Summary: Recent studies have questioned the use of high‐throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi‐quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS‐like fragments of varying lengths and guanine‐cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under‐represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.

Background: Several challenges, e.g. global trade, population growth, and climate change create future challenges for food production and food safety. In order to meet this, we need to secure and increase agricultural production with minimal environmental impact. Potato (Solanum tuberosum) ranks as one of the world’s most important crops for human consumption. While potato production and consumption have decreased in Europe and North America, global production has grown in the last decades due to the expansion of potato consumption in Asia. Potato is vulnerable to a wide range of pathogenic organisms, all of which can cause severe quality and yield losses. As a consequence, potato production is highly reliant on pesticide use, and this has a negative effect on the sustainability of the crop. To mitigate these problems, effective and evidence based crop protection recommendations need to be provided to growers. Methods and output: The overarching aim of this project is to support the development of better methods of integrated pest management (IPM), as well as to identify alternative control methods for potato diseases to contribute to effective plant protection solutions and a more sustainable potato production. The specific objective of this systematic map is to provide a worldwide overview of plant disease protection measures available for potato production. All methods to control diseases within different cropping systems will be considered, such as pesticide application, biological control methods, resistant cultivars as well as disease support systems and tools for diagnosis. The systematic map will be presented as a searchable database where the volume and main characteristics of the relevant scientific literature will be described. We will identify evidence clusters and knowledge gaps in potato disease management and identify future research areas, and in this way contribute to new and innovative solutions. The map will provide important information and support for researchers and stakeholders, in particular authorities and advisory organizations. It will also help to select topics for future systematic reviews and meta-studies within potato research.

Predicting fungal community assembly is partly limited by our understanding of the factors driving the composition of deposited spores. We studied the relative contribution of vegetation, geographical distance, seasonality and weather to fungal spore deposition across three vegetation types. Active and passive spore traps were established in agricultural fields, deciduous forests and coniferous forests across a geographic gradient of ∼600 km. Active traps captured the spore community suspended in air, reflecting the potential deposition, whereas passive traps reflected realized deposition. Fungal species were identified by metabarcoding of the ITS2 region. The composition of spore communities captured by passive traps differed more between vegetation types than across regions separated by >100 km, indicating that vegetation type was the strongest driver of composition of deposited spores. By contrast, vegetation contributed less to potential deposition, which followed a seasonal pattern. Within the same site, the spore communities captured by active traps differed from those captured by passive traps. Realized deposition tended to be dominated by spores of species related to vegetation. Temperature was negatively correlated with the fungal species richness of both potential and realized deposition. Our results indicate that vegetation may be able to maintain similar fungal communities across distances, and likely be the driving factor of fungal spore deposition at landscape level.

Puccinia graminis, the causal agent of stem rust, was collected from its alternate host barberry (Berberis spp.) and two different uredinial hosts, oats (Avena sativa) and rye (Secale cereale). The samples were analyzed using 11 polymorphic simple sequence repeat (SSR) markers. There were large differences between fungal populations on oats (P. graminis f. sp. avenae) and rye (P. graminis f. sp. secalis), and the genetic variation within the different formae speciales was also high. It was possible to distinguish between the two formae speciales on barberry. Additional genotypic groups not present in the field samples from oats and rye were also identified on barberry. Our results confirm the importance of barberry in maintaining the populations of P. graminis in Sweden and the importance of the sexual stage for the survival of the pathogen.

Barberry (Berberis spp.) hosts the aecial stage of several rust species, including Puccinia graminis, which causes stem rust on grasses and cereals. The aecial stage of this pathogen has received less attention because it is not as economically important compared with the uredinial and telial stages. The main objective of this study was to identify and describe the rust species that were found on Berberis spp. collected in different parts of Sweden. A morphological study, including spore measurements and aecia descriptions, was conducted, as well as DNA sequence analyses (using the internal transcribed spacer region and the EF1-α gene). Based on spore and aecia morphology as well as the genetic analyses, three different taxa could be distinguished on barberry: P. graminis f. sp. avenae, P. graminis f. sp. tritci/secalis, and P. arrhenatheri. The genetic analysis revealed little or no differentiation between P. graminis f. sp. tritici and P. graminis f. sp. secalis and, thus, this group of samples was denominated P. graminis f. sp. tritici/secalis. Aecial morphology may be used to differentiate between different taxa. In particular, examination of aecial cross-sections may be used to distinguish between P. graminis f. sp. avenae and P. graminis f. sp. tritici/secalis. A clear differentiation in the mode of growth on barberry was also found; P. arrhenatheri always appeared systemic whereas P. graminis always appeared localized.