Scientists Find the Largest Known Genome Inside a Small Plant (nytimes.com) 45
An anonymous reader quotes a report from the New York Times: Last year, Jaume Pellicer led a team of fellow scientists into a forest on Grande Terre, an island east of Australia. They were in search of a fern called Tmesipteris oblanceolata. Standing just a few inches tall, it was not easy to find on the forest floor. "It doesn't catch the eye," said Dr. Pellicer, who works at the Botanical Institute of Barcelona in Spain. "You would probably step on it and not even realize it." The scientists eventually managed to spot the nondescript fern. When Dr. Pellicer and his colleagues studied it in the lab, they discovered it held an extraordinary secret. Tmesipteris oblanceolata has the largest known genome on Earth. As the researchers described in a study published on Friday, the fern's cells contain more than 50 times as much DNA as ours do. [The analysis revealed the species T. oblanceolata to have a record-breaking genome size of 160.45 Gbp, which is about 7% larger than that of P. japonica (148.89 Gbp). For comparison, the human genome contains about 3.1 Gbp distributed across 23 chromosomes and when stretched out like a ball of yarn, the length of DNA in each cell only measures about 2m.] "Surprisingly, having a larger genome is usually not an advantage," notes Phys.org in a report. "In the case of plants, species possessing large amounts of DNA are restricted to being slow growing perennials, are less efficient at photosynthesis (the process by which plants convert the sun's energy into sugars) and require more nutrients (especially nitrogen and phosphates) to grow and compete successfully with their smaller-genomed neighbors. In turn, such effects may influence the ability of a plant to adapt to climate change and their risk of extinction."
"In animals, some of the largest genomes include the marbled lungfish (Protopterus aethiopicus) at 129.90 Gbp and the Neuse River waterdog (Necturus lewisi) at 117.47 Gbp," reports Phys.org. "In stark contrast, six of the largest-known eukaryotic genomes are held by plants, including the European mistletoe (Viscum album) at 100.84 Gbp."
"In animals, some of the largest genomes include the marbled lungfish (Protopterus aethiopicus) at 129.90 Gbp and the Neuse River waterdog (Necturus lewisi) at 117.47 Gbp," reports Phys.org. "In stark contrast, six of the largest-known eukaryotic genomes are held by plants, including the European mistletoe (Viscum album) at 100.84 Gbp."
Clearly the Result (Score:3)
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Because most animals have to move quickly to avoid predators or hunt, weight is a premium. Plants can afford to be DNA pack-rats.
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Maybe those plants offset those disadvantages by having a handy library of genetic ideas ready to activate when it comes time to adapt. They lasted this long for a reason.
Re:Clearly the Result (Score:5, Interesting)
For mammals, it's easy. Enzymes have to work at body temperature. End of complexity.
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It might even be an experiment that has been done - IANA biochemist or geneticist. I don't know. But I'd be unwilling to make a prediction mys
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We may have too many genes as it is. How many overlapping control systems or different proteins do we need? Much of our DNA is the result of virus like activity of HERVs and LINE transposons
An important discovery, although less celebrated, is that more than half the human genome is derived from mobile pieces of DNA called transposable elements (colloquially known as “jumping genes”). https://www.ncbi.nlm.nih.gov/p... [nih.gov]
We also utilize other organisms. We have 2-10x the number of gut bacteria as cells in our body, which produce beneficial substances that we canno
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There is a huge blank space in the human genome that serves no known purpose. It isn't a guard of any kind, it doesn't shorten, it's just the same letter repeated for a very long time. So long, it's not been possible to sequence until recently, as there was no way to tell how long a stretch it was.
I wonder what would happen if you used gene editing tools to reduce or remove it. Would cells copy faster? Would it make a measurable improvement to cell function?
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Ummm, citation required.
There are long sequences (plural; many, not one) of repeating short sequences of base pairs (e.g. AGTTAGCTAGCTAGCTAGCTAGCT...), which indeed are hard to measure, and of unknown function. If, indeed, any function.
