Host Adaptation Through Hybridization: Genome Analysis of Triticale Powdery Mildew Reveals Unique Combination of Lineage-Specific Effectors

The emergence of new fungal pathogens through hybridization represents a serious challenge for agriculture. Hybridization between the wheat mildew (Blumeria graminis f. sp. tritici) and rye mildew (B. graminis f. sp. secalis) pathogens has led to the emergence of a new mildew form (B. graminis f. sp. triticale) growing on triticale, a man-made amphiploid crop derived from crossing rye and wheat, which was originally resistant to the powdery mildew disease. The identification of the genetic basis of host adaptation in triticale mildew has been hampered by the lack of a reference genome. Here, we report the 141.4-Mb reference assembly of triticale mildew isolate THUN-12 derived from long-read sequencing and genetic map-based scaffolding. All 11 triticale mildew chromosomes were assembled from telomere-to-telomere and revealed that 19.7% of the hybrid genome was inherited from the rye mildew parental lineage. We identified lineage-specific regions in the hybrid, inherited from the rye or wheat mildew parental lineages, that harbor numerous bona fide candidate effectors. We propose that the combination of lineage-specific effectors in the hybrid genome is crucial for host adaptation, allowing the fungus to simultaneously circumvent the immune systems contributed by wheat and rye in the triticale crop. In line with this, we demonstrate the functional transfer of the SvrPm3 effector from wheat to triticale mildew, a virulence effector that specifically suppresses resistance of the wheat Pm3 allelic series. This transfer is the likely underlying cause for the observed poor effectiveness of several Pm3 alleles against triticale mildew and exemplifies the negative implications of pathogen hybridizations on resistance breeding. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license

The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen

Background: Worldwide wheat production is under constant threat by fast-evolving fungal pathogens. In the last decades, wheat breeding for disease resistance heavily relied on the introgression of chromosomal segments from related species as genetic sources of new resistance. The Pm8 resistance gene against the powdery mildew disease has been introgressed from rye into wheat as part of a large 1BL.1RS chromosomal translocation encompassing multiple disease resistance genes and yield components. Due to its high agronomic value, this translocation has seen continuous global use since the 1960s on large growth areas, even after Pm8 resistance was overcome by the powdery mildew pathogen. The long-term use of Pm8 at a global scale provided the unique opportunity to study the consequences of such extensive resistance gene application on pathogen evolution. Results: Using genome-wide association studies in a population of wheat mildew isolates, we identified the avirulence effector AvrPm8 specifically recognized by Pm8. Haplovariant mining in a global mildew population covering all major wheat growing areas of the world revealed 17 virulent haplotypes of the AvrPm8 gene that grouped into two functional categories. The first one comprised amino acid polymorphisms at a single position along the AvrPm8 protein, which we confirmed to be crucial for the recognition by Pm8. The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame such as disruptions of the start codon, gene truncations, gene deletions, and interference with mRNA splicing. With the exception of a single, likely ancient, gain-of-virulence mutation found in mildew isolates around the world, all AvrPm8 virulence haplotypes were found in geographically restricted regions, indicating that they occurred recently as a consequence of the frequent Pm8 use. Conclusions: In this study, we show that the broad and prolonged use of the Pm8 gene in wheat production worldwide resulted in a multitude of gain-of-virulence mechanisms affecting the AvrPm8 gene in the wheat powdery mildew pathogen. Based on our findings, we conclude that both standing genetic variation as well as locally occurring new mutations contributed to the global breakdown of the Pm8 resistance gene introgression

Recent Experimental Tests of Special Relativity

We review our recent Michelson-Morley (MM) and Kennedy-Thorndike (KT) experiment, which tests Lorentz invariance in the photon sector, and report first results of our ongoing atomic clock test of Lorentz invariance in the matter sector. The MM-KT experiment compares a cryogenic microwave resonator to a hydrogen maser, and has set the most stringent limit on a number of parameters in alternative theories to special relativity. We also report first results of a test of Lorentz invariance in the SME (Standard Model Extension) matter sector, using Zeeman transitions in a laser cooled Cs atomic fountain clock. We describe the experiment together with the theoretical model and analysis. Recent experimental results are presented and we give a first estimate of components of the $\tilde{c}^p$ parameters of the SME matter sector. A full analysis of systematic effects is still in progress, and will be the subject of a future publication together with our final results. If confirmed, the present limits would correspond to first ever measurements of some $\tilde{c}^p$ components, and improvements by 11 and 14 orders of magnitude on others.Comment: 29 pages. Contribution to Springer Lecture Notes, "Special Relativity - Will it survive the next 100 years ?", Proceedings, Potsdam, 200

