Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish

AbstractPhenotypic plasticity is an important aspect of an organism’s response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative as a result of increases or decreases in the amounts of specific transcripts, or qualitative as a result of the expression of alternative transcripts from the same gene (e.g., via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for between 426 and 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a conserved set of genes with expression patterns that respond qualitatively to prolonged cold temperatures across fishes.Summary statementQualitative changes in gene expression, such as those mediated by alternative splicing of mRNAs, are involved in phenotypic plasticity in response to prolonged cold acclimation in ectothermic animals

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Phenotypic plasticity

10.1093/oso/9780198797500.003.0005 ◽

2018 ◽

Author(s):

Karen D. Williams ◽

Marla B. Sokolowski

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

Environmental Change ◽

Behavioral Plasticity ◽

Behavioral Flexibility ◽

Insect Behavior ◽

Behavioral Variability ◽

Gene By Environment Interactions ◽

Affect Gene Expression

Why is there so much variation in insect behavior? This chapter will address the sources of behavioral variability, with a particular focus on phenotypic plasticity. Variation in social, nutritional, and seasonal environmental contexts during development and adulthood can give rise to phenotypic plasticity. To delve into mechanism underlying behavioral flexibility in insects, examples of polyphenisms, a type of phenotypic plasticity, will be discussed. Selected examples reveal that environmental change can affect gene expression, which in turn can affect behavioral plasticity. These changes in gene expression together with gene-by-environment interactions are discussed to illuminate our understanding of insect behavioral plasticity.

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Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations ofFundulus heteroclitus

Molecular Ecology ◽

10.1111/mec.13188 ◽

2015 ◽

Vol 24 (13) ◽

pp. 3345-3359 ◽

Cited By ~ 56

Author(s):

David I. Dayan ◽

Douglas L. Crawford ◽

Marjorie F. Oleksiak

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity

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Evidence for the up-regulation of stearoyl-ACP (Δ9) desaturase gene expression during cold acclimation

American Journal of Potato Research ◽

10.1007/bf02853610 ◽

2004 ◽

Vol 81 (2) ◽

pp. 125-135 ◽

Cited By ~ 32

Author(s):

Sandra E. Vega ◽

Alfonso H. del Rio ◽

John B. Bamberg ◽

Jiwan P. Palta

Keyword(s):

Gene Expression ◽

Cold Acclimation ◽

Desaturase Gene ◽

Δ9 Desaturase

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Signal Transduction and Gene Expression During Cold Acclimation of Alfalfa

Advances in Plant Cold Hardiness ◽

10.1201/9781351069526-4 ◽

2018 ◽

pp. 57-71

Author(s):

Rajinder S. Dhindsa ◽

Antonio Monroy ◽

Lawrence Wolfraim ◽

Guangyuan Dong

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Cold Acclimation

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Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

10.1101/116012 ◽

2017 ◽

Cited By ~ 1

Author(s):

Marina Pais ◽

Kentaro Yoshida ◽

Artemis Giannakopoulou ◽

Mathieu A. Pel ◽

Liliana M. Cano ◽

...

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

South American ◽

Nucleotide Polymorphisms ◽

Natural Ecosystems ◽

Asexual Lineage ◽

Irish Famine ◽

Eukaryotic Microbes ◽

And Migration ◽

Potato Famine

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012,Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013,Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

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