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Largest genome sequenced so far is 30 times bigger than a human's. The
South American lungfish has a whopping 180 gigabases of DNA in each cell
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|u/dethb0y - 1 month
|
|>“It’s a real enigma how these fish are able to tolerate such a large
|genome,” says Meyer. The nucleus inside each cell has to be very large
|to fit in so much DNA, he says, which means each cell is larger than
|normal. Replicating so much DNA also takes a lot of energy each time
|cells divide. >There is no evidence that all this extra DNA does
|anything useful. Rather, it appears to be a result of “genetic
|parasites” making endless copies of themselves. It is probably mostly
|junk, says Meyer. >His team found that mechanisms that other organisms
|use to curtail the spread of genetic parasites seem to be damaged or
|missing in all the lungfish species. As a result, the genome of the
|South American lungfish has been growing by 3.7 Gb – more than a single
|copy of the human genome – every 10 million years. I wonder if in a few
|million years it'll get to big of a genome and just die out.
|u/tocksin - 1 month
|
|What are genetic parasites and how do other species defend against
|them?
|u/knvn8 - 1 month
|
|Not just viruses. Transposable elements are self replicating
|segments of DNA that can move or copy themselves around the genome.
|Sometimes they carry neighboring segments with them. Can accumulate
|over generations, though selective pressure probably results in most
|being inactive.
|u/Ghostman1887 - 1 month
|
|It's actually believed that many helpful traits are incidentally
|made by this.
|u/Mooshan - 1 month
|
|Including the placenta
|u/FilDM - 1 month
|
|Placentas are from an ancient strand of retrovirus, in the
|same family of HIV if I’m not mistaken.
|u/WonderNo8544 - 1 month
|
|Do you know of any books on this or similar subjects that would be
|worth reading. I find this and things like it fascinating.
|u/570N3814D3 - 1 month
|
|Nessa Carey's Junk DNA is fascinating:
|https://www.goodreads.com/book/show/25083866-junk-dna
|u/matdex - 1 month
|
|This is genetics 101. Pickup a first year genetics book or go
|down a Wikipedia hole.
|u/Cluelesswolfkin - 1 month
|
|~Cue in the fox's x men soundtrack as Patrick Stewart gives the
|intro ~
|u/Lithorex - 1 month
|
|> Not just viruses. Transposable elements are self replicating
|segments of DNA that can move or copy themselves around the
|genome. That is, if viruses themselves aren't transposable
|elements.
|u/Darkmorphos - 1 month
|
|Genetic parasites are pieces of DNA that are able to replicate
|themselve inside a genome. This generally occurs by the piece of DNA
|encoding a protein that allows it to reverse transcribe an RNA copy
|of itself back to DNA and randomly insert itself in the genome,
|hereby copying itself. Over the course of evolution most species
|genomes have become littered with genetic parasites. For instance
|over 50% of the human genome comprises of them (although the vast
|majority has been inactivated through mutations). Many of these
|genetic parasites originate from a retro virus inserting itself into
|a genome, and then mutating over time. This is not necessarily a
|bad thing as they have often evolved to perform functions for the
|organism, such as in regulation of gene expression levels. There is
|even a gene (Syncytin) that is crucial for formation of the placenta
|that has evolved from a retroviral gene. This originates from the
|viral gene that normally allows a retro virus to fuse to the cell
|membrane to enter and infect the cell. Now this gene allows cells of
|the placenta to fuse and form one giant cell around the placenta to
|serve as a barrier between mother and child. The spread of genetic
|parasites is generally inhibited by the cell as the random genomic
|insertion can cause harmful mutations. Furthermore, the RNA
|transcribed from these pieces of DNA can often be stimulatory to the
|Innate immune system. Inhibition of these genetic parasites occurs
|firstly through silencing their genomic regions (by packaging the
|DNA tightly to prevent transcription). Secondly, a defense system of
|the cell called RNA interference can recognise and destroy RNAs
|transcribed from the genetic parasites, preventing them from
|inserting back into the genome. Probably a way more detailed answer
|than you ere looking for, but I couldn't help myself. ;)
|u/tocksin - 1 month
|
|Actually just the right amount.  Just enough so I can look up more
|if I want.  The cellular world is just incredible with its
|complexity.
