Ecology and Evolution of the Sudden Oak Death Pathogen <i>Phytophthora ramorum</i>

Grünwald, Niklaus J.; LeBoldus, Jared M.; Hamelin, Richard

doi:10.1146/annurev-phyto-082718-100117

Cited by 70 publications

(46 citation statements)

References 70 publications

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“…Plant pathogens are ubiquitous in the environment and can cause severe damage to both cultivated and wild plant species [28][29][30][31]. Plant pathogens are often specialized on a specific host species or taxon.…”

Section: Introductionmentioning

confidence: 99%

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus

Langner

Harant

Gómez-Luciano

et al. 2020

Preprint

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Supernumerary mini-chromosomes-a unique type of genomic structural variation-have been implicated in the emergence of virulence traits in plant pathogenic fungi. However, the mechanisms that facilitate the emergence and maintenance of mini-chromosomes across fungi remain poorly understood. In the blast fungus Magnaporthe oryzae, mini-chromosomes have been first described in the early 1990s but, until very recently, have been overlooked in genomic studies. Here we investigated structural variation in four isolates of the blast fungus M. oryzae from different grass hosts and analyzed the sequences of mini-chromosomes in the rice, foxtail millet and goosegrass isolates. The mini-chromosomes of these isolates turned out to be highly diverse with distinct sequence composition. They are enriched in repetitive elements and have lower gene density than core-chromosomes. We identified several virulence-related genes in the mini-chromosome of the rice isolate, including the polyketide synthase Ace1 and the effector gene AVR-Pik. Macrosynteny analyses around these loci revealed structural rearrangements, including inter-chromosomal translocations between core-and mini-chromosomes. Our findings provide evidence that mini-chromosomes independently emerge from structural rearrangements of core-chromosomes and might contribute to adaptive evolution of the blast fungus. Author summaryThe genomes of plant pathogens often exhibit an architecture that facilitates high rates of dynamic rearrangements and genetic diversification in virulence associated regions. These regions, which tend to be gene sparse and repeat rich, are thought to serve as a cradle for adaptive evolution. Supernumerary chromosomes, i.e. chromosomes that are only present in some but not all individuals of a species, are a special type of structural variation that have been observed in plants, animals, and fungi. Here we identified and studied supernumerary mini-chromosomes in the blast fungus Magnaporthe oryzae, a pathogen that causes some of the most destructive plant diseases. We found that rice, foxtail millet and goosegrass isolates of this pathogen contain mini-chromosomes with distinct sequence composition. All minichromosomes are rich in repetitive genetic elements and have lower gene densities than core-chromosomes. Further, we identified virulence-related genes on the mini-chromosome of the rice isolate. We observed large-scale genomic rearrangements around these loci, indicative of a role of mini-chromosomes in facilitating genome dynamics. Taken together, our results indicate that mini-chromosomes facilitate genome rearrangements and possibly adaptive evolution of the blast fungus.

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Section: Introductionmentioning

confidence: 99%

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus

Langner

Harant

Gómez-Luciano

et al. 2020

Preprint

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“…This result is expected because of the higher sensitivity of the multi-copy mitochondrial assay than the single-copy nuclear assay (Feau et al, 2019;Bilodeau et al, 2014). Since there were no false positives and no false negatives in our testing, this experiment provides support for the suitability of this approach for fast and accurate detection and identification of this pathogen and could become a core tool in the management, mitigation, and containment of current infection centers and in preventing new invasions [37]. The Mitochondrial assay (left) targets a P. ramorum mitochondrial DNA sequence while the nuclear assay (right) targets a single copy P. ramorum nuclear locus Identification of Asian and European gypsy moth.…”

Section: Detection Of Phytophthora Ramorum On Infected Rhododendron Lmentioning

confidence: 51%

In Situ Processing and Efficient Environmental Detection iSPEED of pests and pathogens of trees using point-of-use real-time pcr

Hamelin

Stewart

Hrywkiw

et al. 2019

Preprint

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The increase in global trade is responsible for a surge in foreign invasive species introductions across the world. Early detection and surveillance activities are essential to prevent future invasions. Molecular diagnostics by DNA testing has become an integral part of this process.However, for environmental applications, there is a need for cost-effective and efficient pointof-use DNA testing that would allow for the collection of results in real-time away from laboratory facilities. To achieve this requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We conducted a series of tests using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions to address the first two requirements. We chose to demonstrate the use of this approach with organisms that cover a broad spectrum of known undesirable insects and pathogens: the ascomycete Sphaerulina musiva, the oomycete Phytophthora ramorum, the basidiomycetes Cronartium ribicola and Cronartium comandrae and the insect Lymantria dispar. Tests performed from either infected leaf material or spores (pathogens), or legs and antenna (insects). We were able to obtain positive amplification for the targeted species in all the samples tested. The shelflife of the lyophilized reactions was assessed, confirming the stability of over a year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable plastics, demonstrating the suitability of the method, named in Situ Processing and Efficient Environment Detection (iSPEED), for field testing. This kit is ideally adapted to field testing as it fits in a backpack and can be carried to remote locations.

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“…Sudden oak death is an invasive disease caused by Phytophthora ramorum, a pathogen that was discovered simultaneously on oaks in California and rhododendron in Europe in the mid-1990s [30,31]. The pathogen is believed to be native to Indochina and the source of the two introductions was recently discovered to be in Vietnam [32].…”

Section: Introductionmentioning

confidence: 99%

“…In North America, the pathogen sporulation and host infection appear to be restricted to the rainy season in the Pacific Northwest and the annual variation in precipitation is likely to be an important factor influencing the epidemic [31]. The disease has so far been reported in western North America, throughout Europe and recently in Japan and Vietnam [30,32].…”

Section: Introductionmentioning

confidence: 99%

Assessing Niche Shifts and Conservatism by Comparing the Native and Post-Invasion Niches of Major Forest Invasive Species

Srivastava

Liang

Keena

et al. 2020

Insects

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Invasive species experience biotic and abiotic conditions that may (or may not) resemble their native environment. We explored the methodology of determining climatic niches and compared the native and post-invasion niches of four invasive forest pests to determine if these species experienced shifts or changes in their new climatic niches. We used environmental principle components analysis (PCA-env) method to quantify climatic niche shifts, expansions, and temporal changes. Furthermore, we assessed the effect of variable selection in the delineation and comparison of niche space. We found that variable selection influenced the delineation and overlap of each niche, whereas the subset of climatic variables selected from the first two PCA-env axes explained more variance in environmental conditions than the complete set of climatic variables for all four species. Most focal species showed climatic niche shifts in their invasive range and had not yet fully occupied the available niche within the invaded range. Our species varied the proportion of niche overlap between the native and invasive ranges. By comparing native and invasive niches, we can help predict a species’ potential range expansion and invasion potential. Our results can guide monitoring and help inform management of these and other invasive species.

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Ecology and Evolution of the Sudden Oak Death Pathogen Phytophthora ramorum

Cited by 70 publications

References 70 publications

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus

In Situ Processing and Efficient Environmental Detection iSPEED of pests and pathogens of trees using point-of-use real-time pcr

Assessing Niche Shifts and Conservatism by Comparing the Native and Post-Invasion Niches of Major Forest Invasive Species

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