scholarly journals Genetic redundancy fuels polygenic adaptation in Drosophila

PLoS Biology ◽  
2019 ◽  
Vol 17 (2) ◽  
pp. e3000128 ◽  
Author(s):  
Neda Barghi ◽  
Raymond Tobler ◽  
Viola Nolte ◽  
Ana Marija Jakšić ◽  
François Mallard ◽  
...  
Keyword(s):  
Genetic Redundancy ◽  
Polygenic Adaptation

scholarly journals Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation

2021 ◽  
Author(s):  
Claire Burny ◽  
Viola Nolte ◽  
Marlies Dolezal ◽  
Christian Schl&oumltterer
Keyword(s):  
Drosophila Melanogaster ◽  
Experimental Evolution ◽  
Selection Response ◽  
Adaptive Responses ◽  
Genetic Redundancy ◽  
Powerful Approach ◽  
Polygenic Adaptation ◽  
Parallel Selection ◽  
Sufficient Variation ◽  
Genomic Regions

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype than needed are segregating in populations to express a phenotypic optimum. Experimental evolution provides a powerful approach to study polygenic adaptation using replicated populations adapting to a new controlled environment. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequencing (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.

scholarly journals Polygenic adaptation fuels genetic redundancy in Drosophila

2018 ◽  
Author(s):  
Neda Barghi ◽  
Raymond Tobler ◽  
Viola Nolte ◽  
Ana Marija Jaksic ◽  
Francois Mallard ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Genotypic Variation ◽  
Natural Populations ◽  
Genetic Redundancy ◽  
Adaptive Traits ◽  
Testing Strategies ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Phenotypic Responses ◽  
Phenotypic Convergence

AbstractThe genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic – i.e. result from selection on a large number of genetic loci – but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes across many contributing loci. To resolve this, we use laboratory natural selection, a framework that is powerful enough to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among adaptive alleles. We observed convergent phenotypic responses, e.g. fitness, metabolic rate and fat content, and a strong polygenic response (99 selected alleles; mean s=0.061). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses. The observed genetic redundancy potentiates this genotypic variation through multiple genetic pathways leading to phenotypic convergence. This key property of adaptive alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.

scholarly journals Evolution of gene expression variance during adaptation to high temperature in Drosophila

2021 ◽  
Author(s):  
Wei-Yun Lai ◽  
Christian Schlötterer
Keyword(s):  
Gene Expression ◽  
Natural Populations ◽  
Selection Response ◽  
Phenotypic Variance ◽  
Adaptive Responses ◽  
Genetic Redundancy ◽  
Before And After ◽  
Polygenic Adaptation ◽  
The Impact ◽  
Expression Variance

AbstractShifts in trait means are widely considered as evidence for adaptive responses, but the impact on phenotypic variance remains largely unexplored. Here, we studied gene expression variance of Drosophila simulans males before and after 100 generations of adaptation to a novel hot laboratory environment. In each of the two independently evolved replicate populations the variance of about 150 genes changed significantly (mostly reduction). Although different genes were affected in both replicates, these genes are related to digestion in the gut. This non-parallel selection response on the gene level in combination with a convergent response at a higher phenotypic level reflects genetic redundancy, a characteristic hallmark of polygenic adaptation. We propose that the constant and simple food source in the laboratory resulted in selection for reduced variance in digestive genes. In natural populations adaptation to diverse types of food may be beneficial, resulting in higher phenotypic variance. This empirical evidence of phenotypic variance being the direct target of selection during adaptation has important implications for strategies to identify selection signatures.

scholarly journals Combinatorial CRISPR screen identifies fitness effects of gene paralogues

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicola A. Thompson ◽  
Marco Ranzani ◽  
Louise van der Weyden ◽  
Vivek Iyer ◽  
Victoria Offord ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cell Lines ◽  
Unknown Function ◽  
Single Copy ◽  
Genetic Redundancy ◽  
Synthetic Lethal ◽  
Fitness Effects ◽  
Synthetic Lethal Interactions ◽  
Crispr Screen ◽  
Multiple Cell

AbstractGenetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. Our studies reveal the fitness effects of FAM50A/FAM50B in cancer cells.

scholarly journals Two Putative RNA-Binding Proteins Function with Unequal Genetic Redundancy in the MOS4-Associated Complex

