Discovery of a Novel Leaf Rust (Puccinia recondita) Resistance Gene in Rye (Secale cereale L.) Using Association Genomics

Leaf rust constitutes one of the most important foliar diseases in rye (Secale cereale L.). To discover new sources of resistance, we phenotyped 180 lines belonging to a less well-characterized Gulzow germplasm at three field trial locations in Denmark and Northern Germany in 2018 and 2019. We observed lines with high leaf rust resistance efficacy at all locations in both years. A genome-wide association study using 261,406 informative single-nucleotide polymorphisms revealed two genomic regions associated with resistance on chromosome arms 1RS and 7RS, respectively. The most resistance-associated marker on chromosome arm 1RS physically co-localized with molecular markers delimiting Pr3. In the reference genomes Lo7 and Weining, the genomic region associated with resistance on chromosome arm 7RS contained a large number of nucleotide-binding leucine-rich repeat (NLR) genes. Residing in close proximity to the most resistance-associated marker, we identified a cluster of NLRs exhibiting close protein sequence similarity with the wheat leaf rust Lr1 gene situated on chromosome arm 5DL in wheat, which is syntenic to chromosome arm 7RS in rye. Due to the close proximity to the most resistance-associated marker, our findings suggest that the considered leaf rust R gene, provisionally denoted Pr6, could be a Lr1 ortholog in rye

Barberry plays an active role as an alternate host of Puccinia graminis in Spain

Stem rust, caused by Puccinia graminis, is a destructive group of diseases. The pathogen uses Berberis species as alternate hosts to complete its life cycle. B. vulgaris and the endemic species B. hispanica and B. garciae are present in Spain. The objective of this study was to investigate the functionality of the indigenous barberry as alternate hosts. Field surveys were conducted in 2018 and 2019 in Huesca, Teruel and Albacete provinces of Spain. Aecial samples on barberry were analysed via infection assays and DNA analysis. B. garciae was predominant in Huesca and Teruel provinces, often found in the field margins of cereal crops. Aecial infections on B. garciae were observed in May and uredinial infections on cereal crops in June. Scattered B. hispanica bushes were occasionally found near cereal crops in Albacete, where aecial infections on B. hispanica were observed in June when most cereal crops were mature. Infection assays using aeciospores resulted in stem rust infections on susceptible genotypes of wheat, barley, rye and oat, indicating the presence of the sexual cycle for P. graminis f. sp. tritici, f. sp. secalis and f. sp. avenae. Sequence analyses from aecial samples supported this finding as well as the presence of Puccinia brachypodii. This study provides the first evidence that indigenous Berberis species play an active role in the sexual cycle of P. graminis under natural conditions in Spain

p3d – Python module for structural bioinformatics

<p>Abstract</p> <p>Background</p> <p>High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code.</p> <p>Results</p> <p>p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures.</p> <p>Conclusion</p> <p>p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.</p

Wheat Stem Rust Back in Europe: Diversity, Prevalence and Impact on Host Resistance

The objective of this study was to investigate the re-emergence of a previously important crop pathogen in Europe, Puccinia graminis f.sp. tritici, causing wheat stem rust. The pathogen has been insignificant in Europe for more than 60 years, but since 2016 it has caused epidemics on both durum wheat and bread wheat in local areas in southern Europe, and additional outbreaks in Central- and West Europe. The prevalence of three distinct genotypes/races in many areas, Clade III-B (TTRTF), Clade IV-B (TKTTF) and Clade IV-F (TKKTF), suggested clonal reproduction and evolution by mutation within these. None of these genetic groups and races, which likely originated from exotic incursions, were detected in Europe prior to 2016. A fourth genetic group, Clade VIII, detected in Germany (2013), was observed in several years in Central- and East Europe. Tests of representative European wheat varieties with prevalent races revealed high level of susceptibility. In contrast, high diversity with respect to virulence and Simple Sequence Repeat (SSR) markers were detected in local populations on cereals and grasses in proximity to Berberis species in Spain and Sweden, indicating that the alternate host may return as functional component of the epidemiology of wheat stem rust in Europe. A geographically distant population from Omsk and Novosibirsk in western Siberia (Russia) also revealed high genetic diversity, but clearly different from current European populations. The presence of Sr31-virulence in multiple and highly diverse races in local populations in Spain and Siberia stress that virulence may emerge independently when large geographical areas and time spans are considered and that Sr31-virulence is not unique to Ug99. All isolates of the Spanish populations, collected from wheat, rye and grass species, were succesfully recovered on wheat, which underline the plasticity of host barriers within P. graminis. The study demonstrated successful alignment of two genotyping approaches and race phenotyping methodologies employed by different laboratories, which also allowed us to line up with previous European and international studies of wheat stem rust. Our results suggest new initiatives within disease surveillance, epidemiological research and resistance breeding to meet current and future challenges by wheat stem rust in Europe and beyond.info:eu-repo/semantics/publishedVersio

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

BACKGROUND: Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. RESULTS: To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. CONCLUSIONS: Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens

Pathotype variation of barley powdery mildew in Western Australia

Barley powdery mildew caused by the fungus Blumeria graminis f. sp. hordei (Bgh) has emerged as the most damaging disease of barley in Western Australia (WA). Many of the available cultivars display high levels of disease in the field when climatic conditions are conducive. As a result, fungicides have become the main method of disease control in the last 10 years. Different types and sources of genetic disease resistance are available but to optimise their deployment it is necessary to evaluate the spectrum of pathotypes present in the pathogen population. Sixty isolates of Bgh were collected in the 2009 season from 9 locations, single spored and characterised by infection on reference barley lines and cultivars. Eighteen unique pathotypes were resolved. Virulence against many of the R-genes in the reference lines was present in at least one pathotype. Isolates were virulent against 16 out of a total of 23 resistance gene combinations. Undefeated resistance genes included the major R-genes Mla-6, Mla-9, Ml-ra and the combinations of Mla-1 plus Mla-A12 and Mla-6 plus Mla-14 and Mla-13 plus Ml-Ru3 together with the recessive resistance gene mlo-5. There was significant pathotype spatial differentiation suggesting limited gene flow between different regions with WA or localised selection pressures and proliferation. On the basis of the results we recommend a number of strategies to manage powdery mildew disease levels within WA

Fabrication of Massive Sheets of Single Layer Patterned Arrays Using Lipid Directed Reengineered Phi29 Motor Dodecamer

The bottom-up assembly of patterned arrays is an exciting and important area in current nanotechnology. Arrays can be engineered to serve as components in chips for a virtually inexhaustible list of applications ranging from disease diagnosis to ultra-high-density data storage. Phi29 motor dodecamer has been reported to form elegant multilayer tetragonal arrays. However, multilayer protein arrays are of limited use for nanotechnological applications which demand nanoreplica or coating technologies. The ability to produce a single layer array of biological structures with high replication fidelity represents a significant advance in the area of nanomimetics. In this paper, we report on the assembly of single layer sheets of reengineered phi29 motor dodecamer. A thin lipid monolayer was used to direct the assembly of massive sheets of single layer patterned arrays of the reengineered motor dodecamer. Uniform, clean and highly ordered arrays were constructed as shown by both transmission electron microscopy and atomic force microscopy imaging

Deciphering the Preference and Predicting the Viability of Circular Permutations in Proteins

Circular permutation (CP) refers to situations in which the termini of a protein are relocated to other positions in the structure. CP occurs naturally and has been artificially created to study protein function, stability and folding. Recently CP is increasingly applied to engineer enzyme structure and function, and to create bifunctional fusion proteins unachievable by tandem fusion. CP is a complicated and expensive technique. An intrinsic difficulty in its application lies in the fact that not every position in a protein is amenable for creating a viable permutant. To examine the preferences of CP and develop CP viability prediction methods, we carried out comprehensive analyses of the sequence, structural, and dynamical properties of known CP sites using a variety of statistics and simulation methods, such as the bootstrap aggregating, permutation test and molecular dynamics simulations. CP particularly favors Gly, Pro, Asp and Asn. Positions preferred by CP lie within coils, loops, turns, and at residues that are exposed to solvent, weakly hydrogen-bonded, environmentally unpacked, or flexible. Disfavored positions include Cys, bulky hydrophobic residues, and residues located within helices or near the protein's core. These results fostered the development of an effective viable CP site prediction system, which combined four machine learning methods, e.g., artificial neural networks, the support vector machine, a random forest, and a hierarchical feature integration procedure developed in this work. As assessed by using the hydrofolate reductase dataset as the independent evaluation dataset, this prediction system achieved an AUC of 0.9. Large-scale predictions have been performed for nine thousand representative protein structures; several new potential applications of CP were thus identified. Many unreported preferences of CP are revealed in this study. The developed system is the best CP viability prediction method currently available. This work will facilitate the application of CP in research and biotechnology

Updated Iberian archeomagnetic catalogue: new full vector paleosecular variation curve for the last three millennia

In this work, we present 16 directional and 27 intensity high‐quality values from Iberia. Moreover, we have updated the Iberian archeomagnetic catalogue published more than 10 years ago with a considerable increase in the database. This has led to a notable improvement of both temporal and spatial data distribution. A full vector paleosecular variation curve from 1000 BC to 1900 AD has been developed using high‐quality data within a radius of 900 km from Madrid. A hierarchical bootstrap method has been followed for the computation of the curves. The most remarkable feature of the new curves is a notable intensity maximum of about 80 μT around 600 BC, which has not been previously reported for the Iberian Peninsula. We have also analyzed the evolution of the paleofield in Europe for the last three thousand years and conclude that the high maximum intensity values observed around 600 BC in the Iberian Peninsula could respond to the same feature as the Levantine Iron Age Anomaly, after travelling westward through Europe

Unravelling surface and interfacial structures of a metal–organic framework by transmission electron microscopy

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules