scholarly journals Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici

2021 ◽  
Vol 7 (10) ◽  
Author(s):  
Nikhil Kumar Singh ◽  
Petteri Karisto ◽  
Daniel Croll
Keyword(s):  
Fungal Pathogens ◽  
Population Level ◽  
Growing Season ◽  
Stable Gene ◽  
Gene Pools ◽  
Effective Population ◽  
Zymoseptoria Tritici ◽  
Wheat Field ◽  
Global Food Security ◽  
Significant Difference

Pathogens cause significant challenges to global food security. On annual crops, pathogens must re-infect from environmental sources in every growing season. Fungal pathogens have evolved mixed reproductive strategies to cope with the distinct challenges of colonizing growing plants. However, how pathogen diversity evolves during growing seasons remains largely unknown. Here, we performed a deep hierarchical sampling in a single experimental wheat field infected by the major fungal pathogen Zymoseptoria tritici. We analysed whole genome sequences of 177 isolates collected from 12 distinct cultivars replicated in space at three time points of the growing season to maximize capture of genetic diversity. The field population was highly diverse with 37 SNPs per kilobase, a linkage disequilibrium decay within 200–700 bp and a high effective population size. Using experimental infections, we tested a subset of the collected isolates on the dominant cultivar planted in the field. However, we found no significant difference in virulence of isolates collected from the same cultivar compared to isolates collected on other cultivars. About 20 % of the isolate genotypes were grouped into 15 clonal groups. Pairs of clones were disproportionally found at short distances (<5 m), consistent with experimental estimates for per-generation dispersal distances performed in the same field. This confirms predominant leaf-to-leaf transmission during the growing season. Surprisingly, levels of clonality did not increase over time in the field although reproduction is thought to be exclusively asexual during the growing season. Our study shows that the pathogen establishes vast and stable gene pools in single fields. Monitoring short-term evolutionary changes in crop pathogens will inform more durable strategies to contain diseases.

scholarly journals Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici

2020 ◽  
Author(s):  
Nikhil Kumar Singh ◽  
Emilie Chanclud ◽  
Daniel Croll
Keyword(s):  
Fungal Pathogens ◽  
Population Level ◽  
Genotypic Diversity ◽  
Growing Season ◽  
Diversity Indices ◽  
Stable Gene ◽  
Gene Pools ◽  
Zymoseptoria Tritici ◽  
Wheat Field ◽  
Global Food Security

AbstractPathogens can rapidly surmount crop resistance challenging global food security. On annual crops, pathogens must re-infect from environmental sources at the beginning of every growing season. Fungal pathogens evolved mixed reproductive strategies to cope with the distinct life cycle challenges of colonizing plants, spreading within fields and ultimately producing propagules for survival in winter. However, how genotypic diversity evolves over this period remains largely unknown. Here, we performed a deep hierarchical sampling in a single experimental wheat field infected by the major fungal pathogen Zymoseptoria tritici. We analyzed whole genome sequences of 177 isolates collected from twelve distinct cultivars replicated in space at three time points of the growing season. The field population was highly diverse with 37 SNPs per kilobase and a linkage disequilibrium decay within 200-700 bp. We found that ~20% of the individual isolates were grouping into 15 clonal groups. Pairs of clones were disproportionally found at short distance (<5m) but a low degree of dispersal occurred also at the scale of the entire field consistent with a predominant leaf-to-leaf dispersal. We found no association of wheat cultivars and clonal genotypes with the exception of one cultivar. Surprisingly, levels of clonality did not increase over time in the field although reproduction is thought to be exclusively asexual during the growing season. Our study shows that the pathogen establishes vast and stable gene pools in single fields over the growing season. Monitoring short-term evolutionary changes in crop pathogens will inform more durable strategies to contain diseases.Data summaryAll Illumina sequencing datasets are available from the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra). The Supplementary Tables S1-S3 list the exact strain names, collection location, genotype and genetic diversity indices.

