Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of wine yeast strains, parental and adaptively evolved for selective increase in aroma compounds originating in branched-chain or aromatic amino acid pathway

ABSTRACT: Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the concept of tacking trait enabling natural selection of fitness-costly metabolic traits. The concept is inspired from the tacking maneuver used in sailing for traversing upwind. We use first-principle metabolic models to design an evolution niche wherein the tacking trait and fitness become correlated. Adaptive evolution in this niche, when followed by the reversal to the original niche, manifests in the improvement of the desired trait due to biochemical coupling between the tacking and the desired trait. We experimentally demonstrated this strategy, termed EvolveX, by evolving wine yeasts for increased aroma production. RNA-sequencing was performed for parental and evolved strains in the respective evolution niche and in natural grape must.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Filipa Pereira

PROVIDER: E-MTAB-10019 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Trait tacking for predictive evolution of metabolic pheotypes

Project description:Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the concept of tacking trait enabling naturalÂ selection of fitness-costly metabolic traits. The concept is inspired from the tacking maneuver used in sailing for traversing upwind.Â We use first-principle metabolic models to design an evolution niche wherein the tacking trait and fitness become correlated. Adaptive evolution in this niche, when followed by the reversal to the original niche, manifests in the improvement of the desired trait due to biochemical coupling between the tacking and the desired trait. We experimentally demonstrate this strategy, termed EvolveX, by evolving wine yeasts for increased aroma production. Our results pave the way for precision laboratory evolution for biotechnological and ecological applications.

2022-07-12 | PXD023171 | Pride

Heritability of the expression of defense-related genes in the outer stem of Interior spruce (Picea glauca x engelmannii)

Project description:Inferring the heritability of gene expression is one of the main areas of the field of genetical genomics. With the possibility to treat the abundances of gene transcripts as a suite of quantitative traits, genetical genomics can make an extensive use of the microarray technology. Here we extended a major method for estimating the heritability of a quantitative trait, single parent-offspring regression, to assess the heritability of the expression of genes with two-channel microarrays. In a series of maternal parent-offspring pairs of Interior spruce (Picea glauca x engelmannii, our focus in the outer stem tissues is the expression of defense-related genes, the heritability of which can affect fitness and necessary for evolution by natural selection.

2010-07-15 | GSE22921 | GEO

Bacterial Fitness Landscapes Stratify Based on Proteome Allocation Associated with Discrete Aero-types

Project description:The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism and protein Expression (ME-models) to study the distribution of Escherichia coli phenotypes on the rate-yield plane. We found that the measured phenotypes distribute non-uniformly to form a highly stratified fitness landscape. Systems analysis of ME-model simulations suggest that this stratification results from discrete ATP generation strategies. Accordingly, we define "aero-types", a phenotypic trait that characterizes how a balanced proteome can achieve a given growth rate by modulating 1) the relative utilization of oxidative phosphorylation, glycolysis, and fermentation pathways; and 2) the differential employment of electron-transport-chain enzymes. This global, quantitative, and mechanistic systems biology interpretation of fitness landscape formed upon proteome allocation offers a fundamental understanding of bacterial physiology and evolution dynamics.

2021-01-05 | GSE164236 | GEO

Network analysis of wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions

Project description:High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Each single wood trait was found to be highly polygenic in its nature. However, gene hierarchies need to be assessed with the most important gene variants controlling a specific trait within the complex network of interacting secondary cell wall characteristics that defines the overall wood phenotype. We tested the available genetic and genomic information in an integrative approach to effectively predict wood properties in Populus trichocarpa.Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49K Nimblegen array elements and for 28,831 polymorphic SNPs. Pre-selected transcripts and SNPs with high statistical dependency on the phenotypic trait were used in a Bayesian network learning procedure with stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at much lower logBF threshold than SNPs and were not accommodated in the networks. Complexity of phenotype-centric networks with 100% predictive accuracy ranged from 7 (glucose) to 39 SNPs (alpha-cellulose). Pleiotropic gene actions were accommodated in genetic networks of correlated traits; such gene variants help to understand independent evolution of trait values, and they represent new tools to support the maximization of correlated response to selection. Developing xylem harvested at breast height from the north side of each tree stem from 17 genotypes with two biological replicates and from two additional genotypes without a second replicate previously identified as most extreme phenotypes in six wood traits was individually profiled for transcriptome analysis totaling 36 hybridizations to three NimbleGen 12-plex poplar arrays.

