6 ms·

An Onion's Genome Has Five Times More DNA Than Humans (2019)

51 points by disqard 6y ago

pvaldes 6y ago
Is typical in plants, yes. Because plants can reproduce asexually.
LatteLazy 6y ago
Most of human dna is garbage, it doesn't code for anything. A full 8% of the Human genome is just viruses. If you want efficiency, there are viruses with only 2 genes. 2. 1 for their shell and one for the enzyme that copies dna...
- echelon 6y ago
  > Most of human dna is garbage, it doesn't code for anything. It's not garbage. If you remove it, you won't have a functional human. "Junk" DNA does quite a bit: Shield from damage, change spatial conformation of DNA in 3D space, change histone wrapping offsets, provide a basis for gene duplication and mutation (which is fertile ground for evolution), etc. The spatial effects have a nonnegligible impact on gene transcription. Imagine gutting your PC and throwing just the essential components into a cardboard box and expecting them to work. A better analogy: do the same to an automobile factory, because that's a better proxy for a cell. > A full 8% of the Human genome is just viruses. Which have contributed to our evolution. The placenta has been theorized to be of viral origin. The immune system, which in places uses complex gene rearrangement, also benefits from viral genes.
  - jhbadger 6y ago
    We know from the Fugu (pufferfish) genome that vertebrate genomes can get away with almost no junk. And before people say "well, that's just a fish, not an amazing human", realize that from the larger evolutionary perspective, the difference between a fish and a human is almost nothing. There is no particular reason to imagine that "you won't have a functional human" without the vast majority of junk DNA. Obviously there would be ethical concerns for doing this experiment, but the fact that onions can have huge genomes and fish small ones is pretty good evidence that there is no correlation with the amount of junk and functionality.
    - echelon 6y ago
      An organism can evolve without junk DNA. But to take human genetic code and remove the junk would change transcription that currently expects it. Portions of the DNA that might be wound would be exposed, or vice versa. It impacts DNA repair, transposition, promoter kinetics, etc. It's a vargus nerve situation. We evolved around our junk DNA. It's a part of our machine.
- globular-toast 6y ago
  Some of them, like HIV, encode multiple genes in overlapping sections. If ever there was a case for intelligent design it would be in these viruses, not complex organisms with huge genomes like plants and humans.
  - ericbarrett 6y ago
    Wouldn’t a virus be hard-selected for short, efficient genetic code? They are so tiny that extra base pairs must have an enormous effect on their physical and mechanical condition.
    - globular-toast 6y ago
      It really depends on the virus. Some like the famous bacteriophages have relatively large DNA genomes and they are the most abundant viruses on Earth. There are also giant viruses with genomes bigger than some bacteria. It's all very strange. This leads people to think these viruses evolved via different mechanisms. Some are likely ancient and have been around since before other life started using DNA while others seem to be more like highly specialised bacteria that have lost their own ability to reproduce (hence rendering them viruses).
- yters 6y ago
  I believe the ENCODE project has shown the junk dna hypothesis is not clearly true. A large portion of the genome codes for something, somewhere above 70 percent, even if most of it doesn't create proteins directly. As an analogy, a piece of well written code often has a lot of extra info not directly tied to its core function, such as logging, error handling, etc. Much could be removed without impacting the core function, but that doesn't mean it is junk code.
throwawaygal7 6y ago
This is unsurprising since we often observe plants with a larger number of chromosomes, and a higher number of sets of chromosomes than animals. I believe this is theorized to be a product of domestication (domesticated crops often have a higher number of copies than their wild relatives).
magicalhippo 6y ago
So assuming most of this 5x is "junk" (as the article seems to indicate), how much energy/nutrients does it cost an onion plant to keep copying the "extra junk" compared to if it had the same relative amount of "junk" as that of a human? I imagine not a lot, given that a cell contains a lot more than the DNA itself, but yeah...
mrfusion 6y ago
I think there are trade offs here that we don’t understand yet.
oji0hub 6y ago
This explains a lot.
zepto 6y ago
This is why, after human civilization collapses, onions will inherit the earth.
coding123 6y ago
I was planning on chopping up an onion a little later. Now I'm totally scared of the consequences.
- teh_klev 6y ago
  It's why they make you cry :)
simpleguitar 6y ago
The difference between animals and plants is that animals can "do life" with movement, whereas plants, being stuck in place, use chemistry. Take self defense for example. Animals will run or fight. An onion will make you cry with chemistry. Think of any life function you do with movement. There are equivalent function for a tree that doesn't require movement, and they are all chemistry. Plants do a lot of amazingly sophisticated, almost impossible (photosynthesis!), chemistry to live. More chemistry means they need more genes.
- sscarduzio 6y ago
  Why photosynthesis is "almost impossible"? Genuine question!
  - curtis3389 6y ago
    Although the overall chemistry of photosynthesis seems simple (mH₂0 + nCO₂ => Cₙ(H₂0)ₘ + nO₂), it is driven by a pretty complex arrangement of parts, called the reaction centre: https://en.wikipedia.org/wiki/Photosynthetic_reaction_centre https://en.wikipedia.org/wiki/Photosynthetic_reaction_centre > The energy of the photon is used to excite an electron of a pigment. The free energy created is then used to reduce a chain of nearby electron acceptors, which have progressively higher redox-potentials. These electron transfer steps are the initial phase of a series of energy conversion reactions, ultimately resulting in the conversion of the energy of photons to the storage of that energy by the production of chemical bonds.
  - simpleguitar 6y ago
    > Why photosynthesis is "almost impossible"? Genuine question https://www.discovermagazine.com/technology/physicists-see-quantum-effects-in-photosynthesis https://www.discovermagazine.com/technology/physicists-see-q...
- Out_of_Characte 6y ago
  I dont doubt that plants have more utility for keeping genetic information. Animals also have much more tricks to reduce their need for genetic information. Think of newborn animals often shaking untill their cerebellum develops more and is able to provide smooth motion while balancing against gravity. or birds singing songs to increase transient information. and one of the biggest information breaktrough ofcourse being the written word and now artificial intelligence
smitty1e 6y ago
> yet the human genome turns out to contain only 20,000 or so genes (roughly the same number of genes as a fruit fly or nematode worm). So the amount of static data isn't a full measure of the question of life. Protein folding, anyone?
- arrosenberg 6y ago
  Close, but not quite - more likely that DNA transcription occurs at multiple sites on the same genetic code allowing for different reads/proteins.
  - smitty1e 6y ago
    There needn't be a single answer.
- ravi-delia 6y ago
  An enormous amount of it comes from development, just the physical and chemical interactions of lots of dumb components making a pretty complicated whole.
- approaching236 6y ago
  Compression is weird. https://en.m.wikipedia.org/wiki/Kolmogorov_complexity https://en.m.wikipedia.org/wiki/Kolmogorov_complexity
LargoLasskhyfv 6y ago
Nothing special. The genome of mistletoe seems to be about 40 times bigger [1], while lacking something deemed essential for any other mulitcellular organism [2], the ability to produce ATP! [3] [1] https://www.ed.ac.uk/news/2020/mistletoe-under-spotlight-of-major-dna-study https://www.ed.ac.uk/news/2020/mistletoe-under-spotlight-of-... [2] https://archive.news.indiana.edu/releases/iu/2015/06/mistletoe-genome.shtml https://archive.news.indiana.edu/releases/iu/2015/06/mistlet... [3] https://www.quantamagazine.org/the-mystery-of-mistletoes-missing-genes-20201221/ https://www.quantamagazine.org/the-mystery-of-mistletoes-mis... GETAFIX!
justaguyOOL 6y ago
That's a pretty cool find :D

