Subscribe
Share
Share
Embed
Talking Biotech is a weekly podcast that uncovers the stories, ideas and research of people at the frontier of biology and engineering.
Each episode explores how science and technology will transform agriculture, protect the environment, and feed 10 billion people by 2050.
Interviews are led by Dr. Kevin Folta, a professor of molecular biology and genomics.
Talking Biotech Podcast 382 with Dr. Kevin Folta
Nature's Transgenics - Evidence of Lateral Gene Transfer i Plants
Dr. Lara Pereira, University of Sheffield
===
[00:00:00] Kevin Folta: Hi everybody, and welcome to this week's Talking Biotech podcast by Colabra. Now, since the turn of the millennium, we've seen the price of DNA sequencing plummet and the amount of DNA sequence available just explode. That's kind of funny because back in the early 1990s, we'd get a CD update now and then with all the data in Gen Bank, and it was like Christmas morning when the damn thing showed.
We would take that and have our queries all ready to roll, and you'd put it into a 2 86 computer and listen to a clunk away with the analysis and maybe spit out an answer the next morning if you're lucky, . But with the advent of next generation sequencing, we saw the amount of DNA sequence information just explode after the year 2000.
And today, sequencing a genome is a breeze with high coverage at a good price. Lots of reference genomes to make the bioinformatic side a lot less hassle. It's really easy to capture lots of sequence information and when you capture lots of sequence information, the rare weirdnesses start to stick out.
Anomalies that ones would've been construed as errors or contamination start to show up at increasing regularity, and a good scientist with a keen eye will start to take these patterns very seriously. That's what spawned today's episode in the massive data sets emerging from the grasses. There's some curious patterns that suggest DNA is moving across Barriers that we previously thought to be really tight or insurmountable.
This phenomenon of lateral gene transfer between species, it's happening in a surprising frequency. And that's the topic of today's podcast. We're speaking with Dr. Lara Pereira. She's a post-doctoral researcher at the University of Sheffield. , welcome to the podcast, Dr. Pereira.
[00:01:56] Lara Pereira: Thank you. I'm very happy to
[00:01:58] Kevin Folta: be here.
I'm happy you're here too because this is a really cool evolving story. And so we're really covering what was presented in a recent review where you were the primary author and we're talking about lateral gene transfer, horizontal gene transfer. So what does that really. What are we talking about?
[00:02:19] Lara Pereira: Well when we talk about horizontal gene transfer or lateral gene transfer, we just, we are just talking about movements of genetic material without sexual reproduction involved.
That's all. So usually the genetic material transfers from parents to pro in a vertical way, let's say, when it's not like, Is what we call lateral gene
[00:02:44] Kevin Folta: transfer. Okay. But this wouldn't be necessarily lateral a gene transfer for something that maybe is atic or, or happening from asexual reproduction.
We're talking about transfer from even one species to another sometimes, right?
[00:02:59] Lara Pereira: Yeah, exactly. That's totally true. We usually say when it's. Sexual reproduction, and we should say when it's not sexual or as sexual reproduction. That's That's right.
[00:03:12] Kevin Folta: Yeah, so this is some other way in which genetic material is moving from one species to another, sometimes even.
Well, what's one species to another? Crossing these lines that usually are very strong barriers, correct? I mean, you're going across species sometimes.
[00:03:28] Lara Pereira: Yeah, yeah. Actually we are always across the sp, so the, the ones we identify are always across the species and usually quite distant species. So that's the way we are Sure that is not coming from hybridization or some kind of sexual reproduction.
[00:03:47] Kevin Folta: Yeah. So this is really cool stuff because when you look across all plants, we know that bacteria do this all the time, right? They, they'll take up back, they'll take up other genes from the environment. But where does lateral gene transfer occur outside of bacteria, let's say plants are in animals.
[00:04:04] Lara Pereira: Yeah.
Well, as you said, in, in procars, has been a known process for a very long time in Arias. It's been more recent. But there are multiple reports across all kingdoms. So we have, we can find examples of movement from bacteria to plants from bacteria to fungi across plants, across animals. So there are many examples.
of course, it's not the most common thing happening in nature, but it happens sometimes. And some of these examples is what scientists are just kind of picking up when they are lucky
[00:04:49] Kevin Folta: and when they're lucky. Right. So, so if you had to take a guess a good hypothesis, why is this idea of lateral gene transfer important as an evolutionary me?
[00:04:58] Lara Pereira: What we see in some of these examples, not in all of them, is that the genes that are transferred give the recipient an evolutionary advantage. Probably we see that in the cases that we are able to identify because if we identify them is because they were. They were selected for, if they were conserved within the species, it's probably because they were offering some kind of advantage.