Since you're talking about human cells, you're going to need to take your experimental proposal to the Ethics Committee before you go mu
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Transposons seem to serve an important role, as each brain cell has a unique genome due to gene migration. However, it's entirely likely we do have an excessively complex genome.
It is possible that the Singularity won't be an advance in AI to superhuman levels, but a refactoring of human DNA to remove instabilities and regions that are carcinogenic if activated. This would result in a hominid that could not interbreed with historic lines, only members of the new species.
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...of nature evolving more advanced compression algorithms in more complex organisms.
lol, I'm guessing you're joking.
But just in case some people don't realize this is a joke, I will add that there are several reasons why it doesn't quite work like that. To name a few:
1. The idea of "more advanced" assumes a linearity to evolution that does not fit with natural selection (the "escalator fallacy" discussed by Mary Midgley)
2. While many genes perform multiple functions, these are not in any way planned, as though a gene becomes established because it does both A and B and therefore can repla
12000 out of 400000 (Score:3)
Since we've only sequenced 0.3% of plant species ... a bigger one might be out there still.
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Since we've only sequenced 0.3% of plant species ... a bigger one might be out there still.
You don't have to sequence a genome to see how big it is.
Also, 12,000 out of 400,000 is 3%, not 0.3%.
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Oops you're right that's 3%. And that's true we don't need to sequence the whole genome (though we probably should) the quote from the article was "botanists have measured the sizes of genomes in only 12,000 species of plants, leaving 400,000 other species to study. "
Feed me ... (Score:2)
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Ever see the alternate ending?
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No. I'm more a fan of the 1960 original release anyway.
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https://www.imdb.com/title/tt0054033/ [imdb.com]
Sadly, they seem to have colorized it.
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Underlords? (Score:2)
"You would probably step on it and not even realize it."
I, for one, welcome our new underfoot overlords.
I read "largest known gnome"... (Score:3)
... and I got excited.
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Do we really need another film in the gnome series?
been around for a while (Score:2)
Perhaps it (or its ancestors) have been around for a while. And acquired more and more code without a rewrite ... except to find three different implementations of photosynthesis, four incompatible tables with color values, two quicksort libraries, a Gopher server, a partially complete GNU/Hurd kernel and a small "game of life" implementation :-)
That's New Caledonia you POS NYtimes "journalist" (Score:3)
"Grande Terre" is the nickname of the main island of New Caledonia, an overseas territory of France, you piece of shit pseudo-journalist.
I've never seen anyone make such contorsions to avoid mentioning that fact when speaking about New Caledonia.
Source:
"Here, we report the discovery of an even larger eukaryotic genome in Tmesipteris oblanceolata, a New Caledonian fork fern."
New Caledonia separated millions of years ago from Australia (it isn't a coral reef/volcanic spurt) and is home to a lot of endemic species, meaning that you cannot find those anywhere else on the planet.
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The presumption is that they are avoiding saying it because of the current unrest there and the French putting it down by force.
YA colony that doesn't want to be one.
That's incredible! (Score:2)
How do they fit such a large genome in such a small plant???
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I didn't actually expect a serious answer there :) I thought a lot of tiny creatures would have dna longer than the creature itself.
With my experience though the real miracle is how it doesn't get into a knot.
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A very good point.
Which suggests a question to put to experiment - is there some efficient tangle-prevention mechanism (e.g. tie-points in the folding, whose breaking can be sequenced to control unfolding sequencing), or is there an untangling mechanism?
The answer could be "both". For strands of DNA (which already have a complex packaging system, in eukaryotes) there is already a cutting+ splicing mechanism (which could form the core of a tangle-removal mechanism) ; but to untangle a complex
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I'm surprised that there are untangling mechanisms. I mainly imagined mechanisms to avoid getting tangled up. Like reading your newspaper in a crowded subway and meanwhile sorting the pages so you end up with two newspapers half the thickness.
With sperm tails you can still think of relatively random nearby rejoining.
