Population Structure of Peronospora effusa in the Southwestern United States

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales

Complementation of CTB7 in the maize pathogen Cercospora zeina overcomes the lack of in vitro Cercosporin production

Gray leaf spot (GLS), caused by the sibling species Cercospora zeina or Cercospora zeae-maydis, is cited as one of the most important diseases threatening global maize production. C. zeina fails to produce cercosporin in vitro and, in most cases, causes large coalescing lesions during maize infection, a symptom generally absent from cercosporin-deficient mutants in other Cercospora spp. Here, we describe the C. zeina cercosporin toxin biosynthetic (CTB) gene cluster. The oxidoreductase gene CTB7 contained several insertions and deletions as compared with the C. zeae-maydis ortholog. We set out to determine whether complementing the defective CTB7 gene with the full-length gene from C. zeae-maydis could confer in vitro cercosporin production. C. zeina transformants containing C. zeae-maydis CTB7 were generated by Agrobacterium tumefaciens–mediated transformation and were evaluated for in vitro cercosporin production. When grown on nitrogen-limited medium in the light—conditions conducive to cercosporin production in other Cercospora spp.—one transformant accumulated a red pigment that was confirmed to be cercosporin by the KOH assay, thin-layer chromatography, and ultra performance liquid chromatography-quadrupole-time-of-flight mass spectrometry. Our results indicated that C. zeina has a defective CTB7, but all other necessary machinery required for synthesizing cercosporin-like molecules and, thus, C. zeina may produce a structural variant of cercosporin during maize infection.The National Research Foundation (NRF), Genomics Research Institute of University of Pretoria (UP), United States Department of Agriculture Norman E. Borlaug International Agricultural Science and Technology Fellowship.http://apsjournals.apsnet.org/loi/mpmihj2017Forestry and Agricultural Biotechnology Institute (FABI)Plant Production and Soil Scienc

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicolawas sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed “mesosynteny” is very different from synteny seen between other organisms. A surprising feature of the M. graminicolagenome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors

Planetary system around the nearby M dwarf GJ 357 including a transiting, hot, Earth-sized planet optimal for atmospheric characterization

We report the detection of a transiting Earth-size planet around GJ 357, a nearby M2.5 V star, using data from the Transiting Exoplanet Survey Satellite (TESS). GJ 357 b (TOI-562.01) is a transiting, hot, Earth-sized planet (Teq = 525 ± 11 K) with a radius of Rb = 1.217 ± 0.084 R⊕ and an orbital period of Pb = 3.93 d. Precise stellar radial velocities from CARMENES and PFS, as well as archival data from HIRES, UVES, and HARPS also display a 3.93-day periodicity, confirming the planetary nature and leading to a planetary mass of Mb = 1.84 ± 0.31 M⊕. In addition to the radial velocity signal for GJ 357 b, more periodicities are present in the data indicating the presence of two further planets in the system: GJ 357 c, with a minimum mass of Mc = 3.40 ± 0.46 M⊕ in a 9.12 d orbit, and GJ 357 d, with a minimum mass of Md = 6.1 ± 1.0 M⊕ in a 55.7 d orbit inside the habitable zone. The host is relatively inactive and exhibits a photometric rotation period of Prot = 78 ± 2 d. GJ 357 b isto date the second closest transiting planet to the Sun, making it a prime target for further investigations such as transmission spectroscopy. Therefore, GJ 357 b represents one of the best terrestrial planets suitable for atmospheric characterization with the upcoming JWST and ground-based ELTs

Proceedings of the 46th Annual Meeting of the Southern Soybean Disease Workers (March 6-7, 2019, Pensacola Beach, Florida)

