The sources of adaptive variation

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2017, Volume and Issue: 284(1855), P. 20162864 - 20162864

Published: May 31, 2017

The role of natural selection in the evolution adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, can act together with other processes, including random changes frequencies phenotypic differences that are not under strong selection, environment, which may reflect organisms themselves. understanding genetics developed after 1900, new genetic discoveries were incorporated into biology. resulting general principles summarized Julian Huxley his 1942 book Evolution: modern synthesis Here, we examine how recent advances genetics, developmental biology molecular biology, epigenetics, relate to today's adaptations. We illustrate careful studies have repeatedly shown apparently puzzling results a wide diversity involve processes consistent neo-Darwinism. They do support important roles adaptation for such as directed mutation or inheritance acquired characters, therefore no radical revision our mechanism is needed.

Language: Английский

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Exploiting induced and natural epigenetic variation for crop improvement

Nature Reviews Genetics, Journal Year: 2017, Volume and Issue: 18(9), P. 563 - 575

Published: July 3, 2017

Language: Английский

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DNA methylation dynamics during early plant life

Genome biology, Journal Year: 2017, Volume and Issue: 18(1)

Published: Sept. 19, 2017

Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals plants. While this epigenetic mark extensively reprogrammed the germline early embryos mammals, extent to which DNA reset between generations plants remains largely unknown. Using Arabidopsis as a model, we uncovered distinct dynamics over element sequences during stages plant development. Specifically, their relics show invariably high at CG sites but increasing CHG CHH sites. This non-CG culminates mature embryos, where it reaches saturation large fraction methylated sites, compared typical 10-20% level observed seedlings or adult Moreover, increase embryogenesis matches hypomethylated state endosperm. Finally, that interfering with embryo-to-seedling transition results persistence levels after germination, specifically are targeted by RNA-directed (RdDM) machinery. Our findings indicate absence extensive resetting patterns life point instead an important role RdDM reinforcing every cell embryo. Furthermore, provide evidence elevated activity specific property embryogenesis.

Language: Английский

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New Insights into 5hmC DNA Modification: Generation, Distribution and Function

Frontiers in Genetics, Journal Year: 2017, Volume and Issue: 8

Published: July 19, 2017

Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition the common methylation 5th position of pyrimidine ring cytosine (5mC), other types modifications at same position, 5-hydroxymethyl (5hmC), 5-formyldeoxy (5fC), 5-carboxy (5caC), also important. Recently, 5hmC, a product 5mC demethylation by Ten-Eleven Translocation (TET) family proteins, was shown regulate many cellular developmental processes, including pluripotency embryonic stem cells, neuron development, tumorigenesis mammals. Here, we review recent advances generation, distribution function 5hmC modification mammals discuss its potential roles plants.

Language: Английский

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Gene Body Methylation in Plants: Mechanisms, Functions, and Important Implications for Understanding Evolutionary Processes

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(4)

Published: March 16, 2022

Gene body methylation (gbM) is an epigenetic mark where gene exons are methylated in the CG context only, as opposed to CHG and CHH contexts (where H stands for A, C, or T). transmitted transgenerationally plants, opening possibility that gbM may be shaped by adaptation. This presupposes, however, has a function affects phenotype, which been topic of debate literature. Here, we review our current knowledge plants. We start presenting well-elucidated mechanisms plant establishment maintenance. then more controversial topics: evolution potential selective pressures act on it. Finally, discuss functions affect organismal phenotypes: expression stabilization upregulation, inhibition aberrant transcription (reverse internal), prevention intron retention, protection against TE insertions. To bolster these topics, include novel analyses assess effect transcripts. Overall, growing literature finds correlates with levels patterns expression. It not clear, if this causal relationship. Altogether, functional work suggests effects gbM, any, must relatively small, but there nonetheless evidence it natural selection. conclude discussing adaptive character its implications updated view adaptation

Language: Английский

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Multilayered regulation of secondary metabolism in medicinal plants

Molecular Horticulture, Journal Year: 2023, Volume and Issue: 3(1)

Published: June 6, 2023

Abstract Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining remains challenge due to their low-yield accumulation in medicinal plants; moreover, these are produced through tightly coordinated pathways involving many spatiotemporally environmentally regulated steps. The first regulatory layer involves complex network transcription factors; second, more recently discovered complexity the regulation SMs is epigenetic modification, such as DNA methylation, histone modification small RNA-based mechanisms, which can jointly or separately influence by regulating gene expression. Here, we summarize findings fields genetic special emphasis on plants, providing new perspective multiple layers Graphical

Language: Английский

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The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana

Genome biology, Journal Year: 2017, Volume and Issue: 18(1)

Published: May 18, 2017

Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 DNA methylation. The origin significance these profiles remain largely unknown. methylation enrichment over gene correlated both have a similar dependence on transcription levels. This suggests mechanistic link between body

Language: Английский

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Spontaneous epimutations in plants

New Phytologist, Journal Year: 2018, Volume and Issue: 221(3), P. 1253 - 1259

Published: Sept. 14, 2018

Contents Summary 1253 I. Introduction II. What is the rate and molecular spectrum of spontaneous epimutations? 1254 III. Do epimutations have phenotypic consequences? 1257 IV. Conclusion discussion 1258 Acknowledgements References SUMMARY: Heritable gains or losses cytosine methylation can arise stochastically in plant genomes independently DNA sequence changes. These so-called 'spontaneous epimutations' appear to be a byproduct imperfect maintenance epigenome reinforcement events that occur specialized cell types. There continued interest epigenetics community trying understand broader implications these stochastic events, as some been shown induce heritable gene expression changes, shape patterns diversity within among populations, responsive multi-generational environmental stressors. In this paper we synthesized our current knowledge basis functional consequences plants, discuss technical conceptual challenges, highlight emerging research directions.

Language: Английский

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A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Jan. 25, 2018

Abstract Epigenetic variation has been proposed to facilitate adaptation changing environments, but evidence that natural epialleles contribute adaptive evolution lacking. Here we identify a retrotransposon, named “NMR19” (naturally occurring DNA methylation region 19), whose and genomic location vary among Arabidopsis thaliana accessions. We classify NMR19 as NMR19-4 NMR19-16 based on its location, uncover an epiallele controls leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE ( PPH ). find status is stably inherited independent genetic variation. In addition, further analysis indicates correlates with local climates, implying environmentally associated epiallele. summary, discover novel epiallele, provide mechanistic insights into origin potential function in climate adaptation.

Language: Английский

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Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Nov. 2, 2020

Abstract DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines the maize genome, but variation and evolution landscape during domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) bisulfite (WGBS) data on populations modern maize, landrace, teosinte ( Zea mays ssp. parviglumis) to estimate epimutation rates selection coefficients. We find weak evidence for direct any context, thousands differentially methylated regions (DMRs) are identified population-wide that correlated with recent selection. For two trait-associated DMRs, vgt1 -DMR tb1 -DMR, HiChIP indicate interactive loops between DMRs respective downstream genes B73, line, absent teosinte. Our results enable better understanding evolutionary forces acting patterns suggest role adaptive evolution.

Language: Английский

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