|u/Nemisis_the_2nd - 1 month
|
|The bit that I really like about this is that bacteria have a
|similar problem, and their answer is to use a group of proteins
|called Restriction Enzymes to cut up the unwanted genetic code.
|The thing is, though, that there is another group of enzymes
|called ligases which exist to stick bits of broken genetic code
|back together. Scientists realised that they could use the
|Restriction Enzymes to selectively cut apart 2 bits of different
|DNA, then use the ligases to stick those different bits
|together, making a completely new DNA sequence. This was how
|modern genetic engineering was born. As a result, gene editing
|is fairly standardised and often no more difficult than using a
|computer code like python, it is just a bit more labour
|intensive.
|u/NadjaLuvsLaszlo - 1 month
|
|Wow... this was such an interesting read! Thank you! Genetics are
|ENDLESSLY FASCINATING!
|u/Randall_Flaggg - 1 month
|
|I enjoyed the hell outta this. Sounds like a rad sci-fi about an
|alien world but nay, it’s all in ME.
|u/Darkmorphos - 1 month
|
|Happy to hear! :D And yeah its crazy, I love researching our
|crazy biology.
|u/SimoneNonvelodico - 1 month
|
|"Boss, a hacker tried to break into our system!" "Damn it! Have
|you erased anything he left behind, for safety?" "Actually, this
|guy was good. I'm stealing his code and putting it in production."
|u/centizen24 - 1 month
|
|So cells have a genetic antivirus to protect against these
|parasitic RNA's? How do they detect and differentiate between
|them, is it signature based or heuristic observation of what the
|code will attempt to do?
|u/Izawwlgood - 1 month
|
|Viruses.
|u/Collin_the_doodle - 1 month
|
|Transposons could also be a possibility
|u/BigBad01 - 1 month
|
|It's mostly transposons.
|u/weaselmaster - 1 month
|
|It’s all transposons these days — perhaps you need a refresher
|course!
|u/TheGnarWall - 1 month
|
|Before even seeing this article I was running this morning and
|thinking about this very thing. How DNA is so heavily formed by
|interactions with viruses. Do you happen to know of any good books
|or papers on the subject?
|u/Wheelchair_Legs - 1 month
|
|Google "retroviral elements" or "endogenous retrovirus"
|u/Crash_Test_Dummy66 - 1 month
|
|Hey that's what my dad used to call me!
|u/Thunderous_grundle - 1 month
|
|Tune in tonight at 7 where we will discuss genetic parasites, and
|how they could potentially hurt democrats at the polls this
|November.
|u/oojacoboo - 1 month
|
|Probably similar to an mRNA vaccine.
|u/Hanuman_Jr - 1 month
|
|I imagine it's a lot like "mad cow" disease. Someone didn't know
|how to fold the proteins right and now they are all screwed up.
|u/phlipped - 1 month
|
|Unfortunately your imagination is incorrect - not really related
|to protein misfolding at all.
|u/Hanuman_Jr - 1 month
|
|I didn't say it was related, I said it was comparable.
|u/expanding_crystal - 1 month
|
|Lungfish got a memory leak problem
|u/Kulban - 1 month
|
|Lungfish don't know how to uninstall the parasite software when
|they're done. When they start moving too slow they'll ask their
|grandkid for help and the first thing they'll see is the huge amount
|of parasite icons in their system tray.
|u/zarawesome - 1 month
|
|Computer over?! Virus equals Very Yes?!
|u/Kulban - 1 month
|
|My mouth was a broken jpeg.
|u/FuccYoCouch - 1 month
|
|Or evolve to make use of all that extra data
|u/SeeMarkFly - 1 month
|
|A genetic Peter Principle.
|u/helm - 1 month
|
|New organs out of noise? More likely to cause cancer or prions than
|anything useful
|u/FernandoMM1220 - 1 month
|
|how do you know its more likely to cause cancer and prions?
|u/Gatzlocke - 1 month
|
|So you're telling me there's a chance?...
|u/helm - 1 month
|
|Toss a bunch of sticks and some glass panes on the ground to get
|a log cabin with windows? Prions are very simple proteins.
|Organs are complex.
|u/FernandoMM1220 - 1 month
|
|whats the actual math you’re using to determine likelihood?
|or are you just using random metaphors?
