Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

Hessenauer, Pauline; Feau, Nicolas; Gill, U. S.; Schwessinger, Benjamin; Brar, Gurcharn S.; Hamelin, Richard

doi:10.1094/phyto-08-20-0358-fi

Cited by 30 publications

(27 citation statements)

References 219 publications

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“…This study raises questions about the strategy for effectorinformed breeding. We know that clonal lineages predominate in strawberry, as has often been described in other agriculturalassociated pathosystems (Hessenauer et al, 2021). We have shown that there are highly expressed lineage-specific effectors within the clonal lineage of CR along with CNV in highly expressed effectors.…”

Section: Discussionsupporting

confidence: 62%

Comparative Analysis of Host-Associated Variation in Phytophthora cactorum

et al. 2021

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Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.

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Section: Discussionsupporting

confidence: 62%

Comparative Analysis of Host-Associated Variation in Phytophthora cactorum

et al. 2021

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“…This study raises questions about the strategy for effector-informed breeding. We know that clonal lineages predominate in strawberry, as has often been described in other agricultural-associated pathosystems (Hessenauer et al, 2021). We have shown that there are highly expressed lineagespecific effectors within the clonal lineage of CR along with CNV in highly expressed effectors.…”

Section: Resultssupporting

confidence: 62%

Comparative analysis of host-associated variation in Phytophthora cactorum

Nellist

Armitage

Bates³

et al. 2021

Preprint

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Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well supported non-recombing clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologs in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.

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“…The loss of sexual reproduction, caused by demographic events or selection against sex, is a frequent change in the life history traits of invasive fungal pathogens (Gladieux et al 2015;Hessenauer et al 2021). However, the underlying changes and driving factors remain largely unexplored.…”

Section: Pestification Can Foster Lineage Divergencementioning

confidence: 99%

Ecological Differentiation Among Globally Distributed Lineages of the Rice Blast Fungus Pyricularia oryzae

Thierry

Charriat

Milazzo

et al. 2020

Preprint

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12Natural variation in plant pathogens has an impact on food security and ecosystem health. The rice 13 blast fungus Pyricularia oryzae, which limits rice production in all rice-growing areas, is structured into 14 multiple lineages. Diversification and the maintenance of multiple rice blast lineages have been 15 proposed to be due to separation in different areas and differential adaptation to rice subspecies. 16However, the precise world distribution of rice blast populations, and the factors controlling their 17 presence and maintenance in the same geographic areas, remain largely unknown. We used 18 genotyping data for 886 isolates from more than 185 locations in 51 countries to show that P. oryzae is 19 structured into one recombining and three clonal lineages, each with broad geographic distributions. 20No evidence was found for admixture in clonal lineages, and crossing experiments revealed that female 21 sterility and early postmating genetic incompatibilities acted as strong barriers to gene flow between 22 these lineages. An analysis of climatic and geographic data indicated that the four lineages of P. oryzae 23 were found in areas differing in terms of the prevailing environmental conditions and types of rice 24 2 grown. Pathogenicity tests with representatives of the five main rice subspecies revealed differences 25 in host range between pathogenic lineages, highlighting a contribution of specialization to niche 26 separation between lineages, despite co-existence on the same host species. Our results demonstrate 27 that the spread of a pathogen across heterogeneous habitats and divergent populations of a crop 28 species can lead to niche separation and incipient speciation in the pathogen. 29 Short title: Incipient speciation in the rice blast pathogen 30 31

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Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

Cited by 30 publications

References 219 publications

Comparative Analysis of Host-Associated Variation in Phytophthora cactorum

Comparative Analysis of Host-Associated Variation in Phytophthora cactorum

Comparative analysis of host-associated variation in Phytophthora cactorum

Ecological Differentiation Among Globally Distributed Lineages of the Rice Blast Fungus Pyricularia oryzae

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