Contents List of SSDW Officers Agenda for March 6-7, 2019 Abstracts for presented/contributed papers Evaluating phytotoxicity in response to fungicide by adjuvant combinations. TW Allen and TH Wilkerson Effect of delayed harvest on the seed quality of commercial soybean cultivars. JC Rupe, JA Rojas, R Holland, SR Segalin, RD Bond, and JA Still Virome of Macrophomina phaseolina isolates collected from soybean fields in Mississippi. Nina Aboughanem-Sabanadzovic, Tessie Wilkerson, Tom Allen, and Sead Sabanadzovic Genomic evidence for interspecific hybridization in Cercospora cf. flagellaris strains associated with Cercospora leaf blight of soybean. Alex Zaccaron, Kona Swift, Ahmad Fakhoury, and Burt Bluhm Identification of QoI-resistant Septoria glycines isolates. DL Neves, A Wang, JD Weems, DS Mueller, HM Kelly, and CA Bradley Genome-wide polymorphic microsatellite markers in Phytophthora sojae. Guohong Cai, Tomara J. Fleury, and Ning Zhang Identifying soybean varietal resistance to Cercospora leaf blight and describing a leaf disk assay for rapid resistance screening. Brian Ward, Paul Price III, and Thanos Gentimis Early detection of soybean sudden death syndrome using high-resolution satellite imagery. Muhammad Mohsin Raza, Sharon K. Eggenberger, Forrest W. Nutter, Jr., and Leonor F. Leandro Nematodes population distribution and densities as affected by soil type and crop rotation in Tennessee row crops. Rufus Akinrinlola and Heather Kelly The effects of Soybean vein necrosis virus (Bunyaviridae: Tospovirus) on soybean (Glycine max) yield. Rachel Guyer, Larissa Visioli, and Heather Kelly Has Cercospora kikuchii vanished in the U.S.? Comparative genomics provides new clues. Burt Bluhm, Alex Zaccaron, Kona Swift, and Ahmad Fakhoury Student papers Evaluation of field soils collected from the Mid-southern United States for differences in soybean cyst nematode egg density and reproduction. EG Roberts, A Howland, C Meinhardt, TW Allen, TR Faske, PP Price, TN Spurlock, MG Mitchum, and KM Bissonnette Soybean variety response to Xylaria sp., causal agent of taproot decline. Myra A. Purvis, Trey Price, Tom Allen, and Terry Spurlock Identification of alternative hosts for Xylaria sp., the pathogen of taproot decline of soybean. HR Becton, T Wilkerson, TW Allen, and M Tomaso-Peterson Functional genomics in Phomopsis longicolla as a tool to dissect Phomopsis seed decay at the molecular level. Marcio Zaccaron, John Ridenour, Alex Zaccaron, John Rupe, and Burt Bluhm Taxonomic diversity of Diaporthe species associated with soybean in Arkansas. Fakhir Al-Shuwaili, Marcio Zaccaron, John Rupe, and Burt Bluhm Wilting response of soybean leaves to culture filtrates of Corynespora cassiicola isolates from cotton and soybean. MN Rondon and KS Lawrence Analysis of systemic resistance caused by Bacillus sp. in Meloidogyne incognita infested Glycine max. K Gattoni, N Xiang, BR Lawaju, JW Kloepper and KS Lawrence Determining the role of new soybean germplasm in reducing losses associated with poor quality grain in Mississippi soybean. J Fomba, M Tomaso-Peterson, TW Allen, D Cook, R Smith, S Li, and TW Wilkerson Abstracts for presented posters Fungicide sensitivity screening for Corynespora cassiicola and field evaluations. Heather Kelly and Ty Smith Impact of seed treatment and seed quality on soybean emergence and yield. SR Segalin, R Holland, and JC Rupe Southern United States Soybean Disease Loss Estimates for 2018. TW Allen, K Bissonnette, CA Bradley, JP Damicone, NS Dufault, TR Faske, T Isakeit, RC Kemerait, A Koehler, HL Mehl, JD Mueller, GB Padgett, PP Price, EJ Sikora, L Thiessen, and H Young Proceedings of the Southern Soybean Disease Workers are published annually by the Southern Soybean Disease Workers. Text, references, figures, and tables are reproduced as they were submitted by authors. The opinions expressed by the participants at this conference are their own and do not necessarily represent those of the Southern Soybean Disease Workers. Mention of a trademark or proprietary products in this publication does not constitute a guarantee, warranty, or endorsement of that product by the Southern Soybean Disease Workers. Appreciation is given to the Bluhm Lab at the University of Arkansas, Fayetteville, AR, for their assistance in assembling these Proceedings

Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene

Background: Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen, Pyrenophora tritici-repentis, a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis, was analyzed in greater detail. Results: These analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by a hAT DNA transposon, all of which were inactivated by RIP, except for the original. In P. fijiensis the original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera Cercospora, Pseudocercospora and Sphaerulina. Conclusions: These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution.Forestry, Faculty ofNon UBCForest and Conservation Sciences, Department ofReviewedFacult

, sp. nov., is an emerging root-associated pathogen responsible for taproot decline of soybean in the southern United States

Taproot decline (TRD) is a disease of soybean that has been reported recently from the southern United States (U.S.). Symptoms of TRD include foliar interveinal chlorosis followed by necrosis. Darkened, charcoal-colored areas of thin stromatic tissue are evident on the taproot and lateral roots along with areas of necrosis within the root and white mycelia within the pith. Upright stromata typical of can be observed on crop debris and emerging from infested roots in fields where taproot decline is present, but these have not been determined to contain fertile perithecia. Symptomatic plant material was collected across the known range of the disease in the southern U.S., and the causal agent was isolated from roots. Four loci, ⍺-actin (), β-tubulin (), the nuclear rDNA internal transcribed spacers (nrITS), and the RNA polymerase subunit II (), were sequenced from representative isolates. Both maximum likelihood and Bayesian phylogenetic analyses showed consistent clustering of representative TRD isolates in a highly supported clade within the species complex in the HY clade of the family Xylariaceae, distinct from any previously described taxa. In order to understand the origin of this pathogen, we sequenced herbarium specimens previously determined to be based on morphology and xylariaceous endophytes collected in the southern U.S. Some historical specimens from U.S. herbaria collected in the southern region as saprophytes as well as a single specimen from Martinique clustered within the TRD clade in phylogenetic analyses, suggesting a possible shift in lifestyle. The remaining specimens that clustered within the family Xylariaceae, but outside of the TRD clade, are reported. Both morphological evidence and molecular evidence indicate that the TRD pathogen is a novel species, which is described as

STRUCTURE HARVESTER results for downy mildew showing a K value of 5.

<p>STRUCTURE HARVESTER results for downy mildew showing a K value of 5.</p

Principle Coordinates Analysis showing genetic distances between individuals in five clusters.

<p>Each color represents a STRUCTURE cluster. Cluster 1 (red), cluster 2 (blue), cluster 3 (green), cluster 4 (purple), and cluster 5 (orange).</p

STRUCTURE plot of assigned probabilities of 82 unique genotypes.

<p>Each genotype is represented by a bar indicating likelihood of membership in cluster 1 (red), cluster 2 (blue), cluster 3 (green), cluster 4 (purple), and cluster 5 (orange).</p