The Transitional Stripped-Envelope SN 2008ax: Spectral Evolution and Evidence for Large Asphericity

Supernova (SN) 2008ax in NGC 4490 was discovered within hours after shock breakout, presenting the rare opportunity to study a core-collapse SN beginning with the initial envelope-cooling phase immediately following shock breakout. We present an extensive sequence of optical and near-infrared spectra, as well as three epochs of optical spectropolarimetry. Our initial spectra, taken two days after shock breakout, are dominated by hydrogen Balmer lines at high velocity. However, by maximum light, He I lines dominated the optical and near-infrared spectra, which closely resembled those of normal Type Ib supernovae (SNe Ib) such as SN 1999ex. This spectroscopic transition defines Type IIb supernovae, but the strong similarity of SN 2008ax to normal SNe Ib beginning near maximum light, including an absorption feature near 6270A due to H-alpha at high velocities, suggests that many objects classified as SNe Ib in the literature may have ejected similar amounts of hydrogen as SN 2008ax, roughly a few x 0.01 M_sun. Early-time spectropolarimetry (6 and 9 days after shock breakout) revealed strong line polarization modulations of 3.4% across H-alpha, indicating the presence of large asphericities in the outer ejecta. The continuum shares a common polarization angle with the hydrogen, helium, and oxygen lines, while the calcium and iron absorptions are oriented at different angles. This is clear evidence of deviations from axisymmetry even in the outer ejecta. Intrinsic continuum polarization of 0.64% only nine days after shock breakout shows that the outer layers of the ejecta were quite aspherical. A single epoch of late-time spectropolarimetry, as well as the shapes of the nebular line profiles, demonstrate that asphericities extended from the outermost layers all the way down to the center of this SN. [Abridged]Comment: 24 pages, 21 figures, 4 tables, appendix, minor revisions to match version accepted by Ap

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable-a phenomenon that remains poorly understood, as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used quantitative trait locus (QTL) mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of reoccurring gene conversion events and are members of a mildew sublineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sublineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangling complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations become an integral part of introgression breeding to ensure effective and durable resistance in wheat

Deciphering the Biology of \u3ci\u3eCryptophyllachora eurasiatica\u3c/i\u3e gen. et sp. nov., an Often Cryptic Pathogen of an Allergenic Weed, \u3ci\u3eAmbrosia artemisiifolia\u3c/i\u3e

A little known, unculturable ascomycete, referred to as Phyllachora ambrosiae, can destroy the inflorescences of Ambrosia artemisiifolia, an invasive agricultural weed and producer of highly allergenic pollen. The fungus often remains undetectable in ragweed populations. This work was conducted to understand its origin and pathogenesis, a prerequisite to consider its potential as a biocontrol agent. The methods used included light and transmission electron microscopy, nrDNA sequencing, phylogenetic analyses, artificial inoculations, and the examination of old herbarium and recent field specimens from Hungary, Korea, Ukraine and USA. The Eurasian and the North American specimens of this fungus were to represent two distinct, although closely related lineages that were only distantly related to other lineages within the Ascomycota. Consequently, we describe a new genus that includes Cryptophyllachora eurasiatica gen. et sp. nov. and C. ambrosiae comb. nov., respectively. The pathogenesis of C. eurasiaticawas shown in A. artemisiifolia. No evidence was found for either seed-borne transmission or systemic infection. Two hypotheses were developed to explain the interaction between C. eurasiatica and A. artemisiifolia: (i) as yet undetected seed-borne transmissions and latent, systemic infections; or (ii) alternative hosts

Time variation of the fine structure constant in the early universe and the Bekenstein model

We calculate bounds on the variation of the fine structure constant at the time of primordial nucleosynthesis and at the time of neutral hydrogen formation. We use these bounds and other bounds from the late universe to test Bekenstein model. We modify the Kawano code, CAMB and CosmoMC in order to include the possible variation of the fine structure constant. We use observational primordial abundances of \De, \He and \Li, recent data from the Cosmic Microwave Background and the 2dFGRS power spectrum, to obtain bounds on the variation of $\alpha$. We calculate a piecewise solution to the scalar field equation of Bekenstein model in two different regimes; i) matter and radiation, ii) matter and cosmological constant. We match both solutions with appropriate boundary conditions. We perform a statistical analysis using the bounds obtained from the early universe and other bounds from the late universe to constrain the free parameters of the model. Results are consistent with no variation of $\alpha$ in the early universe. Limits on $\alpha$ are inconsistent with the scale length of the theory $l$ being larger than Planck scale. In order to fit all observational and experimental data, the assumption $l>L_p$ implied in Bekenstein's model has to be relaxed.Comment: 13 pages, 8 figures,version accepted to be published in Astronomy and Astrophysic

Serological evidence of influenza a viruses in frugivorous bats from Africa

Bats are likely natural hosts for a range of zoonotic viruses such as Marburg, Ebola, Rabies, as well as for various Corona- and Paramyxoviruses. In 2009/10, researchers discovered RNA of two novel influenza virus subtypes - H17N10 and H18N11 - in Central and South American fruit bats. The identification of bats as possible additional reservoir for influenza A viruses raises questions about the role of this mammalian taxon in influenza A virus ecology and possible public health relevance. As molecular testing can be limited by a short time window in which the virus is present, serological testing provides information about past infections and virus spread in populations after the virus has been cleared. This study aimed at screening available sera from 100 free-ranging, frugivorous bats (Eidolon helvum) sampled in 2009/10 in Ghana, for the presence of antibodies against the complete panel of influenza A haemagglutinin (HA) types ranging from H1 to H18 by means of a protein microarray platform. This technique enables simultaneous serological testing against multiple recombinant HA-types in 5μl of serum. Preliminary results indicate serological evidence against avian influenza subtype H9 in about 30% of the animals screened, with low-level cross-reactivity to phylogenetically closely related subtypes H8 and H12. To our knowledge, this is the first report of serological evidence of influenza A viruses other than H17 and H18 in bats. As avian influenza subtype H9 is associated with human infections, the implications of our findings from

Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade

The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, Sotiropoulos et al. analyze a global sample of 172 mildew genomes, providing evidence that humans drove global spread of the pathogen throughout history and that mildew rapidly evolved through hybridization with local fungal strains.The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global sample of 172 mildew genomes. Our analyses show that B.g. tritici emerged in the Fertile Crescent during wheat domestication. After it spread throughout Eurasia, colonization brought it to America, where it hybridized with unknown grass mildew species. Recent trade brought USA strains to Japan, and European strains to China. In both places, they hybridized with local ancestral strains. Thus, although mildew spreads by wind regionally, our results indicate that humans drove its global spread throughout history and that mildew rapidly evolved through hybridization

Monocyte mitochondrial dysfunction, inflammaging, and inflammatory pyroptosis in major depression

BACKGROUND: The macrophage theory of depression states that macrophages play an important role in Major Depressive Disorder (MDD). METHODS: MDD patients (N = 140) and healthy controls (N = 120) participated in a cross-sectional study investigating the expression of apoptosis/growth and lipid/cholesterol pathway genes (BAX, BCL10, EGR1, EGR2, HB-EGF, NR1H3, ABCA1, ABCG1, MVK, CD163, HMOX1) in monocytes (macrophage/microglia precursors). Gene expressions were correlated to a set of previously determined and reported inflammation-regulating genes and analyzed with respect to various clinical parameters. RESULTS: MDD monocytes showed an overexpression of the apoptosis/growth/cholesterol and the TNF genes forming an inter-correlating gene cluster (cluster 3) separate from the previously described inflammation-related gene clusters (containing IL1 and IL6). While upregulation of monocyte gene cluster 3 was a hallmark of monocytes of all MDD patients, upregulation of the inflammation-related clusters was confirmed to be found only in the monocytes of patients with childhood adversity. The latter group also showed a downregulation of the cholesterol metabolism gene MVK, which is known to play an important role in trained immunity and proneness to inflammation. CONCLUSIONS: The upregulation of cluster 3 genes in monocytes of all MDD patients suggests a premature aging of the cells, i.e. mitochondrial apoptotic dysfunction and TNF "inflammaging", as a general feature of MDD. The overexpression of the IL-1/IL-6 containing inflammation clusters and the downregulation of MVK in monocytes of patients with childhood adversity indicates a shift in this condition to a more severe inflammation form (pyroptosis) of the cells, additional to the signs of premature aging and inflammaging