The way I see it is like a shortcut to evolution. So usually evolution is a. Long process might take millions of years to develop a phenotype because everything comes from very small changes. So usually small mutations that have a very small effect, the ones that are good, are retained, and that generates a pool of natural diversity that at some point can become a new trade or a an advantage.
In, in the species. What we see with lateral genee transfer is that that process is much faster because you are passing from one species to another one again, that is already optimized. So that's, that just gives an, an, an evolutionary advantage to the recipient.
[00:06:20] Kevin Folta: And you know, you and I are both plant biologists.
So we started this conversation without really talking about lateral gene transfer in the context of your review and your research. But what kind of plants are more likely to show evidence of lateral gene transfer?
[00:06:35] Lara Pereira: The truth is that we don't really know that, or I would like to be conservative and say that we don't know that most of the studies have been done in grass.
So we can say that lateral gene transfer is widespread in grass. uh, We see it in, in many different grasses in among different groups between different families. So we have tons of examples in grasses. We are not so sure about other groups. It, that doesn't mean that they don't exist. I think it's more a lack of systematic studies trying to find lateral gene transfer.
[00:07:18] Kevin Folta: Yeah, so we're seeing this predominantly in grasses, maybe because that's where people have looked the hardest that, so if I'm understanding right, but, but it seems to be against dogma. We normally talk about genomes as being very strict about the material that goes in and goes out, and that you don't see a lot of lateral gene.
Or we or they would resist lateral gene transfer. So how does what you're discovering really contradict that dogma?
[00:07:47] Lara Pereira: Yeah, that's a very good question. I would like to know too, how this happens. The truth is that I agree with you is is sometimes difficult to believe that in Aria. Genomes that are very well protected.
So they are inside the nucleus, they are packed. Most organisms are multicellular. So that's an additional layer of, of protection to the D N A material. How can this happen? We don't know exactly how it happens. The review actually. Sets the ground or puts there some of the examples or some of the knowledge that we think that could be related or could pave the, the way to understand lateral gene transfer.
But the truth is that we don't really know. The mechanism, but what is clear is that it's happening. So we do know it happens and we try to make a parallelism with transformation techniques because at the end, nobody's questioning how this happens when we are creating a transgenic plant. But at the end, it's, it's quite a, quite this, quite the same, I would say for example in bio ballistic approach.
in for, to generate transgenic plants, you just have small B particles with dna N you bombard cells and somehow the DNA that was in these particles gets transferred to a new individual. Right? So in that case, we are also overcoming all those barrier. .
[00:09:23] Kevin Folta: And how did the genomics age really contribute to this?
I mean were people looking for this for looking for evidence of lateral gene transfer? Or did it just appear in maybe, you know, think it was contamination or how did researchers really find the solid evidence of lateral gene transfer?
[00:09:42] Lara Pereira: I think this is a very important question. It's, it's actually the key point.
We are able now to see, because of how much genomics has evolved in the last few decades. So the, the option of really investigate many different genomes is what allows us to identify these incongruencies in the, in the phylogeny. Go forward, follow up them to try to see if they are real l g t lateral gene transfer, or what, as you were saying, possible contaminants or any other explanation.
And yeah, of course we always think that it could be contamination because at the end Yeah, we know that when we are working in the lab with samples, it's very easy to make a mistake. Even if you don't make any mistake, you do have organisms around your plant. And when collecting the samples, sometimes it might be impossible to separate the, the target from the contaminant.
We do deal with this kind of contamination issue with, in, in different aspects. One of them is, for example, having several independent replicates for everything. So we try to use sequencing data that come from different plants when we can, even from different labs. That is not that difficult right now because everybody's sequencing at a very fast rhythm.
So we do have tons of sequencing data that we can interrogate and we see that these genes are usually when we find. Lateral gene transfers, they are usually conserved in this independent replicates. We also look for gene expression. So if its second contaminant is pro, probably not expressed. So if we see that the gene is expressed is.
Probably because it, it belongs to that genome. We also tend to, in, in our lab for example, we are focusing on rust to grass transfers. So we are not, Investigating whether bacteria or insects or any other kind of organism, past genes to process, but only from one grass to a different species of grass.
So in that, in that case, I would say that is more difficult to have a contaminant because yeah, most of this case in this, in this situation, we don't. The grass is growing together, for example, so we know that it's nearly impossible to have donor DNA in our sample.
