scholarly journals Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weed Monochoria vaginalis

2021 ◽  
Author(s):  
Shinji Tanigaki ◽  
Akira Uchino ◽  
Shigenori Okawa ◽  
Chikako Miura ◽  
Kenshiro Hamamura ◽  
...  
Keyword(s):  
Gene Expression ◽  
Herbicide Resistance ◽  
Parallel Evolution ◽  
Agricultural Weed

scholarly journals Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

2020 ◽  
Author(s):  
Emily B. Josephs ◽  
Megan L. Van Etten ◽  
Alex Harkess ◽  
Adrian Platts ◽  
Regina S. Baucom
Keyword(s):  
Gene Expression ◽  
Environmental Change ◽  
Herbicide Resistance ◽  
Morning Glory ◽  
Adaptive Plasticity ◽  
Clear Understanding ◽  
Fitness Consequences ◽  
Agricultural Weed ◽  
Selection For ◽  
Plastic Responses

AbstractPlastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide spray to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

scholarly journals Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weedMonochoria vaginalis

2021 ◽  
Author(s):  
Shinji Tanigaki ◽  
Akira Uchino ◽  
Shigenori Okawa ◽  
Chikako Miura ◽  
Kenshiro Hamamura ◽  
...  
Keyword(s):  
Gene Expression ◽  
Herbicide Resistance ◽  
Parallel Evolution ◽  
Acetolactate Synthase ◽  
Duplicate Gene ◽  
Target Site ◽  
Loss Of Function ◽  
Functional Characterisation ◽  
Gene Copies ◽  
Key Factor

AbstractThe evolution of herbicide resistance in weeds is an example of parallel evolution, through which genes encoding herbicide target proteins are repeatedly represented as evolutionary loci. The number of herbicide target-site genes differs among species, and little is known regarding the effects of duplicate gene copies on the evolution of herbicide resistance. We investigated the evolution of herbicide resistance inMonochoria vaginalis, which carries five copies of sulfonylurea target-site acetolactate synthase (ALS) genes. Suspected resistant populations collected across Japan were investigated for herbicide sensitivity andALSgene sequences, followed by functional characterisation andALSgene expression analysis. We identified over 60 resistant populations, all of which carried resistance-conferring amino acid substitutions exclusively inMvALS1orMvALS3. AllMvALS4alleles carried a loss-of-function mutation. Although the enzymatic properties of ALS encoded by these genes were not markedly different, the expression ofMvALS1andMvALS3was prominently higher among allALSgenes. The higher expression ofMvALS1andMvALS3is the driving force of the biased representation of genes during the evolution of herbicide resistance inM. vaginalis. Our findings highlight that gene expression is a key factor in creating evolutionary hotspots.

scholarly journals Repeated origins, gene flow, and allelic interactions of herbicide resistance mutations in a widespread agricultural weed

2021 ◽  
Author(s):  
Julia M Kreiner ◽  
George Sandler ◽  
Aaron J Stern ◽  
Patrick J. Tranel ◽  
Detlef Weigel ◽  
...  
Keyword(s):  
Gene Flow ◽  
Herbicide Resistance ◽  
De Novo ◽  
Parallel Evolution ◽  
Selective Advantage ◽  
Past Century ◽  
Resistance Mutations ◽  
Standing Variation ◽  
Agricultural Weed

Causal mutations and their frequency in nature are well-characterized for herbicide resistance. However, we still lack understanding of the extent of parallelism in the mutational origin of target-site resistance (TSR), the role of standing variation and gene flow in the spread of TSR variants, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 18 agricultural populations of Amaranthus tuberculatus, which we show to have undergone a massive expansion over the past century, with a contemporary Ne estimate of 8x107. We found nine TSR variants, three of which were common—showing extreme parallelism in mutational origin and an important role of gene flow in their geographic spread. The number of repeated origins varied across TSR loci and generally showed stronger signals of selection on de novo mutations, but with considerable evidence for selection on standing variation. Allele ages at TSR loci varied from ~10-250 years old, greatly predating the advent of herbicides. The evolutionary history of TSR has also been shaped by both intra- and inter-locus allelic interactions. We found evidence of haplotype competition between two TSR mutations, their successes in part modulated by either adaptive introgression of, or epistasis with, genome-wide resistance alleles. Together, this work reveals a remarkable example of spatial parallel evolution—the ability of independent mutations to spread due to selection contingent on not only the time, place, and background on which they arise but the haplotypes they encounter.

