Genome-based discovery of polyketide-derived secondary metabolism pathways in the barley pathogen <i>Ramularia collo-cygni</i>

Ramularia collo-cygni causes Ramularia leaf spot (RLS) disease of barley. The fungus develops asymptomatically within its host until late in the growing season, when necrotic lesions become visible on upper leaves. Fungal secondary metabolites (SM) have been proposed as important factors in RLS lesion formation but the biosynthetic pathways involved remain largely unknown. Mining the R. collo-cygni genome revealed the presence of 10 polyketide synthases (PKS), 10 nonribosomal peptide synthetases (NRPS), and 3 hybrid PKS-NRPS (HPS) identified within clusters of genes with predicted functions associated with secondary metabolism. SM core genes along with their predicted transcriptional regulators exhibited transcriptional coexpression during infection of barley plants. Moreover, their expression peaked during early stages of host colonization and preceded or overlapped with the appearance of disease symptoms, suggesting that SM may manipulate the host to promote colonization or protect R. collo-cygni from competing organisms. Accordingly, R. collo-cygni inhibited the growth of several fungi in vitro, indicating that it synthesized and excreted antifungal agents. Taken together, these findings demonstrate that the R. collo-cygni genome contains the genetic architecture to synthesize a wide range of SM and suggests that coexpression of PKS and HPS is associated with competitive colonization of the host and early symptom development. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . </jats:p

The contributions of biodiversity to the sustainable intensification of food production:Thematic Study to support the State of the World’s Biodiversity for Food and Agriculture

Biodiversity supports sustainable food production, although recognition of its roles has been relatively neglected in the sustainable intensification literature. In the current study, the roles of biodiversity in sustainable food production are considered, assessing how these roles can be measured, the current state of knowledge and opportunities for intervention. The trajectory of global food production, and the challenges and opportunities this presents for the roles of biodiversity in production, are also considered, as well as how biodiversitybased interventions fit within wider considerations for sustainable food systems. The positive interactions between a diverse array of organisms, including annual crops, animal pollinators, trees, micro-organisms, livestock and aquatic animals, support food production globally. To support these interactions, a range of interventions related to access to materials and practices are required. For annual crops, major interventions include breeding crops for more positive crop–crop interactions, and the integration of a wider range of crops into production systems. For animal pollinators, major interventions include the introduction of pollinator populations into production landscapes and the protection and improvement of pollinator habitat. For trees, a major required intervention is the greater integration of perennial legumes into farmland. For micro-organisms, the implementation of agronomic practices that support beneficial crop-microbe interactions is crucial. For livestock production, breed and crop feedstock diversification are essential, and the implementation of improved methods for manure incorporation into cropland. Finally, in the case of aquatic production, it is essential to support the wider adoption of multi-trophic production systems and to diversify crop- and animal-based feed resources. These and other interventions, and the research needs around them, are discussed. Looking to the future, understanding the drivers behind trends in food systems is essential for determining the options for biodiversity in supporting sustainable food production. The increased dominance of a narrow selection of foods globally indicates that efforts to more sustainably produce these foods are crucial. From a biodiversity perspective, this means placing a strong emphasis on breeding for resource use efficiency and adaptation to climate change. It also means challenging the dominance of these foods through focusing on productivity improvements for other crop, livestock and aquaculture species, so that they can compete successfully and find space within production systems. New biodiversity-based models that support food production need not only to be productive but to be profitable. Thus, as well as describing appropriate production system management practices that enhance production and support the environment, the labour, knowledge, time required to operationalize, and other costs of new production approaches, must be considered and minimized. To support the future roles of biodiversity in sustainable food production, we recommend that particular attention be given to the longitudinal analysis of food sectors to determine how the diversity of foods consumed from these sectors has changed over time. Analysis is already available for crops, but related research is needed for livestock and aquaculture sectors. This analysis will then support more optimal cross-sectoral interactions, in terms of the contributions each sector provides to supplying the different components of human diets. Additional meta-analyses and synthetic reviews of case studies are required as an evidence base for biodiversity-based food production system interventions, but future studies should pay more attention to articulating the potential biases in case study compilation (the problem of ‘cherry picking’ positive examples) and the measures that have been taken to minimize such effects

Using Chloroplast trnF Pseudogenes for Phylogeography in Arabidopsis Lyrata

The chloroplast trnL-F region has been extensively utilized for evolutionary analysis in plants. In the Brassicaceae this fragment contains 1–12 tandemly repeated trnF pseudogene copies in addition to the functional trnF gene. Here we assessed the potential of these highly variable, but complexly evolving duplications, to resolve the population history of the model plant Arabidopsis lyrata. While the region 5’ of the duplications had negligible sequence diversity, extensive variation in pseudogene copy number and nucleotide composition revealed otherwise cryptic population structure in eastern North America. Thus structural changes can be phylogeographically informative when pseudogene evolutionary relationships can be resolved

Data from: Planting exotic relatives has increased the threat posed by Dothistroma septosporum to the Caledonian pine populations of Scotland

