Bow down before the organism God actually created in his own image: a small fern found on New Caledonia, Tmesipteris oblanceolata. Furthermore, the name of God’s avatar is also unpronounceable.
Tmesipteris oblanceolata
160 billion base pairs! Our genome has only 2% of the complexity of this fern.
We need to make a pilgrimage to a small island east of Australia now.
All I said was “that piece of halibut was good enough for Tmesipteris oblanceolata.”
check out the crows when you are visiting!
Some of the ENCODE junk DNA deniers are still at it.
Revolutionary Genetics Research Shows RNA May Rule Our Genome
Apologies in advance for the utter ignorance of biology.
Doesn’t at some point having that much DNA to lug around and copy and transcribe get in the way of doing things efficiently?
Doesn’t the amount of DNA affect metabolism in some way?
random hypothesizin’ time, my turn: there was a very unusual survival benefit for having a fat slug of chemicals in the middle of your nucleus for this fern at some point, like maybe a DNA-gobbling bacteria evolved and this was their quick-and-dirty solution. who’s next?
It’s a plant. It doesn’t “lug around” anything.
It only needs to be copied during cell division. Yes, this is a cost, but the penalty is not so much as you might think.
Most of it doesn’t need to be transcribed. A small amount will be anyway, see the previous point.
Since it’s mostly just sitting there, it has little effect on efficiency.
Recommended reading: What’s in Your Genome?: 90% of Your Genome Is Junk
by Larry Moran, ISBN: 9781487508593
Hey, so, off-topic but I wanted to share that Robert Evans’ “Behind the Bastards” podcast just dropped part one of a series on Kent Hovind. I’m looking forward to learning a whole new set of reasons to be disgusted by this weird-ass charlatan!
Cool fern btw.
Um.
“The largest living fungus may be a honey fungus[25] of the species Armillaria ostoyae.[26] A mushroom of this type in the Malheur National Forest in the Blue Mountains of eastern Oregon, U.S. was found to be the largest fungal colony in the world, spanning 8.9 km2 (2,200 acres) of area.[27][28] This organism is estimated to be 2,400 years old.”
(https://en.wikipedia.org/wiki/Largest_organisms#Fungi)
It’s my understanding that plants generally have larger genomes than animals. My first guess as to why is that plants don’t have a nervous system so they have to do all that with chemical messaging. They need thousands of messengers while animals only need 100 or so. That’s a lot of synthesis to be managed.
Just give it to me straight for once, PZ. Do I have to work for big brainstem™ now or what?
Should, but won’t, put an end to the “DNA is a code” nonsense from creationists.
Wait… does this mean The 5th Element lied to me?
It’s not surprising at all that Carl Zimmer didn’t shit on himself conveying this. He says:
I’m no expert on this stuff but I’d lean heavily into the ploidy angle myself. Would viral sequences accumulate to that degree? Of course how often do viral sequences confer any benefit to an organism aside from maybe placentation in mammals thanks to an inserted retroviral sequence?
With ploidy as with gene duplication there may be benefits with added genes producing more gene product. Human liver cells can be polyploid, but to what known benefit?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592246/
Adding copies of genes via duplication in meiosis cross-overs or by full genome ploidy could allow copies to diverge in function (cue Susumu Ohno), but just as well might result in the copies degenerating into nonsense, as my reply is kinda doing at this point.
So maybe polyploid plants have a bunch of decayed former genes if the addition of copies adds nothing beyond initial sufficiency?
I really don’t know if this speculation by Zimmer is warranted:
Also this part leads me to another important concept left out:
The onion test?
Reginald Selkirk @6
Didn’t PZ say he was going to review Moran’s book at some point…?
Also a bit off piste for the current topic but isn’t polyploidy a means for plants to undergo instantaneous (dare I say saltational) speciation? A rediscoverer of Mendel Hugo de Vries was smitten by a primrose. I tried skimming this but my post-work brain started glitching:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227404/
If one includes both transposons and viruses as “virus-like stretches”, the answer is: yes, they really would accumulate.
What’s in your genome by L. Moran
This is a brief table of what is in the human genome. Transposons 44%, viruses 9%, and a very small fraction of those are active. In fact, about 10% of the human genome is made up of one family of repetitive sequences (which Moran would classify as transposons, or transposon-like) Alu, with about a million copies.
You probably noticed that he uses a lot of waffle words, “may” this, “may” that. A lengthier discussion would include mention of the nearly-neutral theory of evolution.
Yes, the onion test. Perhaps more interesting than the human::onion comparison is the variation in genome size between species of onion (wikipedia) which do not appear much different.
