Why do parasitic plants appear all over on Phylogenic Trees?

[professor_porcupine]

I’ve noticed a trend where a lot of Phylogenic Trees have Parasitic Plant Families placed all over in different positions from study to study.
In particular Cynomoriaceae.

I suspect this is because Parasitic plants move DNA around between Plant Families & Orders. Since by their parasitic nature, they can faciliate horizontal gene flow, occasionally incorporating some DNA from their hosts.
If this is what’s happening, then it would explain why they appear all over the place, the little DNA from other plant families inside Cynomoriaceae can mess up it’s position right?

Knowing this, is it possible to use Parasitic Plants to connect to distantly related plants in hopes that some genes transfer? Is this how we create Blue Tomatoes or Blue Watermelons? Lycianthes acuplensis, Solanum flaccidum & Persicaria perfoliata make blue fruit (The last 2 are edible, not sure about the first one).

Also, is this effectively creating a natural GMO? If Parasitic plants transfer DNA naturally, is it GMO or no?

Some plants of the Parasitic Plant Family Orobanchaceae are edible like Castilleja coccinea but are suspected to absorb toxins from host plants, especially Poisonous Non-Edible Plant Hosts. This is why You shouldn’t forage them growing next to poisonous plants.

Also how do GMO Plants appear on Phylogenic Trees? Are their positions all over the place just like with Parasytic Plants?

[ljazz]

Generally, for most of parasitic plants, it’s not the horizontal gene transfer that causes the problem, but loss of genes commonly used for construction of gene phylogenies. This can now be avoided by using (partial) genome data, so it’s mostly stabilised.

Up until 2010s the main genes used were chloroplast genes, which have certain properties that make them easier to work with, however there are serious problems in using just those as they are inherited differently than nuclear genes.
And those are exactly the genes parasitic plants loose very fast during evolution.

For some extreme examples, horizontal gene transfer is a problem (Rafflesiaceae), since a large proportion of the genome is stolen from the host (usually Vitaceae).

In Cynomorum, both factors were a huge problem, yes.

The gene transfer goes only one way, from host to parasite, and if it does not provide any benefit for the parasite, it gets lost fast too, so I do not think this would be a good way to transfer genes.
Agrobacter can be used in a similar manner, and that works.

The question of is it GMO or not is dependend of what you consider GMO to be. In strictest sense, it is not, since there was no direct manipulation by humans with processes extremely unlikely to happen by themselves in nature. But if you hold selective breeding for GMO, the yes, they can be natural GMO

[professor_porcupine]

@ljazz

it’s not the horizontal gene transfer that causes the problem, but loss of genes commonly used for construction of gene phylogenies.

ah… that somewhat makes sense. Can the Phylogenic Trees still detect Horizontal Gene Transfer?
On Brassica Phylogenic Trees, I’ve seen Brassica juncea Grouped with B. rapa & B. oleracea but B. nigra was distant from them with many other genera between them.
This is odd since I know Brassica juncea is a B. rapa x B. nigra hybrid.
Same goes with Brassica carinata grouped with B. nigra even tho it contains B. oleracea generics cuz it’s a interspecies hybrid.

@ljazz

And those are exactly the genes parasitic plants loose very fast during evolution.

Ah ha… interesting. What makes nuclear genes different from chloroplast genes?

@ljazz

The question of is it GMO or not is dependend of what you consider GMO to be

I see… does it makes sense to have Nautral GMO vs Artificial GMO? Or are those termsn nonsense & thus aren’t used?

[ljazz]

there are methods to detect HGT, but not directly in gene tree calculation, there has to be a separate analysis, which usually just involves identifying genes that should not be there ( gene phylogenetic trees can be used for this, but you need many gene trees to make a sensible analysis and to even find specific trasferred genes).

Brassica phylogeny is difficult, as humans played a big role even before the advent of agriculture; and it is an economically significant genus, so research was done early, when the methods were not . It would help if you would cite your sources, so I could see how they got to the results.

nuclear genes are inherited from both parents, chloroplast genes are (generally, in most plants) inherited from seed parent (the “mother” plant) only. Nuclear often come in two versions (allelles) in each individual, which complicates analyses. Chloroplast genome copies are generally present in a sngle version.
Additionally, nuclear genes are classicaly arranged in eucaryote chromosomes, chloroplast genome looks and functions like a bacterial genome. Since molecular genetics started and was developed on bacteria, it was also easier to use bacterial methods on chloroplast genmome, and development of methods for the nuclear part took longer.
And lastly. Each cell of a diploid contains just 2 copies of nuclear genome, so each gene comes only in 2 copies (with notable exceptions, which are copied and repeated many time in the genome). Chloroplast genome is present in multiple copies in every chloroplast in the cell. Each cell has many chloroplast, so in the end each cell od a diploid organism usually has many, many copies of the chloroplast genome, which makes it much more easier to sequence it.

I am not too familiar with the GMO debate, I am just aware that there is (or was, when I was in uni) a debate what exactly is GMO. Technically speaking, many of the crops are already man-made genetic freaks; and some proponents, wishing to excuse the usage of modern-molecularly changed GMO organism; argue that its the same thing, so all wheat is a GMO.
To most others there is a significant difference between selective breeding, hybridisation and mutagenesis used since prehistory to pre-WW2; and modern methods of genetic modification. So old kinds of wheat are not GMO, but the ones begotten from genetic manipulation by, e. g. crispr, are.