|u/DrMobius0 - 1 month
|
|Well, the ones that die will be reproducing less, on average, so it
|should just sorta even out if it starts becoming a problem.
|u/GreatScottGatsby - 1 month
|
|Definitely not, the ones who have the mutation wouldn't reproduce or
|won't be viable so it will sort itself out. It's kinda like editing
|the genes of mosquitoes so females can't suck blood or only produce
|males. Eventually due to a nonviable population, either a female that
|is resistant to that gene or has a dominant gene may be born via
|mutation and they repopulate or a population of mosquitoes dwindle to
|the point where they are locally extinct but a neighboring population
|of mosquitoes that don't have that gene repopulate that area. Either
|way, they are not going extinct due to those genes. They have been
|determined to be evolutionary fit enough for their environment with
|that junk dna.
|u/dustofdeath - 1 month
|
|A large genome of junk at the same time means DNA damage to important
|parts is also less likely.
|u/FernandoMM1220 - 1 month
|
|why would scientists claim the dna isnt useful if they arent sure of
|what it actually does?
|u/Jdazzle217 - 1 month
|
|Coding genes are very easy to identify computationally. They share
|elements at the start (start codons) and the end (stop codons).
|Anything that’s not within an open reading frame can’t get turned
|into mRNA or protein. Some of the non-coding DNA are definitely
|regulatory elements, but the vast majority of it in an organism with
|a genome this large can’t be doing it thing (it’s typically lots of
|repetitive sequences and transposons).
|u/FernandoMM1220 - 1 month
|
|so why are they unsure about this then? do they know which virus
|was used to copy itself repeatedly into this dna? they should be
|able to figure that out.
|u/Jdazzle217 - 1 month
|
|1) They literally just published genome. Things take time. 2)
|They know the transpons and repetitive elements are mostly
|garbage, but some of that stuff could have evolved into
|regulatory sequences etc. You have to do actual molecular
|biology experiments to identify those kind of things, and
|realistically nobody is going to go that deep on an economically
|unimportant, non-model organism with a giant genome.
|u/Anderrn - 1 month
|
|Kudos to you for putting in the effort to explain this to
|someone who didn’t read any of the article and still thinks
|they’re smarter than the researchers.
|u/FernandoMM1220 - 1 month
|
|alright hopefully they figure it out. they probably shouldn’t
|be saying its useless if they dont actually know.
|u/sceadwian - 1 month
|
|This sounds like literal genetic cancer. Weird stuff!
|u/NotThatAngel - 1 month
|
|Right. Looks like a fatal mutation that only kills after millions of
|years of junk DNA accumulation. Must have been bundled with a short
|term advantageous adaptation that allowed it to outcompete other fish
|without the genetic parasite in the 'short term'.
|u/MajesticCoconut1975 - 1 month
|
|> His team found that mechanisms that other organisms use to curtail
|the spread of genetic parasites seem to be damaged or missing I hope
|there is no *Wuhan Mechanisms Against DNA Parasites* lab.
|u/Hayred - 1 month
|
|And to think we were proud when we managed to do the \~17gb wheat
|genome! Just for some perspective because money is fun, my facility
|offers sequencing as a service. To do the level of sequencing they did
|for this lungfish with our facility, it would've cost just under
|$250,000.
|u/Hayred - 1 month
|
|The costs of sequencing have indeed been falling spectacularly
|quickly, [observe!](https://www.genome.gov/about-genomics/fact-
|sheets/Sequencing-Human-Genome-cost) The sequencing involved in the
|human genome project cost somewhere in between USD500 million and 1
|billion. While I'm not sure what coverage the HGP was done to,
|Illumina (worlds biggest sequencing company) say you can now
|sequence 96 human genomes at 40x coverage on one flow cell on their
|newest instrument - our facility would charge only $3430 for that!
|A lot of our projects are now getting to the point where the
|preparation of the samples substantially outweighs the cost of
|sequencing which is pretty remarkable considering your prep costs
|might be something like $10-$20 per sample
|u/Acceptable_Pickle893 - 1 month
|
|“Yo go get me another lungfish, we need to backup the internet again”
|u/yParticle - 1 month
|
|Given base 4 vs base two, wouldn't that be the equivalent of about
|360GB?
