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Andrew Armitage - ePortfolio


PhD student - Warwick Crop Centre 

Welcome to my Research Portfolio. In this area I will try to give an overview of my research into the evolutionary history of Alternaria "Black Mould" fungi. This fascinating group of fungi are human allergens and are virulent crop pathogens. Species of fungi within the Alternaria are very diverse often with distinct preferences for particular hosts. Despite these differences in lifestyle it can be very difficult to visually separate an individual that is known to attack one plant host from one which attacks a different plant host. This is very important to the UK Department for Environmental and Rural Affairs who are concerned that non-native Alternaria pathogenic to UK crops, particularly Apples and Pears, may become established in the UK.


Project title: Non-native Alternariafungi threatening EU pome production – Use of molecular phylogenetics to develop diagnostics

Supervisors: J.Clarkson1 & J.Woodhall2

1 Warwick Crop Centre, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK

2FERA York, Sand Hutton, York, YO41 1LZ , UK

Funding: DEFRA


The host range of Alternaria is broad with species groups such as A.alternata recognised on over 100 crops. Small spored Alternaria pathogens cause black spot infections on leaves and stems leading to reduced crop yield and plant defoliation. Similar morphology has left pathogenic Alternaria taxa hard to identify and their evolutionary history is unresolved.

Alternaria pathogens of pome fruits cause significant economic damage in their native ranges, but pathotypes specific to pome fruits have been shown capable of establishing outside of East Asia. For example, the pear pathotype A. gaisen in Southern Europe and the apple pathotype A.mali in North America. Host range of individual pathotypes within A. alternata is not yet understood as pathotypes thought specific to lettuce, tomato and strawberry are capable of causing leaf lesions on European pear. Furthermore, there is evidence that European cultivars may be less resistant to infection than cultivars the diseases are normally associated with. The European and Mediterranean Plant Protection Organisation (EPPO) recognises A.gaisen as a documented pest, it also lists A.mali on the A1 quarantine pests list. Imports are screened to prevent introduction of non-native pathogenic Alternariato Pome fruits (apple, pear and quince) to the UK.

A.mali, A.gaisen and A.alternata species have not been investigated together in a pan-genus phylogeny. ITS, mtSSU, β-tubulin and TEF have proven useful at resolving Alternaria phylogenies at the genus and species-level. These loci and others, such as polygalacturonases and mating-type genes, will be used to characterise pathogen populations and investigate recent evolutionary history. In addition, the online resource FUNYBASE (FUNgal phYlogenomic dataBASE) allows access to information on 246 orthologous genes present in fungi. These novel loci will be screened from the 60 fungal genomes publically available allowing for identification of new loci with high resolution at inter- and intra-specific levels. Identification of key genetic and phenotypic differences between ecologically important Alternaria species will provide the basis to develop diagnostic tests. These would target characteristics such as genes associated with toxin production involved in causing significant damage to pome hosts from less-aggressive pathotypes. This would allow for improved monitoring of Alternaria plant pathogens and assist in their control.


Andrew Armitage 

Andrew Armitage

Contact me:

A dot D dot Armitage at warwick dot ac dot uk

Warwick HRI,
University of Warwick,
Wellesbourne, Warwickshire,
CV35 9EF.
United Kingdom

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