[00:12:28] Kevin Folta: Yeah, it's a really important point. I know my first instinct when we got strange sequencing information was to throw away the stuff that looked like a contaminant.
And it turns out that it really was a contaminant. When we first did some sequencing of gene expression throughout a strawberry plant, we found all kinds of evidence of the pathogens and the insects and snail eggs and everything else that were there present on the plant. We came up with a population study of a plant just from the stuff that our bioinformatics folks wanted to throw away.
So pretty cool. Yeah. So we're , so there's a lot of interesting things sometimes. So we're, we're speaking with Dr. Laura Perera and she's a postdoc at University of Sheffield. And we're covering her recent paper that came out in Plants, people, and Planet in December of 2022, which goes into the interesting intricacies of lateral gene transfer and the surprising appearance of d n a sequence from one species in another.
Even things that appear to be unrelated. So this is the Talking Biotech podcast by Collabora, and we'll be back in just a.
And now we're back on the Talking Biotech podcast. We're speaking with Dr. Laura Perera. She's a postdoc at the University of Sheffield, and we're covering the idea of lateral gene transfer. That in her work and the work of her laboratory, there is significant evidence that grasses tend to exchange genetic material with each other, not through sexual means.
So it suggests that we're living in a world surrounded by transgenic organisms, , that nobody really cares about. So that's pretty good. So this is all really great work. It's a really good review because it's, it's right to the point and really interesting. . And so who are the other collaborators on this type of.
[00:14:32] Lara Pereira: In, in this review I've worked with Luke Tanning and Pascal, Antoine. Kristin. They are, they were both at that point, my supervisors and they have an stent career working on lateral gene transfer. I'm actually quite new to the topic. So yeah, they, Pascal Antoine was the first one starting this research line while he was working on c4 Photosynth.
in a species called alloy ola. And just while studying phylogenetics of, of C4 genes, he by chance discovered that one of of the main enzymes of the C4 pathway in alloy was transferred from another grass. And this was very cool because is a species. Has a huge interspecific diversity in photos, synthetic type, and we, he was able to show that part of that incredible diversity was due to lateral gene transfer among grasses.
After that Luke has continued this line of research and yeah, we, I'm, I'm opposed looking in his lab and we are working also in trying to identify. , how important lateral gene transfer is in panum variations. So we know that individuals have different gene content even if they are from the same species, and we are trying to identify whether part of that difference in, in gene content is due to lateral gene transfer.
[00:16:13] Kevin Folta: Yeah. And if you're interested in the original PO time when Dr. Dunning was on with me on the podcast, that was episode 295, seems like years ago now. But he was a guest not that long ago where we started to cover this topic. And when we look at Across grasses or across plants. And we kind of touched on this before I was suggesting, you know, how does this happen?
And you know, and really your answer was a good one. It, it doesn't really matter because we do it with bios and other things all the time. D n a gets integrated. But is there a good hypothesis of how that DNA, n a, gets from one grass to another? Is it happening possibly through the gamete or, or how, how do, how is it thought that this might.
[00:16:54] Lara Pereira: That's what we cover in the review. Exactly. Just go through all the possible hypothesis or what we thought that there, there were the possible hypothesis. One of them would be vector mediator, and the vector could be a virus, bacteria, some kind of pathogen, insect that is sucking in one plant and then infecting another one or sucking in another one and somehow transfers the material.
So that's one possibility. Another possibility we consider is through Ines escalation. That is natural rafting among plants. in this case, there is also physical contact among cells, so it could potentially offer the opportunity to interchange ins and the other or for us, I would say the most reliable hypothesis would be what we are calling now reproductive contamination.
So it, it could be kind of illegitimate pollination. So a pollen from a different species is somehow contaminating the, the, the reproductive process. .
[00:18:08] Kevin Folta: Yeah. I'm really interested in this idea of natural grafting. So this would be maybe two plants that. Living next to each other that grew together? Or is this happening underground in the roots?
What, what do you think is happening there?
[00:18:21] Lara Pereira: We think that it might happen on the roots at least in, in some species. That's what we see in Ola, for example. That is one of the main models we use and we see that these allo plants grow. Multi species clumps. So somehow they are very close together and in, in physical contact with other species they develop valves and they have yeah, they have to some extent vegetative reproduction underground.
So within that, in that scenario, it could be possible that somehow this physical interaction, Physical contact could give rise to gene interchange. But this is all an hypothesis, and it's actually quite controversial talking about grafting in Monocots because until very recently, most people thought it was impossible.