To manage emerging forest diseases and prevent their occurrence in the future, it is essential to determine the origin(s) of the pathogens involved and identify the management practices that have ultimately caused disease problems. One such practice is the widespread planting of exotic tree species within the range of related native taxa. This can lead to emerging forest disease both by facilitating introduction of exotic pathogens, and by providing susceptible hosts on which epidemics of native pathogens can develop. We used microsatellite markers to determine the origins of the pathogen Dothistroma septosporum responsible for the current outbreak of Dothistroma needle blight (DNB) on native Caledonian Scots pine (Pinus sylvestris) populations in Scotland, and evaluated the role played by widespread planting of two exotic pine species in the development of the disease outbreak. We distinguished three races of D. septosporum in Scotland, one of low genetic diversity associated with introduced lodgepole pine (Pinus contorta), one of high diversity probably derived from the DNB epidemic on introduced Corsican pine (Pinus nigra subsp. laricio) in England, and a third of intermediate diversity apparently endemic on Caledonian Scots pine. These races differed for both growth rate and exudate production in culture. Planting of exotic pine stands in the UK appears to have facilitated the introduction of two exotic races of D. septosporum into Scotland which now pose a threat to native Caledonian pines both directly and through potential hybridisation and introgression with the endemic race. Our results indicate that both removal of exotic species from the vicinity of Caledonian pine populations, and restriction of movement of planting material are required to minimise the impact of the current DNB outbreak. They also demonstrate that planting exotic species that are related to native species reduces rather than enhances the resilience of forests to pathogens

Correction: Tedder, A. et al. Using chloroplast trnF pseudogenes for phylogeography in Arabidopsis lyrata. Diversity 2010, 2, 653-678

In the original version of our article [1], insufficient acknowledgement was given for the source of some of the DNA samples used. We apologize for the original error. To correct this oversight, Yvonne Willi has been added as an author, a recent paper by Willi, Y. et al. (2010) has been added, the acknowledgements have been altered to more appropriately recognize support and funding, and the sources of samples collected have been corrected in Table 1. [...

Inbreeding depression in self-incompatible North-American Arabidopsis lyrata : disentangling genomic and S-locus-specific genetic load

Newly formed selfing lineages may express recessive genetic load and suffer inbreeding depression. This can have a genome-wide genetic basis, or be due to loci linked to genes under balancing selection. Understanding the genetic architecture of inbreeding depression is important in the context of the maintenance of self-incompatibility and understanding the evolutionary dynamics of S-alleles. We addressed this using North-American subspecies of Arabidopsis lyrata. This species is normally self-incompatible and outcrossing, but some populations have undergone a transition to selfing. The goals of this study were to: (1) quantify the strength of inbreeding depression in North-American populations of A. lyrata; and (2) disentangle the relative contribution of S-linked genetic load compared with overall inbreeding depression. We enforced selfing in self-incompatible plants with known S-locus genotype by treatment with CO2, and compared the performance of selfed vs outcrossed progeny. We found significant inbreeding depression for germination rate (δ 0.33), survival rate to 4 weeks (δ 0.45) and early growth (δ 0.07), but not for flowering rate. For two out of four S-alleles in our design, we detected significant S-linked load reflected by an under-representation of S-locus homozygotes in selfed progeny. The presence or absence of S-linked load could not be explained by the dominance level of S-alleles. Instead, the random nature of the mutation process may explain differences in the recessive deleterious load among lineages

Comparative analysis of Argentinian and European populations of<i> Ramularia collo‐cygni</i> on barley

Ramularia collo‐cygni (Rcc) is a major barley pathogen that causes yield and grain quality losses worldwide. The main sources of Rcc inoculum are the seed and asexual airborne spores. In Argentina, Rcc is considered to be an emerging threat to barley crops, especially as most varieties are susceptible to Rcc and have a European genetic background. Here, we describe the population genetic diversity and structure of the Argentinian Rcc population, based on 10 simple‐sequence repeat (SSR) markers, in order to compare it with Rcc populations from the Czech Republic and Scotland. The Argentinian Rcc population showed lower genetic diversity, higher level of structuring and higher number of clonal isolates than European populations. Significant differentiation at population origin (country) and region (Europe and South America) level suggests the occurrence of a genetic bottleneck and/or a founder effect on Rcc entry to Argentina and that this population could still be in a state of establishment and emergence. Further research on Rcc genetic structure at local and global scale will be crucial for the understanding of Rcc population dynamics for disease management

Data from: Planting exotic relatives has increased the threat posed by Dothistroma septosporum to the Caledonian pine populations of Scotland

To manage emerging forest diseases and prevent their occurrence in the future, it is essential to determine the origin(s) of the pathogens involved and identify the management practices that have ultimately caused disease problems. One such practice is the widespread planting of exotic tree species within the range of related native taxa. This can lead to emerging forest disease both by facilitating introduction of exotic pathogens, and by providing susceptible hosts on which epidemics of native pathogens can develop. We used microsatellite markers to determine the origins of the pathogen Dothistroma septosporum responsible for the current outbreak of Dothistroma needle blight (DNB) on native Caledonian Scots pine (Pinus sylvestris) populations in Scotland, and evaluated the role played by widespread planting of two exotic pine species in the development of the disease outbreak. We distinguished three races of D. septosporum in Scotland, one of low genetic diversity associated with introduced lodgepole pine (Pinus contorta), one of high diversity probably derived from the DNB epidemic on introduced Corsican pine (Pinus nigra subsp. laricio) in England, and a third of intermediate diversity apparently endemic on Caledonian Scots pine. These races differed for both growth rate and exudate production in culture. Planting of exotic pine stands in the UK appears to have facilitated the introduction of two exotic races of D. septosporum into Scotland which now pose a threat to native Caledonian pines both directly and through potential hybridisation and introgression with the endemic race. Our results indicate that both removal of exotic species from the vicinity of Caledonian pine populations, and restriction of movement of planting material are required to minimise the impact of the current DNB outbreak. They also demonstrate that planting exotic species that are related to native species reduces rather than enhances the resilience of forests to pathogens