I am not aware If there already exist terms for “natural” GMO and “artificial” GMO, but such terms would be useful (albeit with a different semantics, use of natural and artificial is problematic in this case).

[jasonhernandez74]

@ljazz

To most others there is a significant difference between selective breeding, hybridisation and mutagenesis used since prehistory to pre-WW2; and modern methods of genetic modification.

At the molecular level, it’s all the same four nucleotides. Despite all the fear mongering about “Frankenfood,” the guanine, for example, from a plant is exactly the same as the guanine from an animal.

[ljazz]

Yes; and the European languages use the same latin letter, but you would not understand it if I used them like other langugaes do.

At the base level, chemistry is the same, yes; but what it does in the body is not.

There is a significant difference between makeing modern wheat or corn from their wild ancestors by hibridisation and line selection and putting jellyfish gene into a cat so it glows.

I am not against GMO per se; if there would be sensible guidelines what and how to do it; but for now it seems there is none; and corporate greed and scientific curiosity are leading the way.
Making any modern GMO is like introducing a gene into a gene ecosystem; we do not know what are all the possibilities since we are doing it for barely a couple of decades. What if we stumble across a “sugar cane toad”- gene (i. e. a gene taht does not do what we want, but has long reaching negative impacts on what we tried to fix)?
The debate around GMO is poisoned and heavily influenced by extreme opinions on both sides, pro-GMO people often refuse to acknowledge we barely know what we are doing and what will be the long-term consequences. Anti-GMO are a priori against with little to no evidence. It is difficult to arge with both.
I think GMO can be a powerful tool, but before we do anything stupid; I think we should sit down and think about what we are doing and how we are doing it for a bit. It is hard to imagine all of the possible consequences of actions we are taking now; if you told a person 400 years ago if they thought putting frogs or plants on wroong continents would cause environmental disasters, I doubt they’d beleive you.

[professor_porcupine]

@ljazz

Brassica phylogeny is difficult, as humans played a big role even before the advent of agriculture

yea… no kidding. It’s complex cuz so many species hybridize & introgress into each other. Plus not to mention much of the family evolved thru whole genome duplication events (Probably explains a bit as to why they all hybridize so easily & why Mis-matching chromosomes don’t prevent crosses).

@ljazz

It would help if you would cite your sources, so I could see how they got to the results.

There’s this Brassica Triangle of U.

Here’s an Expanded Triangle of U. Potentially many more genera could cross too (Theoretically the whole Brassiceae Tribe too)!

But the main study was this one
https://www.researchgate.net/publication/385242021_Expanding_the_Triangle_of_U_Comparative_analysis_of_the_Hirschfeldia_incana_genome_provides_insights_into_chromosomal_evolution_phylogenomics_and_high_photosynthesis-related_traits

@ljazz

I am not aware If there already exist terms for “natural” GMO and “artificial” GMO, but such terms would be useful (albeit with a different semantics, use of natural and artificial is problematic in this case).

I see perhpas Horizontal Gene Flow is the better term or totally separate thing from facilitating GMO? or maybe Cross Pollination vs Gene editing?

But since Horizontal Gene Flow is a natural way to move genes without cross pollination, where would it fit?
Many times Grafting young scions onto Mature Rootstocks creates horizontal gene flow oppurtunties. This Effect (Known as Mentor Grafting) is more noticable on Young Wide Hybrid Scions grafted onto a Mature Rootstock, where the scion takes on traits of the rootstock in the seeds of the scions fruits. Also noticable when grafting seedlings (Cuz the plants are plastid thus the genes more loosey goosey & hybridization barriers lower.

A little of how Chimera work, they are an example of Horizontal Gene Flow right?

@ljazz

There is a significant difference between makeing modern wheat or corn from their wild ancestors by hibridisation and line selection and putting jellyfish gene into a cat so it glows.

Ah yes! Animals aren’t known to Naturally transfer genes into Plants via Horizontal Gene Flow right? I know Fungi sometimes do when the partner up with plants (Some Gardeners I’ve talked with noticed that their Red Corn made the other grasses around them also have red stems, almost as if the Fungi/soil network horizontally transferred some traits). Also many Parasitic plants do this as well.

Reguardless these types of Horizontal Gene Flow examples are small & unlikely to affect the Phylogenic Trees bigly right? But Identify HGT is a separate analysis so does that mean many of the phylogenic trees have not token that into account?

@ljazz

I think GMO can be a powerful tool, but before we do anything stupid; I think we should sit down and think about what we are doing and how we are doing it for a bit.

I agree. Altho GMO technology like via Crisper seems only useful is very very VERY specific cases. Much of the Breeding effort is still better done thru cross pollination! Lots of genes are crucial & interact in many ways. Simply transfering 1 gene across isn’t as straight forward all the time.
However I wonder how effective is employing Parasytic plants to the job for you? That way you are using “GMO Technology” but doing it naturally. Grafting can also facilitate HGT but really isn’t “GMO Technology”.

Altho I’m now curious how AI is going to help make GMO Technology more accurate?
Apparently researchers are now able to identify which genes have & code for the exact trait they are looking for. Super useful to help hybridize the exact plants you want.