Plants do seem to be more prone to polyploidy than animals, but humans – and other vertebrates have evidence of two whole genome duplications deep in the past.
Polyploidy is most common in plants, though salamanders and leeches are animals that exhibit polyploidy. It is often linked with the ability to reproduce asexually.
Only a small proportion of the plants have been sequenced, but ferns and mosses evolved early in the history of Earth so I wouldn’t be surprised if many species display such enormous genomes.
I wonder how its amount of DNA compares to another fern, Ophioglossum reticulatum, which at a haploid number of 1260 – 1500, holds the record among plants for most chromosomes?
Reginald Selkirk @16
Yeah good point about tranposons and Alu in humans.
I still wonder to what extent ploidy itself contributed to the genome size of this ferm versus viral sequence accumulation. Here’s the original article:
https://www.cell.com/iscience/fulltext/S2589-0042(24)01111-8
This organism is at 160.45 Gbp/1C. They say:
So the octoploid above is 2.01 times larger in genome than the tetraploid which seems a doubling of ploidy equalling a doubling of genome size. T. oblanceolata subsp. linearifolia is 2.19 times larger than T. tannensis above in genome size. Ploidy still seems important.
They say:
I see Joe Felsenstein is here so I defer to him on the details.
Also:
I wonder over time if the gene copies would decay away from being functional sequences.
F.O.@4 — the metabolic cost of DNA replication and storage is surprisingly small. This is one of the reasons antibiotic resistance is such a big problem. I remember being taught at uni (back in the Pleistocene) that if we stopped exposing bacteria to antibiotics they would quickly lose their resistance because of the reproductive advantage of not having to copy all that DNA. We now know that bacteria will happily hold onto their resistance plasmids for many, many generations even when they are not exposed to antibiotics. Preventing antibiotic exposure does help, but only because those resistance genes eventually mutate to become ineffective in the absence of selection pressure — a far slower process than being actively selected against, while allowing quick recovery of functionality with a few point mutations if antibiotic exposure resumes.
Hemidactylus@13– Echoing Reginal Selkirk here: roughly half the human genome is viral remnants or repetitive sequences that we suspect are of viral origin.
Adding to the comment above: When there is a polyploidy event, viral remnants will be duplicated along with the rest of the chromosome. Polyploidy and viral inclusion are not mutually exclusive processes.
chrislawson @20 and @21
Yeah I was more focused on plant ploidy than the case in humans but see your point about ploidy actually multiplying the extent of existing viral remnants.
As for antibiotic resistance with plasmids and also to some extent phages bacteria pretty much excel at file sharing (prokaryotic Napster) so a horizontal gene transfer sort of gene flow is happening. If bacteria lose antibiotic resistance it might not be a big deal to borrow it from another type of bacteria in the future. I guess this could be compared also to crowd sourcing.
In New Caledonia, the crows check you out!
@Hemidactulus #13:
That has a name: diploidization. Duplicate chromosomes diverge, by selection or drift, until it’s hard to tell that they’re homologous.
I believe New Caledonia is also where crested geckos originate, so if we all go, I’ll have to bring my daughter’s gecko Alex so he can visit his homeland. :)
@4 FO
As most others have said, with one caveat – There are cases in which microbes have shed nearly all excess DNA, but this is in environments with massively low levels of available energy, and I think also usually oxygen poor ones. This is due to the fact that they can’t a) get food quickly and efficiently, and b) non-oxygen based metabolic processes, while they work, are themselves less efficient, so such organisms need to conserve energy in all things that they do. Something like this plant though… has basically more than it needs from the soil and sunlight to replicate pretty much any amount of DNA it wants, with, as has been said before, almost no constraint on the costs.
On an aside, and as a joke, its an Australian plant, so obviously all that extra DNA must be there to provide it with new ways to try to kill us in the future, when all the other terrible things on that continent fail! lol
From the link in the OP:
Yes. Much of science seems to be reorientating in this way. Cosmologists used to say, “why is there something rather than nothing”? Now it’s more, “why would there be nothing”?
Likewise in biology it’s becoming less a question of why a thing should exist, and more a question of why it should not.
@ 8 Morales
This thread is about size of genome, not territory doofus.
John Harshman @24
Thanks! That tidbit of info may help me figure out a bit more what may be going on with this fern! Plus it adds to my ongoing education on these fascinating issues.
Cool stuff:
https://en.m.wikipedia.org/wiki/Diploidization
Clearly a case of confirmation bias on my part as the wiki shows diploidization has got more moving parts than this yet:
New Caledonia is undergoing political violence right now. Hope this poor fern survives.