The PLOS Genetics Editors-in-Chief and Senior Editors would like to congratulate: Santiago Naranjo, Justin D. Smith, Carlo G. Artieri, Mian Zhang, Yiqi Zhou, Michael E. Palmer and Hunter B. Fraser, authors of the article chosen as the recipient of the PLOS Genetics Research Prize 2016:
In their article, Santiago Naranjo and colleagues set out to identify the molecular basis of polygenic adaptation. To achieve this goal, the authors use a clever approach: they test for evidence of selection on gene expression (via a sign-test), specifically looking for sets of genes showing allele-specific expression in F1 hybrids between Saccharomyces paradoxus and S. cerevisiae. They found that genes from a pathway involved in resistance to citrinin—a naturally occurring mycotoxin produced by fungi—showed highly significant bias towards the S. paradoxus alleles. To assess the significance of this observation, they used growth assays in several strains to show that S. paradoxus has indeed recently evolved citrinin resistance. Next, the authors performed RNA-seq analysis on hybrids exposed to citrinin to identify candidate genes underlying this resistance. They identified five candidates, and were able to confirm four of them by knockout. They went on to use promoter-replacement experiments to show that the S. paradoxus promoters drive much of the divergence in expression that they had identified. Higher expression of these genes confers a fitness advantage in the presence of citrinin, while exacting a cost in its absence—a fitness trade-off.
Overall, the manuscript makes a major contribution to our understanding of evolutionary processes, and tells a beautifully complete story. It uses an elegant approach to screen for cis-regulatory divergence of expression and then follows up candidate genes with functional tests to better understand their underlying molecular mechanisms. The editors were particularly impressed not only with this specific result—demonstrating how small individual effects of regulatory elements can together have a large impact on fitness—but also the potential of the overall approach to be used to identify the genetic basis of polygenic adaptation in additional conditions or species.
Corresponding author, Hunter Fraser says: “We are honored to receive this award. Our paper identified four genes contributing to the evolution of resistance to a naturally occurring toxin in yeast, providing a detailed view of a complex evolutionary adaptation. Looking ahead, the method we employed can be applied to pinpoint the genes underlying polygenic adaptations in a wide range of species, and may help advance our understanding of how complex traits evolve.”
The PLOS Genetics Research Prize was born from the editors’ desire to recognize the outstanding work published in PLOS Genetics and launched last year as part of our 10-year anniversary celebrations. Members of the genetics community nominated their favourite Research Article published in PLOS Genetics in 2015, and the Senior Editors selected the winning article from these nominations, based on scientific excellence and the community impact of the work.
Further details about the prize can be found here: https://www.staging.plos.org/genetics-research-prize/
Header image credit: Yuan et al. (2015)