And a recent paper from last year showed that this can happen, although it's not very easy. So grafting is possible in MoCo. , but it has to be in embryonic tissue. So it, it, it could be difficult, but it's, it is a plausible hypothesis.
[00:19:38] Kevin Folta: You know, there's so many different types of grasses out there, and so many have been sequenced and so many have been looked at.
Is there any particular combination that, or particular species or maybe, you know, Pairs of species that this happens at a more common frequency that you tend to see, wow, this one always is infected with a little piece of this other one.
[00:20:01] Lara Pereira: Yeah. We are actually seeing these kind of patterns. For example, in a sis we see that one very common donor is another graph called Diandra.
We identified several genomic fragments in sis that come from Theda. Another case, and this is some published, that is my current work. We are also seeing recurrent transfers in Mace from ul that is a Mexican. We from the, from the Centri, oid grasses. So We do think that there is a pattern that is mainly caused by bio geographical pattern.
So plants that grow together in the same region. are probably the ones that are passing jeans to each other, right? That's what makes sense at the end. So in, in the Ma it, it fits really well because Maze was domesticated in Mexico and, and this grass still is distributed in, in the same region where Mace was domesticated.
So it would make sense. Is the actual donor, but this is all preliminary results, so I, I cannot be like super explicit on everything yet.
[00:21:24] Kevin Folta: Yeah, I understand it's still a very early field, but I, you also mentioned in your review, and you touched on this briefly, this idea of multiple pollination, and it seems like a real stretch to me because of what we know about the safeguards that protect the plant from out crossing, but.
How could this happen feasibly? Could you give us like an idea of a, for example, maybe it happens this way to describe this idea of multiple pollination?
[00:21:52] Lara Pereira: Yeah. So there is a paper that made this work in, in rice. So they develop a technique using, as you were saying, multiple pollination, they call it Repeated pollination actually in, in rice.
And what they do is they in escalate they escalate the, the rice flowers from a cultivar. Then they put pollen from a wild species that is a, a very distant relative from rice. They wait for a few hours. Actually I think it was 48 hours. And after 48 hours, they pollinate again the plant. But this time with pollen.
From the same plant. From the same species. And after that progeny develops and they just. Go through the progeny in the paper. I think they talk about thousands of seedlings, so it's still a very rare event, but it happens and it in the progeny, they identified plants that had different phenotypes.
They started to look at those plants that had different phenotypes, and they identified genetic material from. The wild pollen from the wild species. This genetic material was not hybridization in the, in the broad sense of the word, because it was not chromosomes, complete chromosomes or even half of the genome.
It was just, Less than 0.5% of, of the genome in those seedlings was from the donor. So somehow, again, we don't know exactly how, but somehow that foreign pollen is able to get to the nucleus and contaminate the process. Completely because at the end it's not hybridization. So we cannot find a set of chromosomes from the wild species.
We can find only very small parts of the DNA N there and most of it was transposable elements. So what we hypothesize, but again, it's just an hypothesis, is that something like this could happen in nature. So flowers are there. Pollen from many different species can fly around and pollen from a different species could land in a flower and somehow contaminate the reproductive process.
We don't know exactly how. One of the hypothesis could be that the pollen starts, starts growing. At some point it degenerates, so it cannot grow until the micro pillow and, and actually, mm, fertilize the X. But the DNA n somehow gets in the middle, so in, in the, in those tissues and gets hit by, by the new successful pollen tube.
is able to fertilize. So that's one of the, the hypothesis we have. But again, all, all of this is just based on a few studies that we could find in the literature that were doing this kind of stuff in environmental, in experimental settings. And yeah, still we don't know the molecular details. We. , no.
The outcome, so it is happen.
[00:25:31] Kevin Folta: It seems like a plausible mechanism to me, though. It seems like it's the one that isn't supposed to be there, just starts to germinate in aborts and leaves its genetic material behind that might be able to be pushed through by a growing pollen tube, by another successful fertilization event.
So it's plausible, you know, and you're, and like you say, you're not seeing a whole genome, you're seeing part, so interesting stuff. But do you, do you see this in dcos too? Or has this been looked at in dcos, or does it seem to be. Predominantly a grass phenomenon.
[00:26:01] Lara Pereira: I don't think it had, it has been seen. I think the only studies that talk about L G T in dcos to my knowledge e are the ones focusing on transposable elements.
So we do know that transposable elements have moved among l dcos among dicot species. For example, there are cases in in tomato, in, in grapevine, in several other species. . But in those cases, the study was looking specifically to Transp postal elements. To my knowledge, nobody has looked at code engines and coming back to the pollination stuff, I don't recall any studies showing this.
in dcos, but that doesn't mean that it doesn't happen again. It's maybe nobody has done it.
