<i>Cis</i>‐regulatory variation in plant genomes and the impact of natural selection

Meaux, Juliette de

doi:10.1002/ajb2.1180

Cited by 12 publications

(8 citation statements)

References 22 publications

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“…If the enhancer and the gene they regulate are linked then the up-regulating variants will hitch-hike with the allele carrying the lowest number of deleterious mutations, leading to an open-ended escalation in enhancer strength [27]. As selection on expression appears to be primarily stabilizing [24, 28, 29], at least at intermediate evolutionary timescales [30], a compensatory effect of expression in trans is predicted [27, 31]. The relative importance of cis - and trans -regulation can be examined by comparing the relative expression in the parental species with the relative expression of homeologous genes in the newly formed tetraploid [21, 32, 33].…”

Section: Introductionmentioning

confidence: 99%

Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

et al. 2019

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Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to follow similar trajectories and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allotetraploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis . Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis -regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans -regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora . Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers indicates that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load.

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Section: Introductionmentioning

confidence: 99%

Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

et al. 2019

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“…A single master regulator, for example, can change the expression of many genes in the same direction, even in the absence of a selective force 25 . In addition, new mutations can erode pre-existing plastic reactions, if selection is relaxed 26 – 33 , and mutations can have functional effects whose size or direction is not uniformly distributed 31 – 28 . The study of allele-specific expression in F1 hybrids, instead, offers a powerful avenue to identify myriads of cis-regulatory variants that evolved independently at each transcribed locus 27 , 29 , 34 – 38 .…”

Section: Introductionmentioning

confidence: 99%

Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity

Steige

Kováčová

et al. 2021

Nat Commun

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Phenotypic plasticity is the variation in phenotype that a single genotype can produce in different environments and, as such, is an important component of individual fitness. However, whether the effect of new mutations, and hence evolution, depends on the direction of plasticity remains controversial. Here, we identify the cis-acting modifications that have reshaped gene expression in response to dehydration stress in three Arabidopsis species. Our study shows that the direction of effects of most cis-regulatory variants differentiating the response between A. thaliana and the sister species A. lyrata and A. halleri depends on the direction of pre-existing plasticity in gene expression. A comparison of the rate of cis-acting variant accumulation in each lineage indicates that the selective forces driving adaptive evolution in gene expression favors regulatory changes that magnify the stress response in A. lyrata. The evolutionary constraints measured on the amino-acid sequence of these genes support this interpretation. In contrast, regulatory changes that mitigate the plastic response to stress evolved more frequently in A. halleri. Our results demonstrate that pre-existing plasticity may be a stepping stone for adaptation, but its selective remodeling differs between lineages.

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“…A single master regulator, for example, can change the expression of many genes in the same direction, even in the absence of a selective force 25 . In addition, new mutations can erode pre-existing plastic reactions, if selection is relaxed [26][27][28][29][30][31][32][33] , and mutations can have functional effects whose size or direction is not uniformly distributed . The study of allele-specific expression in F1 hybrids, instead, offers a powerful avenue to identify myriads of cisregulatory variants that evolved independently at each transcribed locus 27,29,[34][35][36][37][38] .…”

Section: Introductionmentioning

confidence: 99%

“…A single master regulator, for example, can change the expression of many genes in the same direction, even in the absence of a selective force 25 . In addition, new mutations can erode pre-existing plastic reactions, if selection is relaxed [29][30][31][32][33] , and mutations can have functional effects whose size or direction is not uniformly distributed [26][27][28] . To unravel the general rules governing the evolution of transcriptional plasticity and determine whether plasticity itself directs adaptive evolution, rates of evolution must be compared among lineages to distinguish the action of natural selection from the random accumulation of new regulatory mutations.…”

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confidence: 99%

Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity

Steige

Kováčová

et al. 2020

Preprint

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AbstractPhenotypic plasticity is the variation in phenotype that a single genotype can produce in different environments and, as such, is an important component of individual fitness. However, whether the effect of new mutations, and hence evolution, depends on the direction of plasticity remains controversial. Here, we identify the cis-acting modifications that have reshaped gene expression in response to dehydration stress in three Arabidopsis species. Our study shows that the direction of effects of most cis-regulatory variants differentiating the response between A. thaliana and the sister species A. lyrata and A. halleri depends on the direction of pre-existing plasticity in gene expression. A comparison of the rate of cis-acting variant accumulation in each lineage indicates that the selective forces driving adaptive evolution in gene expression favors regulatory changes that magnify the stress response in A. lyrata. The evolutionary constraints measured on the amino-acid sequence of these genes support this interpretation. In contrast, regulatory changes that mitigate the plastic response to stress evolved more frequently in A. halleri. Our results demonstrate that pre-existing plasticity can be a stepping stone for adaptation, but its selective remodeling differs between lineages.

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Cis‐regulatory variation in plant genomes and the impact of natural selection

Abstract: Citation: Juliette de Meaux. 2018. Cis-regulatory variation in plant genomes and the impact of natural selection.

Cited by 12 publications

References 22 publications

Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity

Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity

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