2010 ◽  
Vol 154 (4) ◽  
pp. 1783-1793 ◽  
Author(s):  
Jacqueline Monaghan ◽  
Fang Xu ◽  
Shaohua Xu ◽  
Yuelin Zhang ◽  
Xin Li
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Genetic Redundancy

scholarly journals PLEIOTROPIC REGULATORY LOCUS 2 exhibits unequal genetic redundancy with its homolog PRL1

2012 ◽  
Vol 53 (9) ◽  
pp. 1617-1626 ◽  
Author(s):  
Tabea Weihmann ◽  
Kristoffer Palma ◽  
Yukino Nitta ◽  
Xin Li
Keyword(s):  
Genetic Redundancy ◽  
Regulatory Locus

scholarly journals Depletion of Undecaprenyl Pyrophosphate Phosphatases Disrupts Cell Envelope Biogenesis in Bacillus subtilis

2016 ◽  
Vol 198 (21) ◽  
pp. 2925-2935 ◽  
Author(s):  
Heng Zhao ◽  
Yingjie Sun ◽  
Jason M. Peters ◽  
Carol A. Gross ◽  
Ethan C. Garner ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Transcriptional Repression ◽  
Cell Envelope ◽  
Turgor Pressure ◽  
Teichoic Acid ◽  
Lethal Gene ◽  
Genetic Redundancy ◽  
Wall Teichoic Acid ◽  
Content Type ◽  
Lipid Ii

ABSTRACTThe integrity of the bacterial cell envelope is essential to sustain life by countering the high turgor pressure of the cell and providing a barrier against chemical insults. InBacillus subtilis, synthesis of both peptidoglycan and wall teichoic acids requires a common C55lipid carrier, undecaprenyl-pyrophosphate (UPP), to ferry precursors across the cytoplasmic membrane. The synthesis and recycling of UPP requires a phosphatase to generate the monophosphate form Und-P, which is the substrate for peptidoglycan and wall teichoic acid synthases. Using an optimizedclusteredregularlyinterspacedshortpalindromicrepeat (CRISPR) system with catalytically inactive (“dead”)CRISPR-associated protein9(dCas9)-based transcriptional repression system (CRISPR interference [CRISPRi]), we demonstrate thatB. subtilisrequires either of two UPP phosphatases, UppP or BcrC, for viability. We show that a third predicted lipid phosphatase (YodM), with homology to diacylglycerol pyrophosphatases, can also support growth when overexpressed. Depletion of UPP phosphatase activity leads to morphological defects consistent with a failure of cell envelope synthesis and strongly activates the σM-dependent cell envelope stress response, includingbcrC, which encodes one of the two UPP phosphatases. These results highlight the utility of an optimized CRISPRi system for the investigation of synthetic lethal gene pairs, clarify the nature of theB. subtilisUPP-Pase enzymes, and provide further evidence linking the σMregulon to cell envelope homeostasis pathways.IMPORTANCEThe emergence of antibiotic resistance among bacterial pathogens is of critical concern and motivates efforts to develop new therapeutics and increase the utility of those already in use. The lipid II cycle is one of the most frequently targeted processes for antibiotics and has been intensively studied. Despite these efforts, some steps have remained poorly defined, partly due to genetic redundancy. CRISPRi provides a powerful tool to investigate the functions of essential genes and sets of genes. Here, we used an optimized CRISPRi system to demonstrate functional redundancy of two UPP phosphatases that are required for the conversion of the initially synthesized UPP lipid carrier to Und-P, the substrate for the synthesis of the initial lipid-linked precursors in peptidoglycan and wall teichoic acid synthesis.

Development and Molecular Genetics of Marchantia polymorpha

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Takayuki Kohchi ◽  
Katsuyuki T. Yamato ◽  
Kimitsune Ishizaki ◽  
Shohei Yamaoka ◽  
Ryuichi Nishihama
Keyword(s):  
Model Organism ◽  
Land Plant ◽  
Marchantia Polymorpha ◽  
Annual Review ◽  
Publication Date ◽  
Molecular Tools ◽  
Genetic Redundancy ◽  
Morphological Differences ◽  
Evo Devo ◽  
Basal Position

Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Polygenic adaptation in changing environments (a)

2018 ◽  
Vol 123 (4) ◽  
pp. 48002 ◽  
Author(s):  
Kavita Jain ◽  
Archana Devi
Keyword(s):  
Changing Environments ◽  
Polygenic Adaptation
Sign in / Sign up

Export Citation Format

Share Document