[00:27:00] Kevin Folta: Right. Nobody's looked at it like a, like an aspiring postdoc who wanted to set out and start her own stellar program. Right. , could build a career on this. Hint hint, right? Yeah. Well, this is what's interesting to me is that, so, and, and this puts it, if you look at the politics of the eu, and how stringent they are about having any kind of plants that are transgenic or even gene edited.
Now, how does your findings, or how do the findings in your laboratory change the perception or do they that here we have pieces of dna, n a, large pieces of D N A, moving from one plant species to another, not regulated, not tested. Does that change the conversation at. .
[00:27:45] Lara Pereira: I think it does. I think this is the most crucial question in my opinion, if this is happening in nature, the regulation should be much more flexible because yeah, the, the, you know, the idea of.
GMOs being dangerous and all that is because we were interfering with nature. We were changing the rules of the game. And what we are seeing now is that we are actually not doing that. It's something that happens in nature, it happens rarely. Sure. But it does happen. And we know that already. Just looking at Aerium to Ians.
So we do know that we are somehow using molecular techniques that are present in the nature to transform in a more targeted way. But that doesn't mean that it doesn't happen. On the other hand I, and I think this coin has two sides. We could also think of the opposite. So until now, we all thought, okay, we can have GMOs out there because they are not gonna transfer the transgen to different species because they cannot cross.
Right now. Maybe we should be a little bit more careful with that statement because we know that genes are trans can be transferred. , even if that's rare, but they can be transferred from one species to a totally different unrelated species. So that could mean that specific genes that are, for example, yeah.
Against wheats or against pathogen herbicides could be transferred to other species that. Growing in the same land. So I think, yeah in my opinion, what we have to do with GMOs is have a, an appropriate level of regulation. We have to be careful, but we cannot push back with a technique that can really help to, to solve all the issues that we are facing.
[00:30:10] Kevin Folta: No, I think that's a really fair statement. I really like the way you show both sides of the coin, right? Because it also seems to me that with weed resistance coming up in the us, especially in places where they grow a lot of herbicide tolerant crops, weed resistance, we know is increasing and that would seem like a perfect place to make that discovery, that you could look at some of these populations of resistant weeds, especially those that are more similar.
to the herbicide resistant crops that are grown and maybe look for evidence of horizontal gene transfer because it would be easy to find and it would be really good to know if this is happening at some sort of regular basis. And you know, there's another really good project for an inspiring postdoc.
Yeah, that's
[00:30:54] Lara Pereira: actually a really cool idea.
[00:30:58] Kevin Folta: It's already been done. The experiment's been happening for 30 years, so. Well, this is really, really good stuff. I appreciate your time very much. On, on this. If people wanted to learn more about your project and maybe find the review are you on Twitter or social media or a place where we could learn more?
Yeah,
[00:31:15] Lara Pereira: I am on Twitter. And yeah, we also have information in the, in the Lab look Tannins Lab website. So we'll be happy to, to talk at any point with anyone that could be interested about this. We are open for collaborations also, if some scientist is listening to us.
[00:31:41] Kevin Folta: No. Very good. And what, what's your Twitter handle?
Your Twitter username?
[00:31:45] Lara Pereira: It's la la, l a l r r l a r r r.
[00:31:52] Kevin Folta: Okay. So l a r r l a r r.
[00:31:56] Lara Pereira: R R R three R . The second one, . Why don't they put it in? It's very difficult to choose a Twitter name because everything was taken, so I had to, yeah, .
[00:32:07] Kevin Folta: Well, what I'll do is I'll put it in the show notes and we'll figure it out later.
No, that sounds perfect. Well, Laura Perrera, thank you so much for your time. This is really interesting stuff. The thing that gets me so excited about it is that. It's a rule breaker, right? It it's showing us that biology isn't playing by the rules that we always thought were there. And really appreciate your time.
So thank you very much for joining me today.
[00:32:30] Lara Pereira: Thank you. It was a real pleasure to be here.
[00:32:34] Kevin Folta: And as always, thank you for listening to The Talking Biotech podcast. Write reviews on iTunes, Spotify, wherever you consume podcast media. It's the increasing number of reviews that help dilute the one negative one
The guy who didn't like it, who was, didn't like that I was making fun of U f O science. So you write a review. Help me defend our Honor as a scientific organization. Thank you very much for listening. It's, it's the weekly listeners that make this possible and really good guests. And so thank you so much for listening, and we'll talk to you again next.