Scientists at SCRI have helped decode the genome of the notorious pathogen that caused the Irish potato famine in the mid-19th century and still costs the world £3 billion a year.

The team at SCRI, led by Dr Stephen Whisson, SCRI Plant Pathology programme and Professor Paul Birch, University of Dundee Division of Plant Sciences at SCRI, were part of a large international research team. The study is published in the September 9 online issue of the prestigious journal Nature.

The study has revealed that the organism boasts an unusually large genome size — more than twice that of closely related species — and an extraordinary genome structure, which together appear to enable the rapid evolution of genes, particularly those involved in plant infection.

These data expose an unusual mechanism that enables the pathogen to outsmart its plant hosts and may help researchers unlock new ways to control this enduring and highly destructive pathogen.

"The utility of the genome sequence in our research against late blight cannot be overstated," said Dr Whisson. "It gives us many clues as to which genes might be absolutely required for late blight disease development.

"The products from these essential ‘disease’ genes are then potentially useful to target for resistance in potato breeding programmes, or in development of more specific and environmentally friendly control chemicals," he added.

The Irish potato famine in the mid 1800s was caused by the pathogen Phytophthora infestans. Long considered a fungus, it is now known to be a member of the oomycetes or “water moulds”, which are more closely related to brown algae than to fungi.

P. infestans thrives in cool, wet weather, and can infect potatoes, tomatoes and other related plants, causing a “late blight” disease that can decimate entire fields in just a few days.

The pathogen is remarkable in its ability to change, quickly adapting to new plant hosts, attacking even genetically resistant potatoes bred to fend off P. infestans infection. How the pathogen can adapt so rapidly to these immune potatoes has long puzzled scientists.

One of the most striking findings to emerge from the study is the expanded nature of the P. infestans genome: it is two and a half to four times the size of its relatives.

Perhaps even more surprising is that the added bulk does not reflect more genes per se, but instead stems from a massive expansion in the amount of repetitive (once considered to be “junk”) DNA.

The researchers gained some key insights into the potential advantages of carrying this glut of repetitive DNA:

• The P. infestans genome comprises alternating repeat-rich (and gene-poor) regions and gene-dense regions;
• These gene-dense regions are shared among other Phytophthora species, preserved over millions of years of evolution, whereas the repeat-rich regions are undergoing relatively rapid changes;
• The repeat-rich regions contain fewer genes compared to other genomic regions, yet those genes they do contain are enriched for those that play crucial roles in plant infection.

Taken together, these findings suggest an unusual genomic strategy to support the rapid evolution of critical genes, known as “effector” genes. Effector genes can disrupt plants’ normal physiology, enabling the pathogen to establish a foothold. However, some can also trigger plants’ immune responses, making them prime targets for combating P. infestans infection.

Importantly, the new P. infestans genome sequence enabled the researchers to identify many previously unknown effector genes.

These findings not only expand the catalogue of known P. infestans genes, they also highlight a critical subset of genes undergoing rapid turnover. Further studies of these genes will foster a deeper understanding of plant infection and help identify potential targets for fighting back.

Notes to editors

Paper cited: Haas et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature DOI:10.1038/nature08358

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