Cranial crassicaudiasis in two coastal dolphin species from South Africa is predominantly a disease of immature individuals

2020 ◽  
Vol 139 ◽  
pp. 93-102 ◽  
Author(s):  
MF Van Bressem ◽  
P Duignan ◽  
JA Raga ◽  
K Van Waerebeek ◽  
N Fraijia-Fernández ◽  
...  
Keyword(s):  
South Africa ◽  
Bone Development ◽  
Bottlenose Dolphins ◽  
Fatal Outcome ◽  
Population Level ◽  
Cape Coast ◽  
Osteolytic Lesions ◽  
Immune Mediated ◽  
Significant Difference ◽  
The Difference

Crassicauda spp. (Nematoda) infest the cranial sinuses of several odontocetes, causing diagnostic trabecular osteolytic lesions. We examined skulls of 77 Indian Ocean humpback dolphins Sousa plumbea and 69 Indo-Pacific bottlenose dolphins Tursiops aduncus, caught in bather-protecting nets off KwaZulu-Natal (KZN) from 1970-2017, and skulls of 6 S. plumbea stranded along the southern Cape coast in South Africa from 1963-2002. Prevalence of cranial crassicaudiasis was evaluated according to sex and cranial maturity. Overall, prevalence in S. plumbea and T. aduncus taken off KZN was 13 and 31.9%, respectively. Parasitosis variably affected 1 or more cranial bones (frontal, pterygoid, maxillary and sphenoid). No significant difference was found by gender for either species, allowing sexes to be pooled. However, there was a significant difference in lesion prevalence by age, with immature T. aduncus 4.6 times more likely affected than adults, while for S. plumbea, the difference was 6.5-fold. As severe osteolytic lesions are unlikely to heal without trace, we propose that infection is more likely to have a fatal outcome for immature dolphins, possibly because of incomplete bone development, lower immune competence in clearing parasites or an over-exuberant inflammatory response in concert with parasitic enzymatic erosion. Cranial osteolysis was not observed in mature males (18 S. plumbea, 21 T. aduncus), suggesting potential cohort-linked immune-mediated resistance to infestation. Crassicauda spp. may play a role in the natural mortality of S. plumbea and T. aduncus, but the pathogenesis and population level impact remain unknown.

Household and Population-Level Behavioural Changes Due to COVID-19 Pandemic: A Smart Thermostat Based Comparative Data Analysis

2021 ◽  
Vol 10 (1) ◽  
pp. 1-6
Author(s):  
Kirti Sundar Sahu ◽  
Arlene Oetomo ◽  
Niloofar Jalali ◽  
Plinio P. Morita
Keyword(s):  
Data Analysis ◽  
Population Level ◽  
World Health ◽  
Motion Sensors ◽  
Household Level ◽  
Work From Home ◽  
Significant Difference ◽  
Health Organization ◽  
Smart Thermostat ◽  
The Impact

The World Health Organization declared the coronavirus outbreak as a pandemic on March 11, 2020. To inhibit the spread of COVID-19, governments around the globe, including Canada, have implemented physical distancing and lockdown measures, including a work-from-home policy. Canada in 2020 has developed a 24-Hour Movement Guideline for all ages laying guidance on the ideal amount of physical activity, sedentary behaviour, and sleep (PASS) for an individual in a day. The purpose of this study was to investigate changes on the household and population-level in lifestyle behaviours (PASS) and time spent indoors at the household level, following the implementation of physical distancing protocols and stay-at-home guidelines. For this study, we used 2019 and 2020 data from ecobee, a Canadian smart Wi-Fi thermostat company, through the Donate Your Data (DYD) program. Using motion sensors data, we quantified the amount of sleep by using the absence of movement, and similarly, increased sensor activation to show a longer duration of household occupancy. The key findings of this study were; during the COVID-19 pandemic, overall household-level activity increased significantly compared to pre-pandemic times, there was no significant difference between household-level behaviours between weekdays and weekends during the pandemic, average sleep duration has not changed, but the pattern of sleep behaviour significantly changed, specifically, bedtime and wake up time delayed, indoor time spent has been increased and outdoor time significantly reduced. Our data analysis shows the feasibility of using big data to monitor the impact of the COVID-19 pandemic on the household and population-level behaviours and patterns of change.

