Genetic Variation of the Pathogen Causing Impatiens Downy Mildew Predating and Including Twenty-first Century Epidemics on Impatiens walleriana

De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing

The plant family Balsaminaceae comprises only two genera, and they are a study in contrasts. While Impatiens is an impressively prolific genus, with over 1,000 species and more being discovered each year, its sister genus, Hydrocera, has one solitary species, H. triflora. The two genera also differ in geographic distribution and habitat type (Impatiens species are widely distributed in much of the Old World and N. America, while H. triflora is confined to wetlands specific to S. India, Sri Lanka, and SE Asia). Other contrasting features include plant habit, habitat, floral architecture, mode of seed dispersal, and a host of other traits. The family Balsaminaceae is therefore an excellent model for studying speciation and character evolution as well as understanding the proximal and evolutionary forces that have driven the two genera to adopt such contrasting evolutionary paths. Various species of the Impatiens genus are also commercially important in the ornamental flower industry and as sources of phytochemicals that are of medicinal and other commercial value. As a preliminary step towards studying the genomic basis of the contrasting features of the two genera, we have sequenced and assembled, de novo, the genome of an iconic Impatiens species from N. America, namely I. capensis, and report our findings here.

Peptide Analogs of a Trichoderma Peptaibol Effectively Control Downy Mildew in the Vineyard

Plasmopara viticola, the agent of grapevine downy mildew, causes enormous economic damage, and its control is primarily based on the use of synthetic fungicides. The European Union policies promote reducing reliance on synthetic plant protection products. Biocontrol agents such as Trichoderma spp. constitute a resource for the development of biopesticides. Trichoderma spp. produce secondary metabolites such as peptaibols, but the poor water solubility of peptaibols limits their practical use as agrochemicals. To identify new potential bio-inspired molecules effective against P. viticola, various water-soluble peptide analogs of the peptaibol trichogin were synthesized. In grapevine leaf disk assays, the peptides analogs at a concentration of 50 μM completely prevented P. viticola infection after zoosporangia inoculation. Microscopic observations of one of the most effective peptides showed that it causes membrane lysis and cytoplasmic granulation in both zoosporangia and zoospores. Among the effective peptides, 4r was selected for a 2-year field trial experiment. In the vineyard, the peptide administered at 100 μM (equivalent to 129.3 g/ha) significantly reduced the disease incidence and severity on both leaves and bunches, with protection levels similar to those obtained using a cupric fungicide. In the second-year field trial, reduced dosages of the peptide were also tested, and even at the peptide concentration reduced by 50 or 75%, a significant decrease in the disease incidence and severity was obtained at the end of the trial. The peptide did not show any phytotoxic effect. Previously, peptide 4r had been demonstrated to be active against other fungal pathogens, including the grapevine fungus Botrytis cinerea. Thus, this peptide may be a candidate for a broad-spectrum fungicide whose biological properties deserve further investigation.

Recent developments in plant-downy mildew interactions

Downy mildews are obligate oomycete pathogens that attack a wide range of plants and can cause significant economic impacts on commercial crops and ornamental plants. Traditionally, downy mildew disease control relied on an integrated strategies, that incorporate cultural practices, deployment of resistant cultivars, crop rotation, application of contact and systemic pesticides, and biopesticides. Recent advances in genomics provided data that significantly advanced understanding of downy mildew evolution, taxonomy and classification. In addition, downy mildew genomics also revealed that these obligate oomycetes have reduced numbers of virulence factor genes in comparison to hemibiotrophic and necrotrophic oomycetes. However, downy mildews do deploy significant arrays of virulence proteins, including so-called RXLR proteins that promote virulence or are recognized as avirulence factors. Pathogenomics are being applied to downy mildew population studies to determine the genetic diversity within the downy mildew populations and manage disease by selection of appropriate varieties and management strategies. Genome editing technologies have been used to manipulate host disease susceptibility genes in different plants including grapevine and sweet basil and thereby provide new soucres of resistance genes against downy mildews. Previously, it has proved difficult to transform and manipulate downy mildews because of their obligate lifestyle. However, recent exploitation of RNA interference machinery through Host-Induced Gene Silencing (HIGS) and Spray-Induced Gene Silencing (SIGS) indicate that functional genomics in downy mildews is now possible. Altogether, these breakthrough technologies and attendant fundamental understanding will advance our ability to mitigate downy mildew diseases.

