Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1008648 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25743579_1.fastq.gz | Fastqsanger.gz | |||
| SRR25743579_2.fastq.gz | Fastqsanger.gz | |||
| SRR25743580_1.fastq.gz | Fastqsanger.gz | |||
| SRR25743580_2.fastq.gz | Fastqsanger.gz | |||
| SRR25743581_1.fastq.gz | Fastqsanger.gz |
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Project description:Despite the progress achieved in elucidating the ecological mechanisms of adaptive radiation, there has been little focus on documenting the extent of adaptive differentiation in physiological functions during this process. Moreover, a thorough understanding of the genomic basis underlying phenotypic adaptive divergence is still in its infancy. One important evolutionary process for which causal genetic mechanisms are largely unknown pertains to life-history trade-offs. We analysed patterns of gene transcription in liver tissue of sympatric dwarf and normal whitefish from two natural lakes, as well as from populations reared in controlled environments, using a 16 006-gene cDNA microarray in order to: (i) document the extent of physiological adaptive divergence between sympatric dwarf and normal species pairs, and (ii) explore the molecular mechanisms of differential life history trade-offs between growth and survival potentially involved in their adaptive divergence. In the two natural lakes, 6.45% of significantly transcribed genes showed regulation either in parallel fashion (2.39%) or in different directions (4.06%). Among genes showing parallelism in regulation patterns, we observed a higher proportion of over-expressed genes in dwarf relative to normal whitefish (70.6%). Patterns observed in controlled conditions were also generally congruent with those observed in natural populations. Dwarf whitefish consistently showed significant over-expression of genes potentially associated with survival through enhanced activity (energy metabolism, iron homeostasis, lipid metabolism, detoxification), whereas more genes associated with growth (protein synthesis, cell cycle, cell growth) were generally down-regulated in dwarf relative to normal whitefish. Overall, parallelism in patterns of gene transcription, as well as patterns of interindividual variation across controlled and natural environments, provide strong indirect evidence for the role of selection in the evolution of differential regulation of genes involving a vast array of potentially adaptive physiological processes between dwarf and normal whitefish. Our results also provide a first mechanistic, genomic basis for the observed trade-off in life-history traits distinguishing dwarf and normal whitefish species pairs, wherein enhanced survival via more active swimming, necessary for increased foraging and predator avoidance, engages energetic costs that translate into slower growth rate and reduced fecundity in dwarf relative to normal whitefish.
2010-03-31 | GSE21130 | GEO
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level. Yeast galactose evolved mutants having improved galactose availability were grown on aerobic batch with glucose as carbon source
2012-07-31 | E-GEOD-39065 | biostudies-arrayexpress
Project description:The evolutionary transition of multicellular life initially involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. This is facilitated by trade-offs between traits determining survival and reproduction, favoring the coexistence of cells with extreme trait values and a convex trade-off curve as the multicellular state dominates. However, these transitions remain poorly characterized at the ecological and genetic level. Here, we studied the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirmed that this trait was heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolved in all cell group isolates which were linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection is sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.
2021-02-13 | GSE166685 | GEO
Project description:Tetranychus urticae is an important pest that causes severe damage on a wide variety of plants and crops, leading to a substantial loss of productivity. Previous research has focused on the study of Arabidopsis short-term response to T. urticae, but a comprehensive evaluation of the interaction through whole plant life cycle has not been previously studied. Here, through a physiological trait, transcriptomic and hormonomic evaluation we uncovered the molecular pathways directing the interaction of T. urticae during the complete plant life cycle. Upon mite infestation, plant suffers a process of adaptation to cope the stress and survive, led by the establishment of defence-growth trade-offs in the plant. Transcriptional and hormonal evaluation reveal how plant defence response upon mite perception determines the later growth responses and plant survival. In addition, a delay in plant development with a negative effect on plant fitness was observed, being fitness negatively affected with seed ageing. Taken together, our findings uncover the dynamics regulating plant-mite interactions and determining plant survival and reproductive success, providing new potential targets for improving plant response. Additionally, trade-offs suppose a cost on final plant fitness, demonstrating the underlying impact of the mite on the establishment of the offspring.
2024-08-31 | GSE255811 | GEO
Project description:The hypothesis that increased fitness within a selective environment must be accompanied by a loss of fitness in other non-selective environments leads to the notion of evolutionary tradeoffs. Experimental evolution provides an approach to test the existence of evolutionary tradeoffs, characterize their general quality, and reveal their genetic origins. To examine the underlying mechanism for a fitness trade-off, we constructed the evolutionary trajectories of Escherichia coli K-12 at increasing temperatures up to 45.3°C, and found diverging mutational histories that led to adaptive phenotypes with and without fitness trade-offs at low temperatures. We identified genetic changes in cellular respiration, iron metabolism and methionine biosynthesis that regulated gene expression to achieve thermal adaptation and determined the presence and absence of a fitness trade-off. Our results suggested that evolutionary trade-off could be generated by a regulatory protein mutation that was beneficial in the selective conditions but forced suboptimal proteome allocation under non-selective environments.