scholarly journals Health state of the citizens of Nothern Kosovska Mitrovica

2010 ◽  
Vol 138 (11-12) ◽  
pp. 746-751
Author(s):  
Momcilo Mirkovic ◽  
Snezana Simic ◽  
Jelena Marinkovic ◽  
Sladjana Djuric
Keyword(s):  
Health Survey ◽  
Health Assessment ◽  
Population Level ◽  
Cross Sectional Study ◽  
Health Condition ◽  
Health State ◽  
Cross Sectional ◽  
Significance Level ◽  
Self Rated Health ◽  
Significant Difference

Introduction. For health assessment, beside the data of routine health statistics, it is necessary to include and data obtained by a health survey of the citizens. Objective. The aim of this study was to establish how northern Kosovska Mitrovica adults assess their health and which diseases are most common among the population, as well as to investigate differences in relation to demographic and socioeconomic characteristics, the characteristics of social interaction and health behavior and habits. Methods. The research was conducted as a cross-sectional study conducted on the representative sample of adult citizens in northern Kosovska Mitrovica in 2006. Two hundred-eighteen respondents were included in the survey. In the research we used a questionnaire identical to the Health Survey conducted in Serbia in 2006. The significance of differences in responses about self-rated health and chronic diseases in relation to the characteristics of respondents? responses were determined by X2-test with the significance level of 0.05. Results. Over half of the respondents (54.7%) assessed their health condition as good or very good. There was a significant difference in self-rated health in relation to the respondents? age (?2=202.036; p=0.000), education (?2=72.412; p=0.000), social support (?2=12.416; p=0.015), smoking (?2=11.675; p=0.020) and physical activity (?2=61.842; p=0.000). The leading health problems among the respondents were high blood pressure, rheumatologic diseases of joints, ulcer of the duodenal or gastric ulcer, gall bladder disease and high blood fat. Conclusion. Adult residents of northern Kosovska Mitrovica assessed their health as better than the residents of Serbia without Kosovo and Metohia. The diseases in which stress plays the major role among etiological factors are in the leading position. The obtained data on the population level of specific areas represent the basis in the planning of health education and health promotion activities.

scholarly journals dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

2014 ◽  
Author(s):  
Jonathan Puritz ◽  
Christopher M. Hollenbeck ◽  
John R. Gold
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Variant Calling ◽  
Population Level ◽  
Model Organisms ◽  
Effective Population ◽  
Reduction Techniques ◽  
Indel Polymorphisms ◽  
Indel Calling ◽  
Population Sizes

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for organisms with large effective population sizes and high levels of genetic polymorphism but for which no genomic resources exist. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is most likely due to the fact that dDocent quality trims instead of filtering and incorporates both forward and reverse reads in assembly, mapping, and SNP calling, thus enabling use of reads with Indel polymorphisms. The pipeline and a comprehensive user guide can be found at (http://dDocent.wordpress.com).

scholarly journals Medical Sciences’ Students Responses During the Late Phase of the COVID-19 Pandemic in Iran: A Comprehensive Investigation of the Risk Perception and Information Exposure

2021 ◽  
Author(s):  
Mahan Shafie ◽  
Mahsa Mayeli ◽  
Hamed Hosseini ◽  
Mahnaz Ashoorkhani
Keyword(s):  
Risk Perception ◽  
Perceived Risk ◽  
Late Phase ◽  
Population Level ◽  
Sources Of Information ◽  
Medical Sciences ◽  
Online Questionnaire ◽  
Significant Difference ◽  
Information Exposure ◽  
Risk Patients

COVID-19 pandemic obligated applying population-level behavioral modifications to effectively prevent the spread of the disease. This necessitated investigating those measures that determine population behavior. Herein we have studied risk perception and information exposure that are among those determinants in Iran. 402 cases from medical sciences students were enrolled during the last week of September 2020. Using an online questionnaire, risk perception and sources of information about COVID-19 were investigated. Although most students considered COVID-19 preventable, merely a few considered the disease curable. A higher risk was perceived concerning the families compared to themselves. Moreover, most of them believed the prognosis good even in high-risk patients. Social media was the most informative source used; however, health professionals were considered the most reliable. The risk perception was equal between those diagnosed with COVID-19 or had a family member diagnosed compared to those without such exposure in most questions. Also, no significant difference was observed in risk perception between those students with serious underlying medical conditions and those without one regarding most items. Lastly, major and grade were the most significant demographic contributors to the risk perception. Moderate risk was perceived overall among the cases in which major and grade were the only remarkable demographic contributors. Unexpectedly, underlying medical history was not significantly correlated with the perceived risk. Lastly, previous COVID-19 exposure merely altered the curability and preventability perception.

