plasticity. Genotype-by-environment interaction for gene expression is common in many organisms: C. elegans (Li et al, 2006), yeast (Smith and Kruglyak, 2008; Landry et al, 2006; Li and Fay, 2017), Arabidopsis genus (He et al, 2016). Here we observed a reduced gain of gene expression plasticity for a significant number of genes for all lineages exposed to fluctuating regime.…”

Section: Discussionmentioning

confidence: 99%

Evolution and plasticity of the transcriptome under temperature fluctuations in the fungal plant pathogen Zymoseptoria tritici

Jallet

Rouzic

Génissel

2019

Preprint

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Background. Species are subjected to variable environment in nature. While 20 the ability to cope with changes has been studied through theoretical approaches, the 21 small number of empirical studies limits our understanding of the evolutionary 22 molecular mechanisms underlying adaptation to fluctuations -Results. Whole 23 transcriptome sequencing of the fungal wheat pathogen Zymoseptria tritici revealed the evolution of gene expression after 48 weeks of experimental evolution under stable or 1 fluctuating temperature. We found that although there is a strong genetic signature of 2 gene expression, fluctuating regime could have a large and pervasive effect on the 3 transcriptome evolution. Results show a few hot spots of significantly differentially 4 expressed genes in the genome, in regions enriched with transposable elements (TE), 5 including on dispensable chromosomes. Further, our results evidenced gene evolution 6 towards robustness associated with the fluctuating regime, suggesting robustness is 7 adaptive in changing environment. Last, an analysis on gene expression correlation 8 revealed a significant set of genes that could act as trans-regulators. -Conclusions. This 9 study is the first evolve and re-sequence experiment of a fungal pathogen, with the goal 10 to describe the potential ability to evolve to changing environment and the molecular 11 changes occurring in response to fluctuating selection. In addition to explore the 12 evolutionary potential of the pathogen under temperature fluctuation this work 13 highlights the important role of transcriptional rewiring that can adjust regulation of cell 14 growth and multiplication.15

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Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species

Cited by 38 publications

References 61 publications

In the presence of population structure: From genomics to candidate genes underlying local adaptation

In the presence of population structure: From genomics to candidate genes underlying local adaptation

The transcriptional aftermath in two independently formed hybrids of the opportunistic pathogenCandida orthopsilosis

Evolution and plasticity of the transcriptome under temperature fluctuations in the fungal plant pathogen Zymoseptoria tritici

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