With dna you don't have that freedom and it would have to act as a shaftpasser https://medium.com/@jasoncomel... [medium.com]
I also imagine topological arguments would help but it would have to be trimmed s
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Consider the humble prokaryote DNA loop (I think it's always a simple loop; but it is always a loop of a two-strand spiral thread.) At several points along it's length DNA is being un-twisted, broken into two strands, one strand being spooled away into the protein transcription engine (a big immobile molecule), while a copy is created on the template of the first strand and re-wound.
I've handled more 100m ropes than most people (caver, 100m shaft ; 100m le
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I use an electrical cable of 15m to mow the grass so I'm aware. Also as I kid I often wondered how the old phone cords would keep coiling up.
I found out about Topoisomerase 1 and 2 now. Pretty close to the shaft passer. They hold the ends they just cut to rejoin them afterwards. haven't found out about untangling the flagellum yet.
It's interesting though, these topological issues.I used to make jokes about a genius mathematician who invented knitting and the sewing machine.
The shaft passer was supposedly us
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I didn't know there were enzymes that could do that, but I'm not terribly surprised. The number of lengths of amino acid chain that that molecule can work on would be fairly restricted (compared to the trillions of possible protein chain sections).
You've got most of the necessary steps :
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Not in WW2, but like I said it would only work if the two parties work together well :)
Topoisomerase 1 and 2 don't work on amino acids, they work on dna. Now, I don't know much about the topic and I don't know whether rna has its own coiling problems but I would think once rna gets translated to amino acids there should be no cutting since the protein has to fold up in a specific manner and I assume it is folding while it is being created.
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, this
, this
and this
are variable.
- While excision of parts of a DNA sequence is a fundamental part of the organisation of eukaryotes, if we are to accept Margulis' "extended symbiosis" idea (where almost all structures of eukaryotes were gained by endosymbiosis of sev
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Concerning the 3d folding I thought the protein chain would just have natural angles causing it fold up and the end result would be limited by what was allowed by that mechanism.
Which once you spell it out has a lot of assumptions...
I understand 'it's always more messy than the clean principles once you look closely' though.
I checked out Margulis once. I only understood it as 'mitochondria were simply adopted and it does not fit our ideas of evolution through selection and competition, now let's generalize
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Quite plausibly. Though I'd also have pointed out that, to destroy a city (say, 10 times a Hiroshima bomb) would take a fairly small meteorite. Somewhere well below a "Cañon Diablo" ("Barringer crater") size meteorite. (Take around 1/2 cu.km of material ; put it in the middle of your target
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Ok you did say more than a city, let's say Belgium.
I liked Margulis' idea a lot and from that the idea that you should replace selection by competition by a more hybrid mechanics which includes symbiosis.
But I was cautious about generalizing it too much.
I got my intuition of the evolution of early life from Stuart Kauffman who studied boolean networks. He defined life (from memory)as 'an autocatalytic set of molecules with a food source'. That was a fabulous idea about getting life started with just a netwo
From what I understand (Score:2)
Many plants with huge genomes have many, many copies of a much shorter functional genome. The purpose of the copies has never been clear to me, but I would imagine it's protection against damage. If a segment gets disabled, it's absolutely no big deal. However, I've seen nothing that shows that's the correct explanation, and as it would inhibit evolution for the same reason, it's probably incorrect.
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I've never heard a good explanation for it, but it is intimately involved in the way that plants can cross-fertilize successfully at taxonomic levels higher than animals can do. For example, some cat species (mammals) can interbreed successfully - which exposes how the "reproductive isolation" way of defining "species" is ... at best, problemati
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Many plants with huge genomes have many, many copies of a much shorter functional genome.
Indeed, and unfortunately the summary left out this important blurb from the paper describing this species of fern as an octoploid,
Tmesipteris oblanceolata subsp. linearifolia has been reported, like P. japonica, to be an octoploid, but it has a much higher chromosome number (2n = 416 versus 2n = 407,19). Its massive genome is thus considered to have arisen through the combined effects of repetitive DNA accumulation and polyploidy, as in other species of the genus.
The purpose of the copies has never been clear to me, but I would imagine it's protection against damage.
It’s certainly an interesting question and actively debated. You may find the perspective of this recent paper interesting,
https://www.ncbi.nlm.nih.gov/p... [nih.gov]