scholarly journals A Microbial Fermentation Mixture Reduces Fusarium Head Blight and Promotes Grain Weight but does not impact Septoria tritici blotch

2021 ◽  
Author(s):  
Tony Twamley ◽  
Mark Gaffney ◽  
Angela Feechan
Keyword(s):  
Fusarium Head Blight ◽  
Fungal Pathogens ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Microbial Fermentation ◽  
In Planta ◽  
Head Blight ◽  
Zymoseptoria Tritici ◽  
The Impact

AbstractFusarium graminearum and Zymoseptoria tritici cause economically important diseases of wheat. F. graminearum is one of the primary causal agents of Fusarium head blight (FHB) and Z. tritici is the causal agent of Septoria tritici blotch (STB). Alternative control methods are required in the face of fungicide resistance and EU legislation which seek to cut pesticide use by 2030. Both fungal pathogens have been described as either hemibiotrophs or necrotrophs. A microbial fermentation-based product (MFP) was previously demonstrated to control the biotrophic pathogen powdery mildew, on wheat. Here we investigated if MFP would be effective against the non-biotrophic fungal pathogens of wheat, F. graminearum and Z. tritici. We assessed the impact of MFP on fungal growth, disease control and also evaluated the individual constituent parts of MFP. Antifungal activity towards both pathogens was found in vitro but MFP only significantly decreased disease symptoms of FHB in planta. In addition, MFP was found to improve the grain number and weight, of uninfected and F. graminearum infected wheat heads.

scholarly journals Prospects of practical use of new potatoes state varietal resources in the north-east Forest-Steppe of Ukraine

2019 ◽  
pp. 15-21 ◽  
Author(s):  
N.S. Kozhushko ◽  
M.M. Sakhoshko ◽  
M.G. Bashtovyi ◽  
D.V. Smilyk ◽  
V.I. Avramenko ◽  
...  
Keyword(s):  
Starch Content ◽  
Growing Season ◽  
Potato Production ◽  
Climatic Conditions ◽  
Forest Steppe ◽  
North East ◽  
The North ◽  
Significant Difference ◽  
New Varieties ◽  
Growing Conditions

According to statistic evaluation of the manifestation of signs of the economic suitability of state sort resources of 2019 registration potatoes when growing it in different agro-climatic conditions, a significant advantage of influence of the forest-steppe conditions was determined. Compared to Polesia the increase of yield rose for 4.1 t/ha or 18 % (НІР05 = 2.18, Ffact= 12.65 > F05 = 4.22) and the amount of trade potato for 22.72 ha or 20 % (Ffact = 58.87). There is also a tendency to increase the number of starch from unit of area for – 17 % and the total consumer properties for – 8 %.  However, there is a significant difference in the reduction of storability of products by 45 % and the lack of it’s resistance to macrosporiosis and late blight. It was proved that the yield of varieties for cultivation in the polesia zone by 25.7 % depended on the duration of the growing season (Ffact = 4.14 > F05  = 0.06). The relationship between yield and starch of potatoes in Polesia zone varieties  was determined – 23.6 % and in forest-steppe – 17.3 % and starch collection, respectively, 33.6 % and 28.0 %. The dependence of storability of potato which grew in the polesia zone and in forest-steppe from the amount of starch for 15 % was mathematically proved (Ffact = 2.11 > F05 = 0.17) і 11.3 % (Ffact = 1.52 > F05 = 0.24); the dependence of storability on the duration of the growing season in the Forest-Steppe conditions was confirmed(Ffact = 0.66 > F05  = 0.43). In addition, the 12 % of tasting grade of the Forest-Steppe varieties depended on the starch content amount (Ffact = 1.65 > F05 = 0.22). According to the results of the regression analysis, mathematical models have been developed to predict yields, culinary and consumer properties, and the storability of new potato varieties under different growing conditions. The project of a conveyor for the consumption of fresh product in summer  period with the involvement of varieties of early ripeness in the Forest-Steppe was presented: 80 days after planting – Sanibel, 90 days after planting – Medison, Paroli, 95 days after planting – Bazalia, Bernina, 100 days after planting – Donata, in the Polesia zone ‒ 80 days after planting – Sanibel, 90 days after planting – Paroli, 95 days after planting –Bazalia, 100 days after planting – Medison, Bernina, Donata. By distribution of varieties by predicted high content of phytonutrients there were bred varieties with red skin and creamy flesh – Bazalia and Sanibel, by high content with yellow flesh – Baltic Rosa and moderate content with white flesh – Oleksandrit, Fotynia, Ricarda. Introduction of new varieties with certain high adaptive potential of storability and content of bioactive compounds in potatoes will provide growth of potato production in the conditions of the northeast forest-steppe and increase its competitiveness in the domestic and foreign markets and will solve the problem of year-round consumption of fresh quality products.

