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Phytophthora genome mapped -

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Phytophthora genome mapped

The genome of Phytophthora has been mapped. Phytophthora is a water mould but behaves like a
fungus. The genome is large and shows areas of repetition, indicating resilience as it attacks
crops like potatoes. This repetition allows it to evolve faster. Phytophthora has been responsible
for destruction of potato crops, the most famous being in Ireland from 1845 when the population was
reduced by nearly 25%.

Transcript

Robyn Williams:So, do you recognise this name; Phytophthora infestans, the mould that changed the
world, causing potato blight in Ireland? Well, the little beast has just had its genome published
in the journal Nature and it shows just how it has managed to be so adaptable to the new potato
strains through the ages. Paul Birch, I used to call this a fungus, why not so now?

Paul Birch: Well, it's actually a water mould and in evolutionary terms it's more distantly related
to fungi than we are.

Robyn Williams: What's the crucial difference then between that water mould and a fungus?

Paul Birch: Genetically speaking it has a very, very distant common ancestor, but if you look at it
superficially it behaves very much like a fungus. It has spores, it grows as a mycelium, so in
evolutionary terms it's evolved to do and look like it's doing many of the same things, but it's
actually very distant.

Robyn Williams: I'll call it a water mould from now on. But what is the genome like? Having made
the announcement in the journal Nature, what have you found?

Paul Birch: We found the genome is very large, it's expanded many, many times bigger than, for
example, a fungal genome. And it looks like it's organised into two speeds, as we've been calling
it. Many of the genes that are in there which are conserved with other water moulds are clustered
together and there are not many repeats in the genome, and these are sort of residing in an ocean
of repetitive sequence right the way through the genome, so there are very, very large repeat
regions.

Robyn Williams: And that gives it a kind of reserve firepower to take on the potato. Whatever the
potato has done, it can then do something to infect it still, despite the new resistance.

Paul Birch: Yes, it would appear that many of the genes in this water mould that are to do with its
ability to affect potato are actually residing in these very repetitive regions of the genome. This
means that they can evolve faster.

Robyn Williams: How similar is this one that you've elucidated to the one that was responsible for
the potato famine in the mid-19th century in Ireland? That changed all sorts of populations,
including the Australian population as well as the American one. We've got all sorts of Irish all
over the world as a result of having to escape that terrible blight. How similar are the two
Phytophthora infestans?

Paul Birch: It's the same species. Without actually being able to sequence the whole genome of some
of those ancient samples it's hard to categorically say it's a brother or sister, but it's
basically the same species.

Robyn Williams: You've still got some samples, haven't you, from the blight.

Paul Birch: There are, yes, in the Natural History Museum, and I think in one of the research
institutes here in Rothamsted there are some ancient infected leaf samples from the 1840s.

Robyn Williams: Now you've got the genome, how useful will it be to take on this very, very clever
mould?

Paul Birch: It's revealed to us all of the genes that it needs to infect a potato. Those particular
genes produce proteins that are exposed to the plant's immune system, and therein lies an
extraordinary evolutionary battle between potato and Phytophthora. What we're looking for are some
of these proteins from the pathogen which are maybe less able to evolve, may be constrained in some
ways that we could actually target the immune system of the potato towards.

Robyn Williams: You can look at the vulnerabilities in the bar code and try to zap them. But there
are lots and lots of different sorts of wild potato. I remember looking at how they evolved in the
Andes, because at each level in the mountainside there'd be a different kind adapted to a different
sort of microclimate. So you've got a huge variety of potatoes. Were they all with their own
lurking Phytophthora waiting for them?

Paul Birch: It's hard to say that all of them are in the perfect environment for Phytophthora
infestans to work at its best, but certainly a huge range of different wild potato species and in a
lot of different climates in South and Central America are coevolving with this organism.

Robyn Williams: And it's still deadly, isn't it, it's still somehow able to wipe out crops, like in
Papua New guinea, did it wipe out the whole crop there?

Paul Birch: Yes, I think that was a couple of years ago. They'd not had any Phytophthora in there,
it was introduced by whatever means, it spread through Papua New Guinea and destroyed the crop very
rapidly and in a way that was reminiscent of what happened in Ireland. So today it's very difficult
to have naturally resistant potatoes grown in monoculture that will stand up to the pathogen, so
people tend to spray the crops and spray them very regularly in order to control the disease.

Robyn Williams: And what about the response of people in various parts of the world to your
publication? What do you think the ripple is going to be like?

Paul Birch: I would hope that people, especially in the farming industry, would be interested to
know that we have this blueprint and we intend to use it to try and defeat this pathogen if we can.

Robyn Williams: Knock it on the head. Finally, next year you've got the genome of the potato, is
that right?

Paul Birch: Yes, 2010, 2011 maybe if there's a bit of slippage there, but I believe that
researchers are looking at both potato and tomato genomes, both of which are hosts of this
pathogen. Those genome sequences will be coming along.

Robyn Williams: I look forward to it. Thank you.

Paul Birch: Thank you.

Robyn Williams: Paul Birch is at the University of Dundee in Scotland, and his paper was published
last week in the journal Nature.