Mitochondrial Loci Enable Specific Quantitative Real-Time PCR Detection of the Pathogen Causing Contemporary Impatiens Downy Mildew Epidemics

Impatiens downy mildew (IDM) disease is a primary constraint on the production of Impatiens walleriana, a popular and economically important floriculture plant. IDM is caused by the biotrophic. oomycete Plasmopara destructor that emerged as a pathogen of I. walleriana in the 2000s. To enable P. destructor detection and quantification, a hydrolysis-probe-based quantitative PCR diagnostic assay was developed based on unique orientation and order of the mitochondrial cytochrome c oxidase subunit1 (cox1) and ATP synthase subunit alpha (atp1) genes in the genus Plasmopara. Nucleotide sequences and analysis of the cox1/atp1 region distinguished P. destructor and its sister-species P. obducens, consistent with prior phylogenetic analyses using cox2 and rDNA markers. Specificity for P. destructor was incorporated into a hydrolysis probe targeting the cox1 gene and flanking primers that amplified across the cox1/atp1 intergenic region. The limit of detection was 0.5 fg/μl of P. destructor DNA (∼100 plasmid copies/μl), with amplification efficiency = 0.95. The assay was validated against a panel of target and nontarget oomycetes, which showed that the primers were specific for Plasmopara spp., while the probe was specific for P. destructor infecting both I. walleriana and I. balsamina. Testing of Impatiens tissue collected from 23 locations across 13 states indicated all samples with IDM symptoms tested positive for P. destructor. Asymptomatic plants from two locations also tested positive for P. destructor.

Occurrence of Plasmopara destructor causing Downy Mildew on Impatiens walleriana in Brazil

Impatiens walleriana (Balsaminaceae), popularly known as Impatiens, is an African succulent and a popular ornamental plant worldwide (GBIF, 2019). In Brazil it is broadly grown indoors and outdoors, including in public parks of Curitiba, State of Paraná (Viezzer et al. 2018). In September 2018, I. walleriana plants showing typical downy mildew symptoms were observed in wastelands and gardens in Curitiba. The symptoms included adaxial chlorotic leaf spots with abundant white sporulation on abaxial side (Supplementary figure 1). The disease led to severe defoliation of the plants and the incidence of the plant disease varied from 20 to 80% of plants in an area ranging from 400 to 40,000 m2. A representative sample was deposited in herbarium of the Museu Botânico Municipal de Curitiba (MBM 331601). The following morphology was observed: Sporangiophores (n = 30), hyaline, thin walled, emerging through stomata, 407.3 to 551.1 μm long, slightly swollen base, first branch at 165.8 to 324.7 μm from base, end branches 5.1 to 13.1 μm long, sporangia (n = 50) hyaline, thin-walled subglobose to ovoid, from 12.8 to 21.9 μm x 12.5 to 17.9 μm, slightly papillate. Due to morphological and genetic variations within the species Plasmopara obducens, Görg et al. (2017) proposed the new species P. velutina and P. destructor. The morphology of the Curitiba specimen was equivalent to that described for P. destructor (Görg et al. 2017). DNA was extracted from LEMIDPRTf-19-02 isolate and the ITS1 and cox2 regions were PCR amplified as described in Görg et al. (2017). The resulting sequences were deposited in GenBank (ITS1, MT680628; cox2, MT952335). A BLASTn analysis of the sequences revealed 100% homology with ITS (MF372742) and cox2 (MF372728) sequences of type strain of P. destructor (GLM-F107554). A Bayesian phylogenetic analysis was performed to compare the sequences from this study with reference sequences for P. obducens, P. destructor and P. velutina (Görg et al. 2017; Salgado-Salazar et al. 2018). The oomycete from Curitiba grouped in a reliable clade with P. destructor (Supplementary figure 2). Pathogenicity was carried out by ex vivo and in vivo tests. For ex vivo, stems with approximately four healthy leaves of I. walleriana (n = 10) were embedded in aluminum grid inside of gerbox with the stem bases immersed in distilled water. The inoculation of five stems was carried out by spraying a suspension with 6 x 104 sporangia mL-1 on the abaxial side of the leaves. Five stems with leaves inoculated with sterile water were used as controls. They were incubated in a growth chamber in the dark for 48 h at 20 °C and another 12 days in a 12 h light photoperiod. The confirmation of pathogenicity in plants (in vivo) was obtained with the inoculation of I. walleriana seedlings (one-month old) grown in 2 dm3 aluminum pots. The inoculation methodology and number of plants were the same as the stems test. After the inoculation, plants were incubated in a growth chamber for 48 h in the dark at 20 °C with 100% RH with nebulization, and another 10 days at a photoperiod of 12 hours of light. For both tests, abundant sporulation was observedwith morphology equivalent to Plasmopara destructor described by Görg et al. (2017). No disease developed on control plants. To our knowledge, this is the first report of P. destructor on I. walleriana in Brazil (Farr and Rossman 2019, Silva et al. 2019) representing a potential loss to flower production and a reduction in flowering period in public gardens and parks.

