RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.

Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline.

Single host plant species may harbour more than one species of - a case study on infecting .

The genus is the largest genus of the oomycetes, fungus-like members of the kingdom that also contains amoeboid (e.g., ) and plant-like (e.

High-throughput time series expression profiling of Plasmopara halstedii infecting Helianthus annuus reveals conserved sequence motifs upstream of co-expressed genes.

Downy mildew disease of sunflower, caused by the obligate biotrophic oomycete Plasmopara halstedii, can have significant economic impact on sunflower cultivation. Using high-throughput whole transcriptome sequencing, four developmental phases in 16 time-points of Pl. halstedii infecting Helianthus annuus were investigated.

Tachysterol increases the synthesis of fibroblast growth factor 23 in bone cells.

Tachysterol (T) is a photoisomer of the previtamin D found in UV-B-irradiated foods such as mushrooms or baker's yeast. Due to its structural similarity to vitamin D, we hypothesized that T can affect vitamin D metabolism and in turn, fibroblast growth factor 23 (FGF23), a bone-derived phosphaturic hormone that is transcriptionally regulated by the vitamin D receptor (VDR). Initially, a mouse study was conducted to investigate the bioavailability of T and its impact on vitamin D metabolism and expression.

Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth.

Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread such capacity is across root-colonizing fungi, we surveyed soils in nutrient-limiting habitats using plant baits to look for fungal community changes in response to nutrient conditions.

A Chromosome-Level Genome Assembly of the European Beech () Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs.

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany).

Prevalence, Genetic Structure, and Antifungal Susceptibility of the Species Complex Strains Collected from the Arboreal Niche in Poland.

Fungi belonging to the species complex (CNGSC) are etiological agents of serious and not infrequently fatal infections in both humans and animals. Trees are the main ecological niche and source of potential exposition concerning these pathogens. With regard to epidemiology of cryptococcosis, various surveys were performed worldwide, enabling the establishment of a map of distribution and genetic structure of the arboreal population of the CNGSC.

Ancestral state reconstruction in Peronospora provides further evidence for host jumping as a key element in the diversification of obligate parasites.

Biotrophic plant parasites cause economically important diseases, e.g. downy mildew of grape, powdery mildew of legumes, wheat stripe rust, and wheat bunt.

: more than a node or a foot-shaped basal cell.

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family . Thus, an alternate hypothesis, namely a very broad concept of the genus was proposed. In doing so, however, a significant body of data that supports distinct genera in based on morphology, biology, and phylogeny is disregarded.

A new desert-dwelling oomycete, sp. nov., on () from Iran.

The obligate biotrophic oomycete genus is one of the four major linages of white blister rusts () identified so far. Species of the genus cause white blister rust on numerous genera in the asterids, represented by several phylogenetically distinct genus-specific lineages, most of which still await formal description. Thus, the observation of the species of on the subfamily pointed out to the existence of a hitherto undescribed species.

The Genome of (Brassicaceae) Provides Insights Into the Adaptation to Highly Calcareous Soils.

is widely distributed in temperate Eurasia, but restricted to Ca-rich habitats, predominantly on white Jurassic limestone, which is made up by calcium carbonate, with little other minerals. Thus, naturally occurring individuals are confronted with a high concentration of Ca ions while Mg ion concentration is relatively low. As there is a competitive uptake between these two ions, adaptation to the soil condition can be expected.

A glimpse into the biogeography, seasonality, and ecological functions of arctic marine .

High-latitude environments are warming, leading to changes in biological diversity patterns of taxa. are a group of fungal-like organisms that comprise a major clade of eukaryotic life and are parasites of fish, agricultural crops, and algae. The diversity, functionality, and distribution of these organisms are essentially unknown in the Arctic marine environment.

Holocarpic oomycete parasitoids of red algae are not .

is a genus of obligate holocarpic endobiotic oomycetes. Most of the species classified in the genus are known only from their morphology and life cycle, and a few have been examined for their ultrastructure or molecular phylogeny. However, the taxonomic placement of all sequenced species is provisional, as no sequence data are available for the type species, , to consolidate the taxonomy of species currently placed in the genus.

Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits.

Regulation of gene expression is an important mechanism through which genetic variation can affect complex traits. A substantial portion of gene expression variation can be explained by both local (cis) and distal (trans) genetic variation. Much progress has been made in uncovering cis-acting expression quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate.

Predictors of long-term survival after hip fractures?-5-year results of a prospective study in Germany.

Unlabelled: The incidence of hip fractures is increasing due to demographic transition. Data on long-term survival and influencing factors are sparse. Our prospective observational study with 395 patients shows a survival of 38% after 5 years.

Antimicrobial Resistance and Biofilm Formation in Enterococcus spp. Isolated from Humans and Turkeys in Poland.

Enterococci are a natural component of the intestinal flora of many organisms, including humans and birds. As opportunistic pathogens, they can cause fatal infections of the urinary tract and endocarditis in humans, whereas in poultry symptoms are joint disease, sepsis, and falls in the first week of life. The study covered 107 Enterococcus strains-56 isolated from humans and 51 from turkeys.

Protists are an integral part of the Arabidopsis thaliana microbiome.

Although protists occupy a vast range of habitats and are known to interact with plants among other things via disease suppression, competition or growth stimulation, their contributions to the 'phytobiome' are not well described. To contribute to a more comprehensive picture of the plant holobiont, we examined cercozoan and oomycete taxa living in association with the model plant Arabidopsis thaliana grown in two different soils. Soil, roots, leaves and wooden toothpicks were analysed before and after surface sterilization.

Radiology Case of the Month: TB or Not TB… That is the Question.

45-year-old female presenting initially with fever, nonproductive cough, night sweats, pleuritic chest pain, fatigue and weight loss over the past month.

High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae.

The largest biological surface on earth is formed by plant leaves. These leaf surfaces are colonized by a specialized suite of leaf-inhabiting microorganisms, recently termed "phyllosphere microbiome". Microbial prey, however, attract microbial predators.

The local environment determines the assembly of root endophytic fungi at a continental scale.

Root endophytic fungi are found in a great variety of plants and ecosystems, but the ecological drivers of their biogeographic distribution are poorly understood. Here, we investigate the occurrence of root endophytes in the non-mycorrhizal plant genus Microthlaspi, and the effect of environmental factors and geographic distance in structuring their communities at a continental scale. We sampled 52 plant populations across the northern Mediterranean and central Europe and used a cultivation approach to study their endophytic communities.

Diversity of exophillic acid derivatives in strains of an endophytic Exophiala sp.

Members of the fungal genus Exophiala are common saprobes in soil and water environments, opportunistic pathogens of animals, or endophytes in plant roots. Their ecological versatility could imply a capacity to produce diverse secondary metabolites, but only a few studies have aimed at characterizing their chemical profiles. Here, we assessed the secondary metabolites produced by five Exophiala sp.

Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci.

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA.

A 34-year retrospective study of equine viral abortion in Poland.

The purpose of the present review was a comparison of the abortions caused by EAV and EHV-1 viruses over the 34 years. A total of 452 tissues samples from aborted fetuses (347) or foals (105) stillborn or newborn that died within 72 hours were investigated. The material for the examinations came from different farms located throughout Poland.

Seed transmission of Pseudoperonospora cubensis.

Pseudoperonospora cubensis, an obligate biotrophic oomycete causing devastating foliar disease in species of the Cucurbitaceae family, was never reported in seeds or transmitted by seeds. We now show that P. cubensis occurs in fruits and seeds of downy mildew-infected plants but not in fruits or seeds of healthy plants.