Phenotypic Variation in Growth and Gene Expression Under Different Photoperiods in Allopatric Populations of the Copepod Tigriopus californicus

AbstractGenetic variation, epigenetic regulation and major environmental stimuli are key contributors to phenotypic variation, but the influence of minor perturbations or “noise” has been difficult to assess in mammals. In this work, we uncover one major axis of random variation with a large and permanent influence: developmental stochasticity. By assaying the transcriptome of wild monozygotic quadruplets of the nine-banded armadillo, we find that persistent changes occur early in development, and these give rise to clear transcriptional signatures which uniquely characterize individuals relative to siblings. Comparing these results to human twins, we find the transcriptional signatures which define individuals exhibit conserved co-expression, suggesting a substantial fraction of phenotypic and disease discordance within mammals arises from developmental stochasticity.One sentence summaryLongitudinal gene expression in identical armadillo quadruplets reveals a major role for developmental stochasticity.

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Phenotypic Variation Between Transgenic Plants: What is Making Gene Expression Unpredictable?

Somaclonal Variation and Induced Mutations in Crop Improvement - Current Plant Science and Biotechnology in Agriculture ◽

10.1007/978-94-015-9125-6_27 ◽

1998 ◽

pp. 539-562 ◽

Cited By ~ 3

Author(s):

A. Caplan ◽

P. H. Berger ◽

M. Naderi

Keyword(s):

Gene Expression ◽

Transgenic Plants ◽

Phenotypic Variation

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Suppression of Engulfment Defects in Bacillus subtilis by Elevated Expression of the Motility Regulon

Journal of Bacteriology ◽

10.1128/jb.188.3.1159-1164.2006 ◽

2006 ◽

Vol 188 (3) ◽

pp. 1159-1164 ◽

Cited By ~ 9

Author(s):

Ana R. Perez ◽

Angelica Abanes-De Mello ◽

Kit Pogliano

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Phenotypic Variation ◽

Cell Separation ◽

Peptidoglycan Hydrolases ◽

Σ Factor ◽

Elevated Expression

ABSTRACT During Bacillus subtilis sporulation, the transient engulfment defect of spoIIB strains is enhanced by spoVG null mutations and suppressed by spoVS null mutations. These mutations have opposite effects on expression of the motility regulon, as the spoVG mutation reduces and the spoVS mutation increases σD-directed gene expression, cell separation, and autolysis. Elevating σD activity by eliminating the anti-σ factor FlgM also suppresses spoIIB spoVG, and both flgM and spoVS mutations cause continued expression of the σD regulon during sporulation. We propose that peptidoglycan hydrolases induced during motility can substitute for sporulation-specific hydrolases during engulfment. We find that sporulating cells are heterogeneous in their expression of the motility regulon, which could result in phenotypic variation between individual sporulating cells.

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Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

BMC Genomics ◽

10.1186/s12864-021-07994-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Christopher P. Kozakiewicz ◽

Alexandra K. Fraik ◽

Austin H. Patton ◽

Manuel Ruiz-Aravena ◽

David G. Hamilton ◽

...

Keyword(s):

Gene Expression ◽

Phenotypic Variation ◽

Population Level ◽

Host Responses ◽

Tasmanian Devil ◽

Population Declines ◽

Transcriptomic Response ◽

Expression Variation ◽

Normal Tissues ◽

Cancer Phenotypes

Abstract Background Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown. Results We sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation. Conclusions Expression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival.

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Embryonic geometry underlies phenotypic variation in decanalized conditions

eLife ◽

10.7554/elife.47380 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 3

Author(s):

Anqi Huang ◽

Jean-François Rupprecht ◽

Timothy E Saunders

Keyword(s):

Gene Expression ◽

Aspect Ratio ◽

Phenotypic Variation ◽

Drosophila Embryo ◽

Wild Type ◽

Gap Gene ◽

Key Factor ◽

Segmentation Gene Expression ◽

Environmental Variations ◽

Anterior Posterior

During development, many mutations cause increased variation in phenotypic outcomes, a phenomenon termed decanalization. Phenotypic discordance is often observed in the absence of genetic and environmental variations, but the mechanisms underlying such inter-individual phenotypic discordance remain elusive. Here, using the anterior-posterior (AP) patterning of the Drosophila embryo, we identified embryonic geometry as a key factor predetermining patterning outcomes under decanalizing mutations. With the wild-type AP patterning network, we found that AP patterning is robust to variations in embryonic geometry; segmentation gene expression remains reproducible even when the embryo aspect ratio is artificially reduced by more than twofold. In contrast, embryonic geometry is highly predictive of individual patterning defects under decanalized conditions of either increased bicoid (bcd) dosage or bcd knockout. We showed that the phenotypic discordance can be traced back to variations in the gap gene expression, which is rendered sensitive to the geometry of the embryo under mutations.

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Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400770 ◽

2020 ◽

Vol 10 (3) ◽

pp. 1019-1028 ◽

Cited By ~ 2

Author(s):

Luke Browne ◽

Alayna Mead ◽

Courtney Horn ◽

Kevin Chang ◽

Zeynep A. Celikkol ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Phenotypic Variation ◽

Foliar Application ◽

Substantial Reduction ◽

Dna Demethylation ◽

Soil Microbiome ◽

Relative Reduction ◽

Tree Seedlings ◽

Genome Wide

Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, Quercus lobata, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3–6% absolute reductions and 6.7–43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (i.e., deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development.

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Stresses affect inbreeding depression in complex ways: disentangling stress-specific genetic effects from effects of initial size in plants

Heredity ◽

10.1038/s41437-021-00454-5 ◽

2021 ◽

Author(s):

Tobias M. Sandner ◽

Diethart Matthies ◽

Donald M. Waller

Keyword(s):

Gene Expression ◽

Inbreeding Depression ◽

Phenotypic Variation ◽

Phenotypic Variability ◽

Nutrient Deficiency ◽

Plant Size ◽

Genetic Effects ◽

Initial Size ◽

Copper Addition ◽

Deleterious Alleles

AbstractThe magnitude of inbreeding depression (ID) varies unpredictably among environments. ID often increases in stressful environments suggesting that these expose more deleterious alleles to selection or increase their effects. More simply, ID could increase under conditions that amplify phenotypic variation (CV²), e.g., by accentuating size hierarchies among plants. These mechanisms are difficult to distinguish when stress increases both ID and phenotypic variation. We grew in- and outbred progeny of Mimulus guttatus under six abiotic stress treatments (control, waterlogging, drought, nutrient deficiency, copper addition, and clipping) with and without competition by the grass Poa palustris. ID differed greatly among stress treatments with δ varying from 7% (control) to 61% (waterlogging) but did not consistently increase with stress intensity. Poa competition increased ID under nutrient deficiency but not other stresses. Analyzing effects of initial size on performance of outbred plants suggests that under some conditions (low N, clipping) competition increased ID by amplifying initial size differences. In other cases (e.g., high ID under waterlogging), particular environments amplified the deleterious genetic effects of inbreeding suggesting differential gene expression. Interestingly, conditions that increased the phenotypic variability of inbred progeny regularly increased ID whereas variability among outbred progeny showed no relationship to ID. Our study reconciles the stress- and phenotypic variability hypotheses by demonstrating how specific conditions (rather than stress per se) act to increase ID. Analyzing CV² separately in inbred and outbred progeny while including effects of initial plant size improve our ability to predict how ID and gene expression vary across environments.

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