Plasmopara elegantissima sp. nov. (Oomycota, Peronosporales), a Downy Mildew Species Specialized to Impatiens textori (Balsaminaceae)

Over the past 15 years, downy mildew became the most destructive foliar disease in cultivated Impatiens species (Balsaminaceae) worldwide. A previous study had revealed that the causal agent was not Plasmopara obducens (Oomycota, Peronosporales) but Plasmopara destructor on Impatiens walleriana, and Plasmopara velutina on Impatiens balsamina. This hints to a relatively high degree of specialization of Plasmopara on Balsaminaceae. Therefore, it was the aim of the present study to perform multigene phylogenetic analysis and detailed morphological investigation for several Korean downy mildew samples parasitic to cultivated I. walleriana, and I. balsamina, but also to a northeast Asian wild plant, Impatiens textori. It was revealed that I. textori harbors a new species, which is introduced and described here as Plasmopara elegantissima.

The complete chloroplast genome sequence of horticultural plant, Impatiens hawkeri (Sect. Balsaminacea, Impatiens)

The complete chloroplast genome sequence of Impatiens hawker, a widely cultivated horticultural species in the world is 151,692 bp, with a typical quadripartite structure including a pair of inverted repeat (IRs, 25,584 bp) regions separated by a small single copy (SSC, 17,494 bp) region and a large single copy (LSC, 83,029 bp) region. The overall GC content of I. hawker plastid genome was 36.8%. The whole chloroplast genome contains 135 genes, including 89 protein-coding genes (PCGs), 38 transfer RNA genes(tRNAs), and 8 ribosomal RNA genes (rRNAs). Among these genes, 15 genes have one intron and 2 genes contain two introns. To investigate its evolution status, the phylogenetic tree based on APGIII reveal that there are close relationships to the same genus species I. uliginosa and I. piufanensis.

Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH)

BACKGROUND

Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the disease. Fluorescence in situ hybridization (FISH) is a sensitive and robust method that uses sequence-specific, fluorescence-labeled oligonucleotide probes to detect target organisms from the environment. To study this important pathogen, we developed and standardized a FISH technique for the visualization of P. obducens from Impatiens walleriana tissues using a species-specific 24-mer oligonucleotide probe designed to target a region of the rRNA internal transcribed spacer 2 (ITS2).

RESULTS

Since P. obducens cannot be propagated in vitro, we developed a custom E. coli expression vector that transcribes the P. obducens rRNA-ITS target sequence (clone-FISH) for use as a control and to optimize hybridization conditions. The FISH assay could detect P. obducens sporangiophores, sporangia and oospores, and hyphae from naturally infected I. walleriana leaves and stems. Cross-reactivity was not observed from plant tissue, and the assay did not react when applied to E. coli with self-ligated plasmids and non-target oomycete species.

CONCLUSIONS

This FISH protocol may provide a valuable tool for the study of this disease and could potentially be used to improve early monitoring of P. obducens, substantially reducing the persistence and spread of this destructive plant pathogen.