Composition of the microbiomes from spinach seeds infested or non-infested with Peronospora effusa or Verticillium dahliae

The worldwide distribution of plant seeds can disseminate beneficial and plant pathogenic microorganisms. This phenomenon is of particular concern where seed production is geographically isolated from crop production, as is the case with spinach in the United States. We aimed to characterize the structure and function of spinach seed microbiomes in commercial spinach seed lots originating from Europe and New Zealand. The seed lots we analyzed were infested with Peronospora effusa and Verticillium dahliae, only infested with V. dahliae, or not infested with either of these pathogens. The microbial taxonomic composition and gene function (assessed by Gene Ontology (GO) terms) of spinach seeds were highly influenced by geographic origin and the status of pathogen infestation. Through taxonomic profiling, we found that potentially plant beneficial bacterial genera such as Pseudomonas and Pantoea were the most abundant taxa both in infested and non-infested seeds, and Stenotrophomonas was observed in seed lots infested with P. effusa and V. dahliae. Many potential plant pathogens that are not known to be associated with spinach seed were also discovered by metagenomic analysis, including Sclerotinia sclerotiorum, Botrytis cinerea, Bipolaris sorokiniana, Fusarium pseudograminearum, Alternaria brassicae, Parastagonospora nodorum, and Pyrenophora teres f. teres. Our analysis of the function of prokaryotic genes in de novo assembled metagenomes revealed distinct GO terms associated with the geographic origin of seed lots. This work provides an important first step toward identifying spinach seed-borne microorganisms that could be utilized to improve plant health and plant pathogens that could be inadvertently carried to new locations.

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Sources of Verticillium dahliae Affecting Lettuce

Phytopathology ◽

10.1094/phyto-04-12-0067-r ◽

2012 ◽

Vol 102 (11) ◽

pp. 1071-1078 ◽

Cited By ~ 14

Author(s):

Zahi K. Atallah ◽

Karunakaran Maruthachalam ◽

Krishna V. Subbarao

Keyword(s):

United States ◽

Population Structure ◽

Verticillium Wilt ◽

Verticillium Dahliae ◽

Crop Production ◽

The United States ◽

Lettuce Seed ◽

Disease Epidemiology ◽

Santa Clara Valley ◽

The Impact

Since 1995, lettuce in coastal California, where more than half of the crop in North America is grown, has consistently suffered from severe outbreaks of Verticillium wilt. The disease is confined to this region, although the pathogen (Verticillium dahliae) and the host are present in other crop production regions in California. Migration of the pathogen with infested spinach seed was previously documented, but the geographic sources of the pathogen, as well as the impact of lettuce seed sparsely infested with V. dahliae produced outside coastal California on the pathogen population in coastal California remain unclear. Population analyses of V. dahliae were completed using 16 microsatellite markers on isolates from lettuce plants in coastal California, infested lettuce seed produced in the neighboring Santa Clara Valley of California, and spinach seed produced in four major spinach seed production regions: Chile, Denmark, the Netherlands, and the United States (Washington State). California produces 80% of spinach in the United States and all seed planted with the majority infested by V. dahliae comes from the above four sources. Three globally distributed genetic populations were identified, indicating sustained migration among these distinct geographic regions with multiple spinach crops produced each year and repeated every year in coastal California. The population structure of V. dahliae from coastal California lettuce plants was heavily influenced by migration from spinach seed imported from Denmark and Washington. Conversely, the sparsely infested lettuce seed had limited or no contribution to the Verticillium wilt epidemic in coastal California. The global trade in plant and seed material is likely contributing to sustained shifts in the population structure of V. dahliae, affecting the equilibrium of native populations, and likely affecting disease epidemiology.

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Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems

BMC Biology ◽

10.1186/s12915-021-01061-w ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Jie-Yin Chen ◽

Dan-Dan Zhang ◽

Jin-Qun Huang ◽

Ran Li ◽

Dan Wang ◽

...

Keyword(s):

Transcriptional Regulation ◽

Verticillium Dahliae ◽

Plant Pathogens ◽

Population Genomics ◽

De Novo ◽

Sequence Divergence ◽

Parental Genome ◽

Nucleotide Polymorphisms ◽

Agricultural Ecosystems ◽

Race 1

Abstract Background Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment. Results In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation. Conclusions Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.

