Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes

Eukaryotic plant pathogens are responsible for the destruction of billions of dollars worth of crops each year. With large-scale genomics of both pathogens and hosts and the corresponding computational analysis, biologists are now able to gain knowledge about many pathogenic and defense genes concur...

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Bibliographic Details
Published in:Briefings in bioinformatics 2009-11, Vol.10 (6), p.654-663
Main Author: Soderlund, Carol
Format: Article
Language:English
Subjects:
Biology
Chromosome Mapping - methods
Eukaryota - physiology
Eukaryotes
Flowers & plants
Fungi - physiology
Genomics
Host-Parasite Interactions - genetics
Pathogens
Plant pathology
Plants - genetics
Plants - microbiology
Software
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Summary:Eukaryotic plant pathogens are responsible for the destruction of billions of dollars worth of crops each year. With large-scale genomics of both pathogens and hosts and the corresponding computational analysis, biologists are now able to gain knowledge about many pathogenic and defense genes concurrently. To study the interactions between these two organism groups, it is necessary to design experiments to elucidate the genes being expressed during the invasion of the pathogen into the host. For the most part, this does not require new software development, though it does require the use of existing software in novel ways. This article provides a broad overview of several key and illustrative experiments and the corresponding computational analyses, outlining the knowledge gained in each. It goes on to describe databases for plant-pathogen data and important initiatives such as Plant-Associated Microbe Gene Ontology. It discusses how various emerging approaches will increase the power of computers in host-pathogen interaction studies.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbp053