Untitled

Funder

Organizational Unit

Publications

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Publication . Van Poucke, Kris; Haegeman, Annelies; Goedefroit, Thomas; Focquet, Fran; Leus, Leen; Horta Jung, Marília; Nave, Corina; Redondo, Miguel A.; Husson, Claude; Kostov, Kaloyan; Lyubenova, Aneta; Christova, Petya; Chandelier, Anne; Slavov, Slavcho; de Cock, Arthur; Bonants, Peter; Werres, Sabine; Palau, Jonàs O.; Marçais, Benoit; Jung, Thomas; Stenlid, Jan; Ruttink, Tom; Heungens, Kurt

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.

2021-07-01Journal article

Open Access

Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal

Publication . Jung, Thomas; Horta Jung, Marília; Cacciola, Santa Olga; Cech, Thomas; Bakonyi, Jozsef; Seress, Diana; Mosca, Saveria; Schena, Leonardo; Seddaiu, Salvatore; Pane, Antonella; Lio, Gaetano Magnano di San; Maia, Cristiana; Cravador, Alfredo; Franceschini, Antonio; Scanu, Bruno

During surveys of Phytophthora diversity in natural and semi-natural Fagaceae forests in Austria, Italy and Portugal, four new cryptic species were isolated from rhizosphere soil samples. Multigene phylogeny based on nuclear ITS, beta-tubulin and HSP90 and mitochondrial cox1 and NADH1 gene sequences demonstrated that two species, P. tyrrhenica and P. vulcanica spp. nov., belong to phylogenetic Clade 7a, while the other two species, P. castanetorum and P. tubulina spp. nov., clustered together with P. quercina forming a new clade, named here as Clade 12. All four new species are homothallic and have low optimum and maximum temperatures for growth and very slow growth rates at their respective optimum temperature. They differed from each other and from related species by a unique combination of morphological characters, cardinal temperatures, and growth rates. Pathogenicity of all Phytophthora species to the root system of their respective host species was demonstrated in soil infestation trials.

2017-12Journal article

Open Access

Extensive morphological and behavioural diversity among fourteen new and seven described species in Phytophthora Clade 10 and its evolutionary implications

Publication . Jung, T.; Milenković, I.; Corcobado, T.; Májek, T.; Janoušek, J.; Kudláček, T.; Tomšovský, M.; Nagy, Z.Á.; Durán, A.; Tarigan, M.; Sanfuentes von Stowasser, E.; Singh, R.; Ferreira, M.; Webber, J. F.; Scanu, B.; Chi, N. M.; Thu, P. Q.; Junaid, M.; Rosmana, A.; Baharuddin, B.; Kuswinanti, T.; Nasri, N.; Kageyama, K.; Hieno, A.; Masuya, H.; Uematsu, S.; Oliva, J.; Redondo, M.; Maia, Cristiana; Matsiakh, I.; Kramarets, V.; O'Hanlon, R.; Tomić, Ž.; Brasier, C. M.; Horta Jung, M.

During extensive surveys of global Phytophthora diversity 14 new species detected in natural ecosystems in Chile, Indonesia, USA (Louisiana), Sweden, Ukraine and Vietnam were assigned to Phytophthora major Clade 10 based on a multigene phylogeny of nine nuclear and three mitochondrial gene regions. Clade 10 now comprises three subclades. Subclades 10a and 10b contain species with nonpapillate sporangia, a range of breeding systems and a mainly soil-and waterborne lifestyle. These include the previously described P. afrocarpa, P. gallica and P. intercalaris and eight of the new species: P. ludoviciana, P. procera, P. pseudogallica, P. scandinavica, P. subarctica, P. tenuimura, P. tonkinensis and P. ukrainensis. In contrast, all species in Subclade 10c have papillate sporangia and are self-fertile (or homothallic) with an aerial lifestyle including the known P. boehmeriae, P. gondwanensis, P. kernoviae and P. morindae and the new species P. celebensis, P. chilensis, P. javanensis, P. multiglobulosa, P. pseudochilensis and P. pseudokernoviae. All new Phytophthora species differed from each other and from related species by their unique combinations of morphological characters, breeding systems, cardinal temperatures and growth rates. The biogeography and evolutionary history of Clade 10 are discussed. We propose that the three subclades originated via the early divergence of pre-Gondwanan ancestors > 175 Mya into water-and soilborne and aerially dispersed lineages and subsequently underwent multiple allopatric and sympatric radiations during their global spread.

2022Journal article

Open Access

Invasive forest pathogens in Europe: cross-country variation in public awareness but consistency in policy acceptability

Publication . Eriksson, Louise; Boberg, Johanna; Cech, Thomas L.; Corcobado, Tamara; Desprez-Loustau, Marie-Laure; Hietala, Ari M.; Horta Jung, Marília; Jung, Thomas; Lehtijarvi, Hatice Tuğba Doğmuş; Oskay, Funda; Slavov, Slavtcho; Solheim, Halvor; Stenlid, Jan; Oliva, Jonàs

Political action can reduce introductions of diseases caused by invasive forest pathogens (IPs) and public support is important for effective prevention. The public's awareness of IP problems and the acceptability of policies aiming to combat these pathogens were surveyed in nine European countries (N = 3469). Although awareness of specific diseases (e.g., ash dieback) varied, problem awareness and policy acceptability were similar across countries. The public was positive towards policies for informational measures and stricter standards for plant production, but less positive towards restricting public access to protected areas. Multilevel models, including individual and country level variables, revealed that media exposure was positively associated with awareness of IP problems, and strengthened the link between problem awareness and policy acceptability. Results suggest that learning about IPs through the media and recognizing the associated problems increase policy acceptability. Overall, the study elaborates on the anthropogenic dimension of diseases caused by IPs.

2018Journal article

Open Access

Eight new Halophytophthora species from marine and brackish-water ecosystems in Portugal and an updated phylogeny for the genus

Publication . Maia, Cristiana; Jung, M. Horta; Carella, G.; Milenković, I.; Janoušek, J.; Tomšovský, M.; Mosca, S.; Schena, L.; Cravador, Alfredo; Moricca, S.; Jung, T.

During an oomycete survey in December 2015, 10 previously unknown Halophytophthora taxa were isolated from marine and brackish water of tidal ponds and channels in saltmarshes, lagoon ecosystems and river estuaries at seven sites along the Algarve coast in the South of Portugal. Phylogenetic analyses of LSU and ITS datasets, comprising all described Halophytophthora species, the 10 new Halophytophthora taxa and all relevant and distinctive sequences available from GenBank, provided an updated phylogeny of the genus Halophytophthora s.str. showing for the first time a structure of 10 clades designated as Clades 1-10. Nine of the 10 new Halophytophthora taxa resided in Clade 6 together with H. polymorphica and H. vesicula. Based on differences in morphology and temperature-growth relations and a multigene (LSU, ITS, Btub, hsp90, rpl10, tigA, cox1, nadh1, rps10) phylo-geny, eight new Halophytophthora taxa from Portugal are described here as H. brevisporangia, H. cele-ris, H. frigida, H. lateralis, H. lusitanica, H. macrosporangia, H. sinuata and H. thermoambigua. Three species, H. frigida, H. macrosporangia and H. sinuata, have a homothallic breeding system while the remaining five species are sterile. Pathogenicity and litter decomposition tests are underway to clarify their pathological and ecological role in the marine and brackish-water ecosystems. More oomycete surveys in yet undersurveyed regions of the world and population genetic or phylogenomic analyses of global populations are needed to clarify the origin of the new Halophytophthora species.

2022-06Journal article

Open Access