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De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

Genes ◽

10.3390/genes12071017 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1017

Author(s):

Mohammed Bakkali ◽

Rubén Martín-Blázquez ◽

Mercedes Ruiz-Estévez ◽

Manuel A. Garrido-Ramos

Keyword(s):

Functional Annotation ◽

Vascular Plants ◽

De Novo ◽

Transcriptome Assembly ◽

Systematic Position ◽

Important Data ◽

Ecological Requirements ◽

Physiological Adaptations ◽

Fern Species ◽

Go Terms

We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.

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A Bibliometric Insight of Genetic Factors in ASD: Emerging Trends and New Developments

Brain Sciences ◽

10.3390/brainsci11010033 ◽

2020 ◽

Vol 11 (1) ◽

pp. 33

Author(s):

Kang Wang ◽

Weicheng Duan ◽

Yijie Duan ◽

Yuxin Yu ◽

Xiuyi Chen ◽

...

Keyword(s):

Genetic Factors ◽

De Novo ◽

Rapid Development ◽

The United States ◽

Research Area ◽

Scientific Output ◽

Autism Spectrum ◽

De Novo Mutations ◽

Emerging Trends ◽

Genetic Abnormalities

Autism spectrum disorder (ASD) cases have increased rapidly in recent decades, which is associated with various genetic abnormalities. To provide a better understanding of the genetic factors in ASD, we assessed the global scientific output of the related studies. A total of 2944 studies published between 1997 and 2018 were included by systematic retrieval from the Web of Science (WoS) database, whose scientific landscapes were drawn and the tendencies and research frontiers were explored through bibliometric methods. The United States has been acting as a leading explorer of the field worldwide in recent years. The rapid development of high-throughput technologies and bioinformatics transferred the research method from the traditional classic method to a big data-based pipeline. As a consequence, the focused research area and tendency were also changed, as the contribution of de novo mutations in ASD has been a research hotspot in the past several years and probably will remain one into the near future, which is consistent with the current opinions of the major etiology of ASD. Therefore, more attention and financial support should be paid to the deciphering of the de novo mutations in ASD. Meanwhile, the effective cooperation of multi-research centers and scientists in different fields should be advocated in the next step of scientific research undertaken.

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Prevalence of systemic lupus erythematosus in Spain: higher than previously reported in other countries?

Rheumatology ◽

10.1093/rheumatology/kez668 ◽

2020 ◽

Vol 59 (9) ◽

pp. 2556-2562 ◽

Cited By ~ 4

Author(s):

Raúl Cortés Verdú ◽

José M Pego-Reigosa ◽

Daniel Seoane-Mato ◽

Mercedes Morcillo Valle ◽

Deseada Palma Sánchez ◽

...

Keyword(s):

Lupus Erythematosus ◽

Adult Population ◽

Geographical Area ◽

Geographic Origin ◽

The United States ◽

Epidemiological Studies ◽

Population Based ◽

Cross Sectional Study ◽

Medical Visit ◽

Cross Sectional

Abstract Objectives Prevalence of SLE varies among studies, being influenced by study design, geographical area and ethnicity. Data about the prevalence of SLE in Spain are scarce. In the EPISER2016 study, promoted by the Spanish Society of Rheumatology, the prevalence estimate of SLE in the general adult population in Spain has been updated and its association with sociodemographic, anthropometric and lifestyle variables has been explored. Methods Population-based multicentre cross-sectional study, with multistage stratified and cluster random sampling. Participants were contacted by telephone to carry out a questionnaire for the screening of SLE. Investigating rheumatologists evaluated positive results (review of medical records and/or telephone interview, with medical visit if needed) to confirm the diagnosis. To calculate the prevalence and its 95% CI, the sample design was taken into account and weighing was calculated considering age, sex and geographic origin. Multivariate logistic regression models were defined to analyse which sociodemographic, anthropometric and lifestyle variables included in the telephone questionnaire were associated with the presence of SLE. Results 4916 subjects aged 20 years or over were included. 16.52% (812/4916) had a positive screening result for SLE. 12 cases of SLE were detected. The estimated prevalence was 0.21% (95% CI: 0.11, 0.40). SLE was more prevalent in the rural municipalities, with an odds ratio (OR) = 4.041 (95% CI: 1.216, 13.424). Conclusion The estimated prevalence of SLE in Spain is higher than that described in most international epidemiological studies, but lower than that observed in ethnic minorities in the United States or the United Kingdom.