No Effect of Soybean Lipoxygenase on Aflatoxin Production in Aspergillus flavus–Inoculated Seeds

2002 ◽  
Vol 65 (12) ◽  
pp. 1984-1987 ◽  
Author(s):  
J. E. MELLON ◽  
P. J. COTTY
Keyword(s):  
Aspergillus Flavus ◽  
Fungal Pathogens ◽  
Seed Viability ◽  
Soybean Seed ◽  
Fungal Growth ◽  
Aflatoxin Production ◽  
Aflatoxin Contamination ◽  
Soybean Seeds ◽  
Heat Treated ◽  
Significant Difference

Soybean lines lacking lipoxygenase (LOX) activity were compared with soybean lines having LOX activity for the ability to support growth and aflatoxin B1 production by the fungal seed pathogen Aspergillus flavus. Whole seeds, broken seeds, and heat-treated (autoclaved) whole seeds were compared. Broken seeds, irrespective of LOX presence, supported excellent fungal growth and the highest aflatoxin levels. Autoclaved whole seeds, with or without LOX, produced good fungal growth and aflatoxin levels approaching those of broken seeds. Whole soybean seeds supported sparse fungal growth and relatively low aflatoxin levels. There was no significant difference in aflatoxin production between whole soybean seeds either with or without LOX, although there did seem to be differences among the cultivars tested. The heat treatment eliminated LOX activity (in LOX+ lines), yet aflatoxin levels did not change substantially from the broken seed treatment. Broken soybean seeds possessed LOX activity (in LOX+ lines) and yet yielded the highest aflatoxin levels. The presence of active LOX did not seem to play the determinant role in the susceptibility of soybean seeds to fungal pathogens. Seed coat integrity and seed viability seem to be more important characteristics in soybean seed resistance to aflatoxin contamination. Soybean seeds lacking LOX seem safe from the threat of increased seed pathogen susceptibility.

Study on Changes of Total Flavonoid Content in Suaeda salsa in Different Months of Growing Season

2014 ◽  
Vol 926-930 ◽  
pp. 1028-1031
Author(s):  
Wei Fang Zhong ◽  
Yue Hong Wang ◽  
Hong Ying Liu ◽  
Jin Hua Feng
Keyword(s):  
Theoretical Basis ◽  
Growing Season ◽  
Total Flavonoid ◽  
Suaeda Salsa ◽  
Uv Spectrophotometry ◽  
Total Flavonoid Content ◽  
Flavonoid Content ◽  
Significant Difference

Objective To investigate the changes of total flavonoid content of Suaeda salsa in different months of growing season, from May to November. Methods UV spectrophotometry was used for determination of the total flavonoid. Results The content of total flavonoid in Suaeda salsa was highest in September (67.75 mg·g-1) and was lowest in May (11.4 mg·g-1).The content was found to increase from May to September, and to decrease from September to November. Conclusion There is significant difference between total flavonoid content in Suaeda salsa from different months, which can be used to provide theoretical basis for harvesting and processing of Suaeda salsa.

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