scholarly journals Parallel evolution of gene expression between trophic specialists despite divergent genotypes and morphologies

2018 ◽  
Vol 2 (2) ◽  
pp. 62-75 ◽  
Author(s):  
Joseph A. McGirr ◽  
Christopher H. Martin
Keyword(s):  
Gene Expression ◽  
Parallel Evolution

scholarly journals Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
María José Rivas ◽  
María Saura ◽  
Andrés Pérez-Figueroa ◽  
Marina Panova ◽  
Tomas Johansson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Sequence ◽  
Population Genomics ◽  
Parallel Evolution ◽  
Ecological Adaptation

scholarly journals Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

2012 ◽  
Vol 22 (3) ◽  
pp. 650-669 ◽  
Author(s):  
Tereza Manousaki ◽  
Pincelli M. Hull ◽  
Henrik Kusche ◽  
Gonzalo Machado-Schiaffino ◽  
Paolo Franchini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Parallel Evolution ◽  
Ecological Divergence ◽  
Cichlid Fishes ◽  
Adaptive Radiations ◽  
Differential Gene

scholarly journals Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 400 ◽  
Author(s):  
Alexandre Rêgo ◽  
Samridhi Chaturvedi ◽  
Amy Springer ◽  
Alexandra M. Lish ◽  
Caroline L. Barton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Allele Frequency ◽  
Development Time ◽  
Callosobruchus Maculatus ◽  
Parallel Evolution ◽  
Frequency Change ◽  
Multiple Traits ◽  
Population Genomic ◽  
Performance Traits ◽  
Frequency Changes

Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

scholarly journals Evolution of Gene Expression and Splicing in Parallel Cold-Adapted Fly Populations

2019 ◽  
Author(s):  
Yuheng Huang ◽  
Justin B. Lack ◽  
Grant T. Hoppel ◽  
John E. Pool
Keyword(s):  
Gene Expression ◽  
Adaptive Evolution ◽  
Parallel Evolution ◽  
Population Variation ◽  
Regulatory Evolution ◽  
Cold Adapted ◽  
Mitochondrial Functions ◽  
Expression Evolution ◽  
Gene Regulatory ◽  
Trans Regulation

AbstractChanges in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find significant although somewhat limited evidence for parallel expression evolution between them, and less evidence for parallel splicing evolution. We find that genes with mitochondrial functions are particularly enriched among candidates for adaptive expression evolution. We also develop a method to estimate cis-versus trans-encoded contributions to expression or splicing differences that does not rely on the presence of fixed differences between parental strains. Applying this method, we infer important roles of both cis-and trans-regulation among our putatively adaptive expression and splicing differences. The apparent contributions of cis-versus trans-regulation to adaptive evolution vary substantially among population pairs, with an Ethiopian pair showing pervasive trans-effects, suggesting that basic characteristics of regulatory evolution may depend on biological context. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.

scholarly journals Parallel Evolution of Opsin Gene Expression in African Cichlid Fishes

2010 ◽  
Vol 27 (12) ◽  
pp. 2839-2854 ◽  
Author(s):  
K. E. O'Quin ◽  
C. M. Hofmann ◽  
H. A. Hofmann ◽  
K. L. Carleton
Keyword(s):  
Gene Expression ◽  
Parallel Evolution ◽  
Opsin Gene ◽  
Cichlid Fishes ◽  
African Cichlid
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