Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora

Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts ( Castanea ), apricots, peaches, plums, almonds and cherries ( Prunus ), apples ( Malus ), oaks ( Quercus ), and beech ( Fagus ). It was one of the first damaging invasive Phytophthora species to be introduced to Europe and North America, although its origin is unknown. We determined its population genetic history in Europe, North and South America, Australia and East Asia (mainly Japan) using genotyping-by-sequencing. Populations in Europe and Australia appear clonal, those in North America are highly clonal yet show some degree of sexual reproduction, and those in East Asia are partially sexual. Two clonal lineages, each of opposite mating type, and a hybrid lineage derived from these two lineages, dominated the populations in Europe and were predominantly found on fagaceous forest hosts ( Castanea , Quercus , Fagus ). Isolates from fruit trees ( Prunus and Malus ) belonged to a separate lineage found in Australia, North America, Europe and East Asia, indicating the disease on fruit trees could be caused by a distinct lineage of P. × cambivora , which may potentially be a separate sister species and has likely been moved with live plants . The highest genetic diversity was found in Japan, suggesting that East Asia is the centre of origin of the pathogen. Further surveys in unsampled, temperate regions of East Asia are needed to more precisely identify the location and range of the centre of diversity

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.info:eu-repo/semantics/publishedVersio

Internal fruit rot (Fusarium spp.) of Greenhouse Bell Peppers

Since 2003 the cultivation of bell peppers in Belgium has to deal with a new disease that leads to internal fruit rot and is caused by Fusarium species. Infection takes place in the flowering stage. The pathogen stays latent during the growth of the fruit after which fungal mycelium can develop during ripening, but mostly after harvest, causing internal and later external fruit rot. Around 75% of the isolates obtained from diseased fruits belonged to the Fusarium lactis species complex (FLASC). F. oxysporum and F. proliferatum were also isolated but less frequently, 14% and 9% respectively. The pathogenicity of these Fusarium species was studied in assays using fruit as well as flower inoculation on different cultivars. Differences in pathogenicity were most clearly observed after fruit inoculation. These results however were not consistent with the results of flower inoculation, which is considered more representative, that showed only very little difference between the Fusarium species. Furthermore there was also an impact of the cultivar on the development of internal fruit rot. To gain a better insight in the latent phase of the infection process and particularly to study the development of the frequency of latent infections during the growing period of the fruit an experiment was set up and repeated three times over the course of the growing season. The presence of Fusarium in the flowers and in the fruits was determined at several time points between flowering and harvest using traditional surface disinfection and plating techniques using either natural infection or artificially inoculated (FLASC) flowers. The frequency of latently infected fruits stayed at a similar level from flower to harvest, indicating only very limited opportunities to affect the disease after initial infection took place. Preventing initial infection will thus be an important factor in the control of internal fruit rot. One way to reduce the amount of initial infections may be the removal of withering tissues such as pistil and petals, as preliminary results have shown that these were frequently saprophytically colonized with FLASC isolates. Several experiments indicated however that such removal was not successful, suggesting that the infection process is quite fast and that the number of airborne spores is insufficiently lowered by the removal of withering flowering structures. As our study to gain more insights into this pathosystem goes on, opportunities for sustainable control of internal fruit rot, such as prevention of flower infection by biological control agents, and screening for disease resistance, are being explored.status: publishe

Data from: Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations