scholarly journals Selective sweeps in populations of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2018 ◽  
Author(s):  
Mark C Derbyshire ◽  
Matthew Denton-Giles ◽  
James K Hane ◽  
Steven Chang ◽  
Mahsa Mousavi-Derazmahalleh ◽  
...  
Keyword(s):  
Positive Selection ◽  
Sclerotinia Sclerotiorum ◽  
Pathogenic Fungus ◽  
Genotypic Diversity ◽  
Global Scale ◽  
Genomic Region ◽  
Broad Host Range ◽  
Selective Sweeps ◽  
South African Isolate ◽  
The World

AbstractThe pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking.We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents - Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps.Among the 25 isolates, there was evidence for four population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), another consisted of five isolates from Australia and one from Morocco (population 2). A further cluster was made up of Australian isolates, and the single South African isolate appeared to be from a separate population. We found that there was evidence of distinct selective sweeps between population 1 and population 2. Many of these sweeps overlapped genes involved in transcriptional regulation, such as transcription factors. It is possible that distinct populations of S. sclerotiorum from differing global environments have undergone selective sweeps at different genomic loci. This study lays the foundation for further work into investigation of the differing selective pressures that S. sclerotiorum populations are subjected to on a global scale.

scholarly journals A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

PLoS ONE ◽  
2019 ◽  
Vol 14 (3) ◽  
pp. e0214201 ◽  
Author(s):  
Mark Charles Derbyshire ◽  
Matthew Denton-Giles ◽  
James K. Hane ◽  
Steven Chang ◽  
Mahsa Mousavi-Derazmahalleh ◽  
...  
Keyword(s):  
Host Range ◽  
Sclerotinia Sclerotiorum ◽  
Pathogenic Fungus ◽  
Genome Scan ◽  
Broad Host Range ◽  
Whole Genome ◽  
Selective Sweeps ◽  
Plant Pathogenic Fungus ◽  
Snp Data ◽  
Whole Genome Scan

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum . In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

Impact of Globalisation on Pandemics: A comparative study on SARS and Covid-19 (Preprint)

2020 ◽  
Author(s):  
Johann Johann And Devika
Keyword(s):  
Comparative Analysis ◽  
Comparative Study ◽  
Descriptive Analysis ◽  
Qualitative Comparative Analysis ◽  
Global Scale ◽  
Global Level ◽  
Economic Stability ◽  
The Past ◽  
The World ◽  
Close Relationship

BACKGROUND Since November 2019, Covid - 19 has spread across the globe costing people their lives and countries their economic stability. The world has become more interconnected over the past few decades owing to globalisation and such pandemics as the Covid -19 are cons of that. This paper attempts to gain deeper understanding into the correlation between globalisation and pandemics. It is a descriptive analysis on how one of the factors that was responsible for the spread of this virus on a global scale is globalisation. OBJECTIVE - To understand the close relationship that globalisation and pandemics share. - To understand the scale of the spread of viruses on a global scale though a comparison between SARS and Covid -19. - To understand the sale of globalisation present during SARS and Covid - 19. METHODS A descriptive qualitative comparative analysis was used throughout this research. RESULTS Globalisation does play a significant role in the spread of pandemics on a global level. CONCLUSIONS - SARS and Covid - 19 were varied in terms of severity and spread. - The scale of globalisation was different during the time of SARS and Covid - 19. - Globalisation can be the reason for the faster spread in Pandemics.

The Reasoning Structure in Legal Disputes on the International Trade of Biotechnology: From a Judicial Balance by Chance to a Judicial Balance by Design

2021 ◽  
pp. 1-16
Author(s):  
Alessandra GUIDA
Keyword(s):  
International Trade ◽  
World Trade Organization ◽  
World Trade ◽  
Technology Innovation ◽  
Global Scale ◽  
Trade Restrictions ◽  
Competing Interests ◽  
The World ◽  
National Economies ◽  
Biotech Products

The international trade in biotech products boosts national economies and advances scientific as well as technology innovation. However, while trading these products increases the spread of benefits on a global scale, it also increases risks to human health and the environment (ie biosafety). This is because the effects of this technology on biosafety are still highly uncertain. Against this background, the judicial bodies under the World Trade Organization (WTO) find themselves in the middle of an intricate and polarised debate in which a proper judicial balance between free trade and biosafety becomes fundamental in order to determine whether requests for ensuring human and environmental health justify trade restrictions. This paper aims to highlight that the WTO is institutionally unready for balancing economic and non-economic values. In suggesting how to rationalise the judicial balance between the competing interests in the context of biotechnology, this paper demonstrates that the judicial adoption of a well-structured proportionality analysis can turn the current balance by chance into a balance by structure.

