scholarly journals The two-speed genomes of filamentous pathogens: waltz with plants

2015 ◽  
Author(s):  
Suomeng Dong ◽  
Sylvain Raffaele ◽  
Sophien Kamoun
Keyword(s):  
Adaptive Evolution ◽  
Plant Pathogens ◽  
Repetitive Sequences ◽  
Model Systems ◽  
Multiple Time Scales ◽  
Multiple Time ◽  
Effector Genes ◽  
Genes Encoding ◽  
Genome Model ◽  
Virulence Effectors

Fungi and oomycetes include deep and diverse lineages of eukaryotic plant pathogens. The last 10 years have seen the sequencing of the genomes of a multitude of species of these so-called filamentous plant pathogens. Already, fundamental concepts have emerged. Filamentous plant pathogen genomes tend to harbor large repertoires of genes encoding virulence effectors that modulate host plant processes. Effector genes are not randomly distributed across the genomes but tend to be associated with compartments enriched in repetitive sequences and transposable elements. These findings have led to the “two-speed genome” model in which filamentous pathogen genomes have a bipartite architecture with gene sparse, repeat rich compartments serving as a cradle for adaptive evolution. Here, we review this concept and discuss how plant pathogens are great model systems to study evolutionary adaptations at multiple time scales. We will also introduce the next phase of research on this topic.

The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens

2018 ◽  
Vol 56 (1) ◽  
pp. 21-40 ◽  
Author(s):  
Andrea Sánchez-Vallet ◽  
Simone Fouché ◽  
Isabelle Fudal ◽  
Fanny E. Hartmann ◽  
Jessica L. Soyer ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Population Genomics ◽  
Gene Evolution ◽  
Point Mutations ◽  
Repetitive Elements ◽  
Genome Biology ◽  
Global Food Security ◽  
Effector Genes ◽  
Genes Encoding ◽  
Global Food

Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host to the pathogen's advantage. Genes encoding such effectors are among the most rapidly evolving genes in pathogen genomes. Here, we review how the major characteristics of the emergence, function, and regulation of effector genes are tightly linked to the genomic compartments where these genes are located in pathogen genomes. The presence of repetitive elements in these compartments is associated with elevated rates of point mutations and sequence rearrangements with a major impact on effector diversification. The expression of many effectors converges on an epigenetic control mediated by the presence of repetitive elements. Population genomics analyses showed that rapidly evolving pathogens show high rates of turnover at effector loci and display a mosaic in effector presence-absence polymorphism among strains. We conclude that effective pathogen containment strategies require a thorough understanding of the effector genome biology and the pathogen's potential for rapid adaptation.

SOME REMARKS ON THE MULTIPLE TIME SCALES OF DIFFUSION IN MINERALS AND MELTS

2018 ◽  
Author(s):  
Yan Liang ◽  
◽  
Daniele J. Cherniak ◽  
Chenguang Sun
Keyword(s):  
Time Scales ◽  
Multiple Time Scales ◽  
Multiple Time

scholarly journals Odor response adaptation in Drosophila—a continuous individualization process

2021 ◽  
Vol 383 (1) ◽  
pp. 143-148
Author(s):  
Shadi Jafari ◽  
Mattias Alenius
Keyword(s):  
Sensory Neurons ◽  
Olfactory System ◽  
Multiple Time Scales ◽  
Multiple Time ◽  
Olfactory Perception ◽  
Adaptation Mechanisms ◽  
Metabolic States ◽  
The Central Nervous System ◽  
Olfactory Adaptation ◽  
Central Adaptation

AbstractOlfactory perception is very individualized in humans and also in Drosophila. The process that individualize olfaction is adaptation that across multiple time scales and mechanisms shape perception and olfactory-guided behaviors. Olfactory adaptation occurs both in the central nervous system and in the periphery. Central adaptation occurs at the level of the circuits that process olfactory inputs from the periphery where it can integrate inputs from other senses, metabolic states, and stress. We will here focus on the periphery and how the fast, slow, and persistent (lifelong) adaptation mechanisms in the olfactory sensory neurons individualize the Drosophila olfactory system.

scholarly journals Are We Doing ‘Systems’ Research? An Assessment of Methods for Climate Change Adaptation to Hydrohazards in a Complex World

2019 ◽  
Vol 11 (4) ◽  
pp. 1163 ◽  
Author(s):  
Melissa Bedinger ◽  
Lindsay Beevers ◽  
Lila Collet ◽  
Annie Visser
Keyword(s):  
Climate Change ◽  
Human Nature ◽  
Climate Change Adaptation ◽  
Time Scales ◽  
Spatial Scales ◽  
Local Context ◽  
Multiple Time Scales ◽  
Future Research ◽  
Multiple Time ◽  
Systems Research

