Cavers, Stephen

Ennos, Richard

Cottrell, Joan

Green, Sarah

Crowson, Daisy

Natural Environment Research Council (NERC)

E4 Doctoral Training Partnership

2026-05-28T13:57:28Z

2026-05-28

Invasive tree pathogens are a growing threat to natural and managed ecosystems, causing severe ecological and economic impacts. The outcome of novel plant-pathogen interactions depends on a complex suite of evolutionary and ecological processes that are unique to each system. Understanding these interactions therefore requires taking diverse and complementary approaches: quantitative genetics can be employed to address questions regarding host resistance; population genetics and genomics can be used to explore key pathogen traits and evolutionary history; and molecular analyses can provide a mechanistic insight into the host-pathogen interaction. This thesis integrates these approaches to investigate the evolutionary and ecological dynamics of the invasive oomycete pathogen Phytophthora austrocedri and its UK-native host juniper (Juniperus communis). In Chapter 1, I outline the framework of my research by introducing the background of the rising problem of invasive plant pathogens, discussing the evolutionary-ecology of novel host-pathogen interactions and describing the pathosystem. Chapter 2 investigates the presence and nature of any resistance to the pathogen in natural host populations. By means of a progeny-provenance inoculation trial I show that: resistance in juniper is a heritable genetic trait; juniper has both qualitative and quantitative variation in resistance; and P. austrocedri is imposing natural selection on juniper populations, with a higher frequency of resistant juniper individuals found in populations previously exposed to the pathogen. In Chapter 3, I present new, high-quality reference genomes for each of the two distinct geographical lineages of P. austrocedri, establishing the first genomic resources for this species. In Chapter 4, I explore large-scale genome evolution, population genomics, and genetic diversity in the pathogen. I use flow cytometry and whole-genome sequence data to show that P. austrocedri is a tetraploid, but that variation in genome size and evidence of large genomic deletions suggest diploidisation and triploidisation is occurring in some isolates. I confirm that P. austrocedri is of hybrid origin, with the hybridisation event likely predating the divergence of the two lineages. I also show that levels of genome-wide genetic diversity and within-subgenome heterozygosity in the pathogen are very low, suggesting a history of self-fertilisation, but that the hybrid nature of the pathogen allows it to maintain high levels of between-subgenome heterozygosity. Chapter 5 investigates the molecular basis of resistance in the host and of virulence in the pathogen using dual RNAseq of the host-pathogen interaction. I show that a successful defence response in juniper is characterised by rapid induction of ethylene signalling and associated production of secondary metabolites and pathogenesis-related proteins, and I identify a candidate transmembrane receptor that may underlie this rapid response. I also show that increased virulence in the pathogen appears linked to enhanced suppression and evasion of host defences, which may also allow an extended biotrophic phase, and I identify candidate genes that may be driving these differences. Finally, in Chapter 6, I synthesise the findings of the previous chapters and set them within the broader context of research into the evolutionary ecology of novel host-pathogen interactions. I conclude by outlining some practical recommendations for managing the juniper-P. austrocedri pathosystem that arise from the results presented in this thesis. In summary, this research integrates quantitative genetics, genomics, and molecular analyses to advance our understanding of the evolutionary dynamics underlying novel plant-pathogen interactions.

https://era.ed.ac.uk/handle/1842/44767

https://doi.org/10.7488/era/7281

en

C​r​e​a​t​i​v​e ​C​o​m​m​o​n​s: ​Attribution-NonCommercial-NoDerivatives 4.0 International (​CC BY-NC-ND 4.0)

https://creativecommons.org/licenses/by-nc-nd/4.0/

Phytophthora austrocedri

Juniper (Juniperus communis)

Genomics

Resistance

Host-pathogen interaction

Ecological genetics of the invasive tree pathogen Phytophthora austrocedri and its native host juniper

Thesis

Doctoral

PhD Doctor of Philosophy