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Assessing the Phytosanitary Risk Posed by an Intraspecific Invasion of Cryphonectria parasitica in Europe

Phytopathology ◽

10.1094/phyto-06-19-0197-r ◽

2019 ◽

Vol 109 (12) ◽

pp. 2055-2063 ◽

Cited By ~ 3

Author(s):

Francesca Dennert ◽

Joana Beatrice Meyer ◽

Daniel Rigling ◽

Simone Prospero

Keyword(s):

United States ◽

South Korea ◽

Plant Pathogens ◽

Castanea Sativa ◽

The United States ◽

Cryphonectria Parasitica ◽

Seedling Mortality ◽

New Host ◽

Phytosanitary Measures

Intraspecific cryptic invasions may occur when new strains of an invasive species are introduced into an area where this species had already been introduced previously. In plant pathogens, such invasions are not well studied, even if, potentially, they can have severe consequences. Here, we investigated the effects of a potential intraspecific invasion in Europe of Cryphonectria parasitica, the causal agent of chestnut blight. Specifically, we tested the hypotheses that (i) non-European strains are more virulent on Castanea sativa than those already present in Europe because they have never encountered this new host, and (ii) the variation in virulence among strains is higher within native than within introduced populations. In a greenhouse, 2-year-old C. sativa seedlings were inoculated with Cryphonectria parasitica strains from South Korea, the United States, and Switzerland, and lesion development and seedling mortality were recorded weekly. Additionally, growth and sporulation of the strains were measured in vitro on agar medium at 15 and 24°C. Although lesion growth was similar for all strains, seedlings inoculated with strains from South Korea and Switzerland died faster than seedlings inoculated with strains from the United States. Moreover, in vitro strains from South Korea grew faster and produced more spores at both temperatures than the strains from the other two countries. In conclusion, our results did not support the two hypotheses. All strains, regardless of their origin, were found to be highly virulent on the inoculated chestnut seedlings. Nevertheless, current phytosanitary measures to avoid the introduction of new genotypes of C. parasitica into Europe should be further implemented.

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Limited Genetic Diversity in North American Isolates of Phytophthora erythroseptica Pathogenic to Potato Based on RAPD Analysis

Plant Disease ◽

10.1094/pd-89-0380 ◽

2005 ◽

Vol 89 (4) ◽

pp. 380-384 ◽

Cited By ~ 10

Author(s):

Rick D. Peters ◽

Rod J. Clark ◽

Albert D. Coffin ◽

Antony V. Sturz ◽

David H. Lambert ◽

...

Keyword(s):

Genetic Diversity ◽

North America ◽

New Brunswick ◽

Prince Edward Island ◽

Random Amplified Polymorphic Dna ◽

Geographic Origin ◽

The United States ◽

Vitro Assay ◽

Phytophthora Erythroseptica

Pink rot of potato (Solanum tuberosum), caused by Phytophthora erythroseptica, is found wherever potatoes are grown, and in the last decade, it has reemerged as an economically important disease in Canada and the United States. A selection of isolates of P. erythroseptica from major potato-growing regions in North America, namely Prince Edward Island and New Brunswick, Canada, and Maine and Idaho, U.S.A., was assessed for genetic diversity with randomly chosen decanucleotide primers which were used to amplify regions of DNA to reveal polymorphisms among templates (random amplified polymorphic DNA [RAPD]). The isolates varied in their geographic origin as well as in their sensitivity to mefenoxam, as determined by an in vitro assay. In three separate RAPD screens (I, II, and III) with 23 isolates of P. erythroseptica chosen from a larger collection, 1,410, 369, and 316 robust, scorable bands were amplified, respectively. However, among the bands amplified in screens I, II, and III, only 3, 1, and 3 bands, respectively, were polymorphic. When three primers yielding polymorphisms were used to screen 106 isolates from Prince Edward Island and New Brunswick, or a representative collection of 32 isolates from Prince Edward Island, New Brunswick, Maine, and Idaho, no major variation was discovered. RAPD markers were not correlated with geographic origin or mefenoxam sensitivity of the isolates. From an evolutionary standpoint, the absence of genetic diversity among the isolates of P. erythroseptica we examined may be attributable to the relatively recent introduction of a small founding population of the pathogen in North America.