Kuehneola loeseneriana.

2021 ◽  
Author(s):  
Keyword(s):  
South America ◽  
Environmental Conditions ◽  
Pathogenic Fungus ◽  
North Central ◽  
Plant Pathogenic Fungus ◽  
The World ◽  
Agricultural Plants

Abstract There is little published information on this plant pathogenic fungus, which is limited to parts of North, Central and South America. It infects Rubus spp., which exist in other regions of the world with similar environmental conditions, therefore this species may pose a threat to native or agricultural plants if introduced.

The Strait of Magellan—a Gateway to New Worlds

2021 ◽  
Author(s):  
Mauricio Onetto Pavez
Keyword(s):  
Global Scale ◽  
Modern World ◽  
American Continent ◽  
The Earth ◽  
Starting Point ◽  
Strait Of Magellan ◽  
The World ◽  
The Strait Of Magellan ◽  
History Of ◽  
First Time

The year 2020 marks the five hundredth anniversary of the “discovery” of the Strait of Magellan. The unveiling of this passage between 1519 and 1522 allowed the planet to be circumnavigated for the first time in the history of humanity. All maritime routes could now be connected, and the idea of the Earth, in its geographical, cosmographic, and philosophical dimensions, gained its definitive meaning. This discovery can be considered one of the founding events of the modern world and of the process of globalization that still continues today. This new connectivity awoke an immediate interest in Europe that led to the emergence of a political consciousness of possession, domination, and territorial occupation generalized on a global scale, and the American continent was the starting point for this. This consciousness also inspired a desire for knowledge about this new form of inhabiting the world. Various fields of knowledge were redefined thanks to the new spaces and measurements produced by the discovery of the southern part of the Americas, which was recorded in books on cosmography, natural history, cartography, and manuscripts, circulating mainly between the Americas and Europe. All these processes transformed the Strait of Magellan into a geopolitical space coveted by Europeans during the 16th century. As an interoceanic connector, it was used to imagine commercial routes to the Orient and political projects that could sustain these dynamics. It was also conceived as a space to speculate on the potential wealth in the extreme south of the continent. In addition, on the Spanish side, some agents of the Crown considered it a strategic place for imperial projections and the defense of the Americas.

scholarly journals Anthropogenic Effects on Forest Ecosystems at Various Spatio-Temporal Scales

2002 ◽  
Vol 2 ◽  
pp. 827-841 ◽  
Author(s):  
Michael Bredemeier
Keyword(s):  
Air Pollution ◽  
Long Range ◽  
Acid Deposition ◽  
Soil Degradation ◽  
Forest Ecosystems ◽  
Global Scale ◽  
Soil Productivity ◽  
Long Term Effects ◽  
The World

The focus in this review of long-term effects on forest ecosystems is on human impact. As a classification of this differentiated and complex matter, three domains of long-term effects with different scales in space and time are distinguished: 1- Exploitation and conversion history of forests in areas of extended human settlement 2- Long-range air pollution and acid deposition in industrialized regions 3- Current global loss of forests and soil degradation.There is an evident link between the first and the third point in the list. Cultivation of primary forestland — with its tremendous effects on land cover — took place in Europe many centuries ago and continued for centuries. Deforestation today is a phenomenon predominantly observed in the developing countries, yet it threatens biotic and soil resources on a global scale. Acidification of forest soils caused by long-range air pollution from anthropogenic emission sources is a regional to continental problem in industrialized parts of the world. As a result of emission reduction legislation, atmospheric acid deposition is currently on the retreat in the richer industrialized regions (e.g., Europe, U.S., Japan); however, because many other regions of the world are at present rapidly developing their polluting industries (e.g., China and India), “acid rain” will most probably remain a serious ecological problem on regional scales. It is believed to have caused considerable destabilization of forest ecosystems, adding to the strong structural and biogeochemical impacts resulting from exploitation history.Deforestation and soil degradation cause the most pressing ecological problems for the time being, at least on the global scale. In many of those regions where loss of forests and soils is now high, it may be extremely difficult or impossible to restore forest ecosystems and soil productivity. Moreover, the driving forces, which are predominantly of a demographic and socioeconomic nature, do not yet seem to be lessening in strength. It can only be hoped that a wise policy of international cooperation and shared aims can cope with this problem in the future.

Sign in / Sign up

Export Citation Format

Share Document