Plant Cell Atlas Launch

Do you know how a plant cell works? This tool should soon answer all your questions.
14 December 2021

Interview with 

Sue Rhee, Carnegie Institution for Science


If you want to know how something works, usually a machine, you open a workshop manual, which displays all the components and how they fit together. So it's logical that we should want something similar for living systems, isn't it? And biologists are busy building the same sort of thing for the human body, mapping out the chemical and genetic nuts and bolts of each individual cell type and how they work together. Surprisingly, though, that's currently not being done for the very thing that keeps the planet alive and probably holds the key to our - and the planet's - future health. I'm referring, of course, to plants; and, as she explains to Chris Smith, this is a shortcoming that Sue Rhee, from the Carnegie Institution for Science, wants to change...

Sue -  Our vision is to create the plant cell atlas. We're hoping to achieve a community of plant biologists, data scientists and technology developers, who are interested in figuring out how plant cells work, so that ultimately we can maybe build or engineer plant cells.

Chris -  Call me slightly naive, but I'm quite surprised that this sort of initiative doesn't exist already, because we have got similar atlases for say, human cells, haven't we? I know Sarah Teichmann at the Sanger has been helping to lead that project.

Sue -  Yeah, the human cell atlas project really got started about five years ago. So it's not been that long since this concept of cell atlases has been around.

Chris -  Is it that you're going to do things differently and do new things, or is it that there are people already doing a lot of this stuff, but they just need a framework to peg it to? So that you are going to deliver all of this in a very organised way, and therefore make the gaps a bit easier to see. So we know what we need to go after?

Sue -  It's a little bit of both, but I would say by far, the majority of plant biologists are not looking at things at this level. And for those who are already doing it, I would say that they're doing it more or less on their own. So there isn't really a community supported standards or rubrics of how we should be defining cells, and states of cells in plants. I would say, we need to do both.

Chris -  How's it actually going to work then? Talk us through what exactly the nuts and bolts of this are going to be. So someone coming from outside seeing this in five years time, what will they experience?

Sue -  First of all, I hope that there will be a very easily accessible web portal, where anyone out there interested in plant biology could access all of this data. This portal, we hope, will present single cell information down from molecules, atomic level, all the way to organ and tissue levels.

Chris -  Is this then that you will say, right, we're going to pick representative species from different groups of plants, and we're going to get representative cells from representative tissues in those things and then we're going to read every single gene that's in there, and how active it is for example. Is that kind of the level of resolution of what you're going for?

Sue -  Yeah, exactly. I think that would be a really great place to be. But ultimately, you know, plants are quite diverse, you know, even just flowering plants, there are over 400,000 species. It would be really great to find these focal reference points, where we can get down to that level of resolution. But ultimately it would be great to be able to expand that, to represent the diversity of plants.

Chris -  Presumably quite a lot of this data do exist for some plants already. And some of it you're going create de novo. So is part of the project going to be going and finding what's already out there and onboarding it, as it were. Bringing it within the portal, so that it's then in the right format, the right context, and you can see what still needs to be to done. And at the same time also showing people where the new avenues, the new vistas to explore are?

Sue -  Yeah, that's exactly right. Yeah. There are already some data out there that we want to bring together, and identify what should be considered minimal requirements in describing the data.

Chris -  A couple of things sort of spring to mind off the back of this. One, it's a huge undertaking. I mean, as you say, there are hundreds of thousands of plant species, and if we want to be comprehensive about it, this is a big undertaking. This is a long-term project, isn't it? So how are you actually going to do this? There must be some bottlenecks which are going to hold this up, which you are going to have to solve along the way. And how long is it going to take to do all of this?

Sue -  Yeah, that's a really good question. I think there are mainly two bottlenecks that we need to overcome, and we need to overcome them pretty fast. The biggest bottleneck that I see, is that there are just very few plant scientists. In the US only about 10% of those working in the field of medicine are those that work in plants. We need to really increase the number of people working on plant biology. The second bottleneck that I see is that most of the genes in these plant genomes, or plant species, are still completely uncharacterised and unknown. So we need to find ways to try to find what these genes are doing in plants.

Chris -  And the time scale?

Sue -  It depends on several factors, but if we can excite new generations of scientists into plant biology, and if we can excite the general public and the politicians to funnel more funds into plant biology, then I think we can achieve it in a relatively reasonable time. But it all depends on what's available.

Chris -  And speaking of what's available, who's actually putting up the funds? I mean, this is a stupendously big project, which is going to run for many years. So how much are you going to really need? If you had to say to somebody very, very rich, indeed, write me a check, which will get this done. How many zeroes on there?

Sue -  The human cell atlas project has a budget of about 3 billion dollars for one organism. So at least the same amount as the human cell atlas would be reasonable.

Chris -  I hope you are good at writing grants! But some people listening to this Sue may say, "well, this is very laudable that people want to comprehensively map out what all these cells are doing in individual plants and so on, but why should I care?" might be their reaction. So why should a young, up and coming biologist decide to put their career in your hands and do this? Why does this matter?

Sue -  Plants are really under-appreciated in our world. The biosphere, as we know today started 3.5 billion years ago by plant ancestors. And agriculture started about 10,000 years ago, which led to the civilisation that we all enjoy today. We will die if plants died. So this planet and everything on it really depends on plants. And now, you know, plants are really becoming the source of bio-renewable energy. And I think in the future plants are going to be a major driver of the economy. I think we're going to have an economy that's based on biology.


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