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.

Cultures as types and the utility of viable specimens for fungal nomenclature.

The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi.

- A New Species of from the East Fjords of Iceland.

There is increasing evidence that holocarpic oomycetes, i.e., those converting their entire vegetative thallus into zoospores upon maturation, are a phylogenetically diverse group in both freshwater and marine ecosystems.

Adding a missing piece to the puzzle of oomycete phylogeny: the placement of ().

Oomycetes are a group of fungus-like organisms, which phylogenetically comprise early diverging lineages that are mostly holocarpic, and two crown classes, the and , including many well-investigated pathogens of plants and animals. However, there is a poorly studied group, the , which placement amongst the crown oomycetes is ambiguous. It accommodates several taxa with a sophisticated vegetative and reproductive cycle, as well as structural organisation, that is arguably the most complex in the oomycete lineage.

and evidence for a novel clade of endobiotic pollen-infecting "lagenidiaceous" .

The genus () contains three species (), and a single variety ( var. ) of obligate endobiotic pollen parasites. These organisms have been first assigned to the green alga genus , as they form very similar spherical structures, but the observation of heterokont zoospores has led to their reclassification to the phylum .

Small-spored Alternaria spp. (section Alternaria) are common pathogens on wild tomato species.

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus.

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.

Evaluating natural medicinal resources and their exposure to global change.

Medicinal plants and their bioactive molecules are integral components of nature and have supported the health of human societies for millennia. However, the prevailing view of medicinal biodiversity solely as an ecosystem-decoupled natural resource of commercial value prevents people from fully benefiting from the capacity of nature to provide medicines and from assessing the vulnerability of this capacity to the global environmental crisis. Emerging scientific and technological developments and traditional knowledge allow for appreciating medicinal plant resources from a planetary health perspective.

: a new species of from Iceland, and report of a co-cultivation system for studying oomycete-diatom interactions.

The genus represents an early-diverging lineage of diatom-parasitic , straminipilous eukaryotes that have evolved fungal features independent from the opisthokont . Recent studies have revealed that diatom parasitoids are much more species-rich than previously thought and may play an important role in limnic and marine ecosystems. Of the different diatom-parasitic lineages, the genus is one of the most abundant in marine ecosystems.

Pontisma blauvikense sp. nov. the first member of the early-diverging oomycete genus Pontisma parasitizing brown algae.

Holocarpic oomycetes have been neglected over several decades, until interest in these organisms has recently resurged. One of the most widespread genera of holocarpic oomycetes is Pontisma, parasitic to red seaweeds throughout all oceans. Recently, the genus Sirolpidium (parasitic to green algae) was found to be congeneric with Pontisma.

species causing downy mildew diseases of , including nomenclature revisions and diagnostic resources.

Downy mildew pathogens of graminicolous hosts () are members of eight morphologically and phylogenetically distinct genera in the ( ). Graminicolous downy mildews (GDMs) cause severe losses in crops such as maize, millets, sorghum, and sugarcane in many parts of the world, especially in tropical climates. In countries where the most destructive GDMs are not endemic, these organisms are often designated as high-risk foreign pathogens and subject to oversight and quarantine by regulatory officials.

and allied fusarioid taxa (FUSA). 1.

Seven species complexes are treated, namely species complex (FASC) (two species), species complex (FBSC) (five species), species complex (FBURSC) (three species), species complex (FCAMSC) (three species), species complex (FCSC) (eight species), species complex (FCCSC) (five species) and the species complex (FCOSC) (four species). New species include from soil (Zimbabwe), and from soil associated with (Netherlands). New combinations include and Newly validated taxa include , , , and .

High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens.

Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, , encountered a recent genome expansion. Using long reads, we assembled genomes of 6 strains and 3 sister species, to study this genome expansion.

Miracula einbuarlaekurica sp. nov., a new holocarpic endoparasitoid species from pennate freshwater diatoms in Iceland.

Holocarpic oomycetes infecting freshwater diatoms are obligate endobiotic parasites reported from a wide range of habitats. So far, the taxonomy of and phylogeny of most species remains unresolved, since most have not been reported throughout the past decades and sequence data are available for only the four species, , and the recently-discovered species . In the current study, a new freshwater diatom parasite resembling in the sense of Scherffel was discovered from pennate diatoms () collected from the small stream Einbúalækur on Víkurskarð, North Iceland and investigated for its life cycle and phylogenetic placement.

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.

Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis.

Tilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming.

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).

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.

Complete Chloroplast Genomes of L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs.

Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution.

A New Marine Species of () Parasitic to sp. in Iceland.

Obligate endoparasitic oomycetes are known to ubiquitously occur in marine and freshwater diatoms, but their diversity is still largely unexplored. Many of these parasitoids are members of the early-diverging oomycete lineages (, ), others are within the of the (, ) and some have been described in the (, ). Even though some species have been recently described and two new genera were introduced ( and ), the phylogeny and taxonomy of most of these organisms remain unresolved.

: 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.