51 points by disqard 6y ago

Is typical in plants, yes. Because plants can reproduce asexually.

Most of human dna is garbage, it doesn't code for anything. A full 8% of the Human genome is just viruses. If you want efficiency, there are viruses with only 2 genes. 2. 1 for their shell and one for the enzyme that copies dna...

echelon 6y ago
> Most of human dna is garbage, it doesn't code for anything. It's not garbage. If you remove it, you won't have a functional human. "Junk" DNA does quite a bit: Shield from damage, change spatial conformation of DNA in 3D space, change histone wrapping offsets, provide a basis for gene duplication and mutation (which is fertile ground for evolution), etc. The spatial effects have a nonnegligible impact on gene transcription. Imagine gutting your PC and throwing just the essential components into a cardboard box and expecting them to work. A better analogy: do the same to an automobile factory, because that's a better proxy for a cell. > A full 8% of the Human genome is just viruses. Which have contributed to our evolution. The placenta has been theorized to be of viral origin. The immune system, which in places uses complex gene rearrangement, also benefits from viral genes.
- jhbadger 6y ago
  We know from the Fugu (pufferfish) genome that vertebrate genomes can get away with almost no junk. And before people say "well, that's just a fish, not an amazing human", realize that from the larger evolutionary perspective, the difference between a fish and a human is almost nothing. There is no particular reason to imagine that "you won't have a functional human" without the vast majority of junk DNA. Obviously there would be ethical concerns for doing this experiment, but the fact that onions can have huge genomes and fish small ones is pretty good evidence that there is no correlation with the amount of junk and functionality.
  - echelon 6y ago
    An organism can evolve without junk DNA. But to take human genetic code and remove the junk would change transcription that currently expects it. Portions of the DNA that might be wound would be exposed, or vice versa. It impacts DNA repair, transposition, promoter kinetics, etc. It's a vargus nerve situation. We evolved around our junk DNA. It's a part of our machine.
globular-toast 6y ago
Some of them, like HIV, encode multiple genes in overlapping sections. If ever there was a case for intelligent design it would be in these viruses, not complex organisms with huge genomes like plants and humans.
- ericbarrett 6y ago
  Wouldn’t a virus be hard-selected for short, efficient genetic code? They are so tiny that extra base pairs must have an enormous effect on their physical and mechanical condition.
  - globular-toast 6y ago
    It really depends on the virus. Some like the famous bacteriophages have relatively large DNA genomes and they are the most abundant viruses on Earth. There are also giant viruses with genomes bigger than some bacteria. It's all very strange. This leads people to think these viruses evolved via different mechanisms. Some are likely ancient and have been around since before other life started using DNA while others seem to be more like highly specialised bacteria that have lost their own ability to reproduce (hence rendering them viruses).
yters 6y ago
I believe the ENCODE project has shown the junk dna hypothesis is not clearly true. A large portion of the genome codes for something, somewhere above 70 percent, even if most of it doesn't create proteins directly. As an analogy, a piece of well written code often has a lot of extra info not directly tied to its core function, such as logging, error handling, etc. Much could be removed without impacting the core function, but that doesn't mean it is junk code.

throwawaygal7 6y ago

This is unsurprising since we often observe plants with a larger number of chromosomes, and a higher number of sets of chromosomes than animals. I believe this is theorized to be a product of domestication (domesticated crops often have a higher number of copies than their wild relatives).

magicalhippo 6y ago

So assuming most of this 5x is "junk" (as the article seems to indicate), how much energy/nutrients does it cost an onion plant to keep copying the "extra junk" compared to if it had the same relative amount of "junk" as that of a human? I imagine not a lot, given that a cell contains a lot more than the DNA itself, but yeah...

mrfusion 6y ago

I think there are trade offs here that we don’t understand yet.

oji0hub 6y ago

This explains a lot.

zepto 6y ago

This is why, after human civilization collapses, onions will inherit the earth.

coding123 6y ago

I was planning on chopping up an onion a little later. Now I'm totally scared of the consequences.

teh_klev 6y ago
It's why they make you cry :)

simpleguitar 6y ago

The difference between animals and plants is that animals can "do life" with movement, whereas plants, being stuck in place, use chemistry. Take self defense for example. Animals will run or fight. An onion will make you cry with chemistry. Think of any life function you do with movement. There are equivalent function for a tree that doesn't require movement, and they are all chemistry. Plants do a lot of amazingly sophisticated, almost impossible (photosynthesis!), chemistry to live. More chemistry means they need more genes.

sscarduzio 6y ago
Why photosynthesis is "almost impossible"? Genuine question!
- curtis3389 6y ago
  Although the overall chemistry of photosynthesis seems simple (mH₂0 + nCO₂ => Cₙ(H₂0)ₘ + nO₂), it is driven by a pretty complex arrangement of parts, called the reaction centre: https://en.wikipedia.org/wiki/Photosynthetic_reaction_centre https://en.wikipedia.org/wiki/Photosynthetic_reaction_centre > The energy of the photon is used to excite an electron of a pigment. The free energy created is then used to reduce a chain of nearby electron acceptors, which have progressively higher redox-potentials. These electron transfer steps are the initial phase of a series of energy conversion reactions, ultimately resulting in the conversion of the energy of photons to the storage of that energy by the production of chemical bonds.
- simpleguitar 6y ago
  > Why photosynthesis is "almost impossible"? Genuine question https://www.discovermagazine.com/technology/physicists-see-quantum-effects-in-photosynthesis https://www.discovermagazine.com/technology/physicists-see-q...
Out_of_Characte 6y ago
I dont doubt that plants have more utility for keeping genetic information. Animals also have much more tricks to reduce their need for genetic information. Think of newborn animals often shaking untill their cerebellum develops more and is able to provide smooth motion while balancing against gravity. or birds singing songs to increase transient information. and one of the biggest information breaktrough ofcourse being the written word and now artificial intelligence

smitty1e 6y ago

> yet the human genome turns out to contain only 20,000 or so genes (roughly the same number of genes as a fruit fly or nematode worm). So the amount of static data isn't a full measure of the question of life. Protein folding, anyone?

arrosenberg 6y ago
Close, but not quite - more likely that DNA transcription occurs at multiple sites on the same genetic code allowing for different reads/proteins.
- smitty1e 6y ago
  There needn't be a single answer.
ravi-delia 6y ago
An enormous amount of it comes from development, just the physical and chemical interactions of lots of dumb components making a pretty complicated whole.
approaching236 6y ago
Compression is weird. https://en.m.wikipedia.org/wiki/Kolmogorov_complexity https://en.m.wikipedia.org/wiki/Kolmogorov_complexity

LargoLasskhyfv 6y ago

Nothing special. The genome of mistletoe seems to be about 40 times bigger [1], while lacking something deemed essential for any other mulitcellular organism [2], the ability to produce ATP! [3] [1] https://www.ed.ac.uk/news/2020/mistletoe-under-spotlight-of-major-dna-study https://www.ed.ac.uk/news/2020/mistletoe-under-spotlight-of-... [2] https://archive.news.indiana.edu/releases/iu/2015/06/mistletoe-genome.shtml https://archive.news.indiana.edu/releases/iu/2015/06/mistlet... [3] https://www.quantamagazine.org/the-mystery-of-mistletoes-missing-genes-20201221/ https://www.quantamagazine.org/the-mystery-of-mistletoes-mis... GETAFIX!

justaguyOOL 6y ago

That's a pretty cool find :D