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Key Insights and Research Prospects at the Dawn of the Population Genomics Era for Verticillium dahliae

Annual Review of Phytopathology ◽

10.1146/annurev-phyto-020620-121925 ◽

2021 ◽

Vol 59 (1) ◽

Author(s):

Jie-Yin Chen ◽

Steven J. Klosterman ◽

Xiao-Ping Hu ◽

Xiao-Feng Dai ◽

Krishna V. Subbarao

Keyword(s):

Population Structure ◽

Verticillium Dahliae ◽

Plant Pathogens ◽

Population Genomics ◽

Population Divergence ◽

Annual Review ◽

Publication Date ◽

Disease Symptoms ◽

Historical Perspectives ◽

Characteristic Features

The genomics era has ushered in exciting possibilities to examine the genetic bases that undergird the characteristic features of Verticillium dahliae and other plant pathogens. In this review, we provide historical perspectives on some of the salient biological characteristics of V. dahliae, including its morphology, microsclerotia formation, host range, disease symptoms, vascular niche, reproduction, and population structure. The kaleidoscopic population structure of this pathogen is summarized, including different races of the pathogen, defoliating and nondefoliating phenotypes, vegetative compatibility groupings, and clonal populations. Where possible, we place the characteristic differences in the context of comparative and functional genomics analyses that have offered insights into population divergence within V. dahliae and the related species. Current challenges are highlighted along with some suggested future population genomics studies that will contribute to advancing our understanding of the population divergence in V. dahliae. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Growing climatic sensitivity of U.S. agriculture linked to technological change and regional specialization

Science Advances ◽

10.1126/sciadv.aat4343 ◽

2018 ◽

Vol 4 (12) ◽

pp. eaat4343 ◽

Cited By ~ 23

Author(s):

Ariel Ortiz-Bobea ◽

Erwin Knippenberg ◽

Robert G. Chambers

Keyword(s):

Climate Change ◽

Crop Production ◽

Agricultural Sector ◽

State Level ◽

The United States ◽

Climate Data ◽

Specialty Crops ◽

Regional Specialization ◽

Vulnerability To Climate Change ◽

Climatic Sensitivity

A pressing question for climate change adaptation is whether ongoing transformations of the agricultural sector affect its ability to cope with climatic variations. We examine this question in the United States, where major increases in productivity have fueled most of agricultural production growth over the past half-century. To quantify the evolving climate sensitivity of the sector and identify its sources, we combine state-level measures of agricultural productivity with detailed climate data for 1960–2004. We find that agriculture is growing more sensitive to climate in Midwestern states for two distinct but compounding reasons: a rising climatic sensitivity of nonirrigated cereal and oilseed crops and a growing specialization in crop production. In contrast, other regions specialize in less climate-sensitive production such as irrigated specialty crops or livestock. Results suggest that reducing vulnerability to climate change should consider the role of policies in inducing regional specialization.

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A review of the biology and ecology of Florida beggarweed (Desmodium tortuosum)

Weed Science ◽

10.1614/ws-03-028r ◽

2004 ◽

Vol 52 (2) ◽

pp. 185-200 ◽

Cited By ~ 7

Author(s):

Theodore M. Webster ◽

John Cardina

Keyword(s):

United States ◽

Plant Pathogens ◽

Cultural Practices ◽

The United States ◽

Western Hemisphere ◽

Southern United States ◽

Southeast United States ◽

Forage Crop ◽

Disturbed Areas ◽

The World

Florida beggarweed is native to the Western Hemisphere but is naturalized around the world. During the last century, the mechanization of agriculture has transitioned Florida beggarweed from an important forage component to a weed of significance in the coastal plain of the southeast United States. This herbaceous annual is naturalized and found in fields and disturbed areas throughout the southern United States. The characteristics that made Florida beggarweed a good forage crop also make it a formidable weed. This review describes the importance of Florida beggarweed as a weed in the southern United States and the taxonomy of this species and details the distribution throughout the world and within the United States. The ecology of Florida beggarweed and its interactions with crop plants, insects, nematodes, and plant pathogens also are summarized. Finally, management of Florida beggarweed in agricultural systems using cultural practices and herbicides is reviewed.

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