2013-02-26 | E-GEOD-44606 | biostudies-arrayexpress

QX recombinant inbred advanced intercross lines of C. elegans

Project description:Mutation generates the heritable variation that genetic drift and natural selection shape. In classical quantitative genetic models, drift is a function of the effective population size and acts uniformly across traits, while mutation and selection act trait-specifically. We identified thousands of quantitative trait loci (QTL) influencing transcript abundance traits in a cross of two C. elegans strains; although trait-specific mutation and selection explained some of the observed pattern of QTL distribution, the pattern was better explained by trait-independent variation in the intensity of selection on linked sites. Our results suggest that traits in C. elegans exhibit different levels of variation less because of their own attributes than because of differences in the effective population sizes of the genomic regions harboring their underlying loci.

2010-10-01 | GSE23857 | GEO

Genome-wide transcriptomic effects of the foraging gene shed light on genetic pathways that regulate pleiotropy and plasticity

Project description:Natural variants of the Drosophila melanogaster foraging (for) gene as a popular model to understand behaviour, plasticity, and pleiotropy at an evolutionary and molecular level. The effects for variants on phenotype, fitness, stimulus-response (e.g., food deprivation), and tissue-specific for expression are well characterized. In contrast, the transcriptome-wide influence that for variants have across different tissues and stimuli remains unknown. In this study, we collected fed and 4-hour food-deprived D. melanogaster samples from the genetic null, the natural sitter variant, and the natural rover variant in the CNS (brain and brain stem), gut, and fat (89 samples total, N=4-5 per condition/genotype/tissue). Paired-end bulk RNA sequencing was then completed in one experimental batch at Genome Quebec using the NovaSeq6000 S4 PE100 Sequencing Lane. Briefly, samples were aligned to the dm6 genome using STAR, duplicates were marked with Picard, and reads that were non-chromosomal, low-quality, or unpaired were filtered with samtools. High-quality reads were then counted to the dm6 genome with the "Drosophila_melanogaster.BDGP6.22.96" genome annotation with featurecounts. These RNA-seq data elucidated how the for locus, and the natural variants of for can influence gene expression and cellular function across tissues and conditions.

2023-03-15 | E-MTAB-12688 | biostudies-arrayexpress

RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production.

Project description:Model-guided chassis strain design has the potential to accelerate cellfactory development. In this experiment genetic targets were identified in silico and implemented in vivo to design a yeast chassis strain for enhanced production of succinic, malic and fumaric acid. The phenotype of engineered chassis strains was further optimised through adaptive laboratory evolution. RNA-seq analysis of engineered yeast chassis strains, evolved strains and wild-type (CEN.PK background)was performed to determine the effect of engineered gene deletions and evolution on the transcriptome.

2021-07-01 | E-MTAB-9499 | biostudies-arrayexpress

The life history of retrocopies illuminates the evolution of new mammalian genes

Project description:New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as useful models for the study of new gene origination. Here we combine extensive mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, the majority evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers or bivalent regulatory elements, as well as from CpG islands not associated to other genes. Altogether, these mechanisms facilitated the birth of up to 280 retrogenes in each therian species. Furthermore, the regulatory evolution of the originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated the cooption of distant promoters and in many cases allowed the expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute their parents during the process of male (meiotic) X inactivation, while others even rendered parental functions completely superfluous, allowing for parental gene loss. Overall, our reconstruction of the complete â??life historyâ?? of mammalian retrogenes highlights the usefulness of retroposition as a general model for understanding new gene birth and functional evolution. Assembly and expression of vertebrate retrogene transcripts

2015-12-16 | E-GEOD-72236 | biostudies-arrayexpress

Network analysis of wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions

2013-02-26 | GSE44606 | GEO

Molecular basis of complex heritability in natural genotype-to-phenotype relationships

Project description:The intrinsic complexity of quantitative traits was evident even before the molecular nature of the gene was understood. Yet we still lack a detailed molecular understanding of complex heritability. Here we alleviated statistical roadblocks to high-resolution genetic mapping by using an inbred population of diploid yeast with very low linkage disequilibrium and more individuals than segregating polymorphisms. We mapped over 18,000 quantitative trait loci, resolving more than 3,300 to single nucleotides. This allowed us to explore the molecular origins of complexity, hybrid vigor, pleiotropy, and gene ´ environment interactions and to rigorously estimate the distribution of fitness effects of natural genetic variation. Our results describe a comprehensive, high-resolution genotype-to-phenotype map and define general principles underlying the complexity of heredity.

2018-12-13 | GSE123702 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data