2020-11-17 | GSE140478 | GEO
Project description:Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level.
2012-08-01 | GSE39065 | GEO
Project description:We studied adaptation of the metabolically versatile bacterium Pseudomonas aeruginosa to standard laboratory conditions by propagating mismatch repair-deficient P. aeruginosa in exponential phase for 24 days in rich medium. In the selective environment of this large-bottleneck mutation accumulation experiment, the bacteria developed shorter lag phases, higher growth rates and higher maximum cell densities. Transcriptional profiling and phenotyping for growth in different media revealed that higher fitness under laboratory conditions evolved via different pathways. Although common adaptive mutations or mutations that define trade-offs were not identified, there was a convergent evolution of transcriptional profiles associated with a shift from biofilm-associated to planktonic lifestyles. Our results indicate that under constant planktonic conditions P. aeruginosa uses several genetic pathways in order to fine-tune adaptation towards faster growth. The selected mutations in the different genetic pathways show a great variety of biofilm, virulence and motility phenotypic trade-offs, thus implying that on the population level, the adaptation of P. aeruginosa to constant conditions does not compromise its versatility. Methods: mRNA profiles were generated for Pseudomonas aeruginosa samples derived from LB-cultures grown to an OD600 =0.4-0.6. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with default settings.
2020-11-26 | GSE146906 | GEO
Project description:The transcriptome and DGE analysis of the fat body and ovary of L. migratoria based on the Illumina short-read sequencing technology and De novo assembly. Research on the trade-offs between immunity and reproduction is contributing significantly to the understanding of the fitness of organisms in nature.
2017-05-01 | GSE57437 | GEO
Project description:Background: Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach. Results: We obtained a total of about 121 million paired-end reads from Illumina RNA sequencing and analyzed 218,541 transcripts obtained from a de novo assembly. We identified 109 transcripts with a significant differential expression between endurant and burst performant individuals (FDR ≤ 0.05 and logFC ≥ 2), and blast searches resulted in 103 protein-coding genes. We found major differences between endurant and burst-performant individuals in the expression of genes involved in the polymerization of actin filaments, cellular trafficking, proteoglycans and extracellular proteins secreted, lipid metabolism, mitochondrial activity and regulators of signaling cascade. Remarkably, we revealed transcripts isoforms of key genes with function in metabolism, apoptosis, nuclear export and as transcriptional corepressor, expressed in either burst-performant or endurant individuals. Lastly, we find two up-regulated transcripts in burst-performant individuals that correspond to the expression of myosin-binding protein C fast-type (mybpc2). This suggests the presence of mybpc2 homoeologs and may have been favored by selection to permit fast and powerful locomotion. Conclusion: Locomotor performance trade-off in Xenopus allofraseri can be attributed to the differential expression of genes belonging to the different pathways of calcium signaling, endoplasmic reticulum stress response and striated muscle contraction, but also attributed to the use of alternative splicing and regulatory processes. Ultimately, our transcriptomic analysis offers new perspectives for future analyses of the role of single nucleotide variants, homoeology and alternative splicing in the evolution of locomotor performance trade-offs.
2021-01-31 | GSE157915 | GEO
Project description:The interplay between phenotypic plasticity and adaptive evolution has long been an important topic of evolutionary biology. This process is critical to our understanding of a species evolutionary potential in light of rapid climate changes. Despite recent theoretical work, empirical studies of natural populations, especially in marine invertebrates, are scarce. In this study, we investigated the relationship between adaptive divergence and plasticity by integrating genetic and phenotypic variation in Pacific oysters from its natural range in China. Genome resequencing of 371 oysters revealed unexpected fine-scale genetic structure that is largely consistent with phenotypic divergence in growth, physiology, thermal tolerance and gene expression across environmental gradient. These findings suggest that selection and local adaptation are pervasive and together with limited gene flow shape adaptive divergence. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and likely favored by selection in organisms facing dynamic environments such as oysters. Divergence in heat response and tolerance implies that the evolutionary potential to a warming climate differs among oyster populations. We suggest that trade-offs in energy allocation are important to adaptive divergence with acetylation playing a role in energy depression under thermal stress.
2018-07-27 | PXD008057 | Pride