Climate change is a product of the Anthropocene, and the human–nature system in which we live. Effective climate change adaptation requires that we acknowledge this complexity. Theoretical literature on sustainability transitions has highlighted this and called for deeper acknowledgment of systems complexity in our research practices. Are we heeding these calls for ‘systems’ research? We used hydrohazards (floods and droughts) as an example research area to explore this question. We first distilled existing challenges for complex human–nature systems into six central concepts: Uncertainty, multiple spatial scales, multiple time scales, multimethod approaches, human–nature dimensions, and interactions. We then performed a systematic assessment of 737 articles to examine patterns in what methods are used and how these cover the complexity concepts. In general, results showed that many papers do not reference any of the complexity concepts, and no existing approach addresses all six. We used the detailed results to guide advancement from theoretical calls for action to specific next steps. Future research priorities include the development of methods for consideration of multiple hazards; for the study of interactions, particularly in linking the short- to medium-term time scales; to reduce data-intensivity; and to better integrate bottom–up and top–down approaches in a way that connects local context with higher-level decision-making. Overall this paper serves to build a shared conceptualisation of human–nature system complexity, map current practice, and navigate a complexity-smart trajectory for future research.

scholarly journals A multistate model incorporating estimation of excess hazards and multiple time scales

2021 ◽  
Vol 40 (9) ◽  
pp. 2139-2154
Author(s):  
Caroline E. Weibull ◽  
Paul C. Lambert ◽  
Sandra Eloranta ◽  
Therese M. L. Andersson ◽  
Paul W. Dickman ◽  
...  
Keyword(s):  
Time Scales ◽  
Multiple Time Scales ◽  
Multiple Time ◽  
Multistate Model

scholarly journals Skipping the Insect Vector: Plant Stolon Transmission of the Phytopathogen ‘Ca. Phlomobacter fragariae’ from the Arsenophonus Clade of Insect Endosymbionts

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 93
Author(s):  
Jessica Dittmer ◽  
Thierry Lusseau ◽  
Xavier Foissac ◽  
Franco Faoro
Keyword(s):  
Plant Pathogens ◽  
Model Systems ◽  
Insect Vector ◽  
Evolutionary Perspective ◽  
Evolutionary Transition ◽  
Strawberry Plant ◽  
Disease Symptoms ◽  
Transmission Electron ◽  
Nutrient Provisioning ◽  
Early Growth Phase

The genus Arsenophonus represents one of the most widespread clades of insect endosymbionts, including reproductive manipulators and bacteriocyte-associated primary endosymbionts. Two strains belonging to the Arsenophonus clade have been identified as insect-vectored plant pathogens of strawberry and sugar beet. The bacteria accumulate in the phloem of infected plants, ultimately causing leaf yellows and necrosis. These symbionts therefore represent excellent model systems to investigate the evolutionary transition from a purely insect-associated endosymbiont towards an insect-vectored phytopathogen. Using quantitative PCR and transmission electron microscopy, we demonstrate that ‘Candidatus Phlomobacter fragariae’, bacterial symbiont of the planthopper Cixius wagneri and the causative agent of Strawberry Marginal Chlorosis disease, can be transmitted from an infected strawberry plant to multiple daughter plants through stolons. Stolons are horizontally growing stems enabling the nutrient provisioning of daughter plants during their early growth phase. Our results show that Phlomobacter was abundant in the phloem sieve elements of stolons and was efficiently transmitted to daughter plants, which rapidly developed disease symptoms. From an evolutionary perspective, Phlomobacter is, therefore, not only able to survive within the plant after transmission by the insect vector, but can even be transmitted to new plant generations, independently from its ancestral insect host.

scholarly journals Structural Disorder and Collective Behavior of Two-Dimensional Magnetic Nanostructures

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1392
Author(s):  
David Gallina ◽  
G. M. Pastor
Keyword(s):  
Interaction Energy ◽  
Time Evolution ◽  
Magnetic Nanostructures ◽  
Thermal Quenching ◽  
Structural Disorder ◽  
Square Lattice ◽  
Multiple Time Scales ◽  
Multiple Time ◽  
Two Dimensional ◽  
Energy Landscapes

Structural disorder has been shown to be responsible for profound changes of the interaction-energy landscapes and collective dynamics of two-dimensional (2D) magnetic nanostructures. Weakly-disordered 2D ensembles have a few particularly stable magnetic configurations with large basins of attraction from which the higher-energy metastable configurations are separated by only small downward barriers. In contrast, strongly-disordered ensembles have rough energy landscapes with a large number of low-energy local minima separated by relatively large energy barriers. Consequently, the former show good-structure-seeker behavior with an unhindered relaxation dynamics that is funnelled towards the global minimum, whereas the latter show a time evolution involving multiple time scales and trapping which is reminiscent of glasses. Although these general trends have been clearly established, a detailed assessment of the extent of these effects in specific nanostructure realizations remains elusive. The present study quantifies the disorder-induced changes in the interaction-energy landscape of two-dimensional dipole-coupled magnetic nanoparticles as a function of the magnetic configuration of the ensembles. Representative examples of weakly-disordered square-lattice arrangements, showing good structure-seeker behavior, and of strongly-disordered arrangements, showing spin-glass-like behavior, are considered. The topology of the kinetic networks of metastable magnetic configurations is analyzed. The consequences of disorder on the morphology of the interaction-energy landscapes are revealed by contrasting the corresponding disconnectivity graphs. The correlations between the characteristics of the energy landscapes and the Markovian dynamics of the various magnetic nanostructures are quantified by calculating the field-free relaxation time evolution after either magnetic saturation or thermal quenching and by comparing them with the corresponding averages over a large number of structural arrangements. Common trends and system-specific features are identified and discussed.

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