|u/eloquent_beaver - 1 month
|
|180 gigabases = 90 billion base pairs. Since DNA is supposed to come
|in pairs (assuming you only consider valid pairings in your
|information theory analysis), with each pair being able to take on 1
|of 4 values, you can think of each base pair as being 2 bits of
|information (also can take on 1 of 4 values). 90 billion base pairs =
|180 billion bits of information = 180 gigabits.
|u/jakkson - 1 month
|
|> A yobibyte can store 83 bits of information A yobibyte is ~10^24
|bits, how does that translate to only 83 bits of information?
|u/eloquent_beaver - 1 month
|
|Whoops I made a mistake. Corrected it.
|u/bibliophile785 - 1 month
|
|You were doing really well until the end. This part is true: >180
|gigabases = 90 billion base pairs. Since DNA is supposed to come in
|pairs (assuming you only consider valid pairings in your information
|theory analysis), with each pair being able to be 1 of 4 values, you
|have 490 * 109 possible values, or roughly 1.8 * 1011 bits of
|information. This part is not: >That's an inconceivable amount of
|information. We don't even have terms for 10^11 bits of information.
|A yobibyte can store 83 bits of information. This is 10^11 bits. A
|yobibyte is [a little under 10^25 bits](https://www.google.com/searc
|h?q=how%20many%20bits%20in%20a%20yobibyte&ie=utf-8&oe=utf-8&client=f
|irefox-b-1-m). Without doing the math, I'm eyeballing 10^11 bits as
|being hundreds of gigabits or maybe a terabit.
|u/eloquent_beaver - 1 month
|
|Whoops I made a mistake. Corrected it.
|u/Symon_Pude - 1 month
|
|I'm sorry, but I disagree. By my understanding, there is no need to
|divide it by 2 to get the number of base pairs, it's more likely
|that the unit 'gigabases' already counts bp (it would be redundant
|to really give the amount of bases, since you can infer the
|information on the counter strand from the original one). So, there
|are 1.8*10^11 bp. And (as you correctly identified) 2 bits can cover
|the four option in the DNA. So, there are 3.6 *10^11 bits of data.
|Since 1 byte can hold 8 bits, if we are effective, we can store 4 bp
|within one byte. Meaning the actual needed safe space is 45 GB.
|u/eloquent_beaver - 1 month
|
|The unit Gb (in the context of DNA information) is ambiguous, as
|the b could refer to base, or base pair. OTOH, given the article
|says this: > There is a new record for the largest genome to be
|sequenced, set at a massive 90 billion letters of DNA. It belongs
|to the South American lungfish. > ... > Each cell in the South
|American lungfish (Lepidosiren paradoxa) has two copies of the
|genome, comprising 180 gigabases (Gb) of DNA That seems to
|indicate the 180 is referrring to bases, and not just pairs,
|because they earlier refer to the same metric by "90 billion
|letters." Also: > That is 30 times more than the 6 Gb of DNA in
|each human cell. Yup, given the human genome contains 3 billion
|base pairs, it's clear in this article "b" refers to individual
|bases, not base pairs.
|u/eloquent_beaver - 1 month
|
|Yeah no. That's not how bits work. 90 billion base pairs = 4^(90
|* 10^9) possible states. Each base pair can be in one 4 states,
|and there's 90 billion of them. 4^(90 * 10^9) = 2^(180 * 10^9).
|Each bit can be in 1 of 2 states, and there's 180 billion of them.
|Another way to think of it is lg(4^(90 * 10^9)) = 180 * 10^(9),
|where lg is the binary logarithm. Or you can avoid computing the
|total number of states and taking binary logs altogether by just
|noticing that 1 base pair has 2 bits of information.
|u/pythonwiz - 1 month
|
|360 Gb, so about 45 GB.
|u/catoftrash - 1 month
|
|Do lungfish have a more drawn out senescence process? I know with hydras
|large amounts of telomerase keep their chromatids from degrading over
|time. Does the massive amount of junk DNA similarly protect lungfish?
|u/Cilad777 - 1 month
|
|WTH. Hey. Lets sequence this lungfish...
|u/Ffslifee - 1 month
|
|They have played us for absolute fools.
|u/beefstewie13 - 1 month
|
|I have to ask, what is meant by this comment?
|u/bremergorst - 1 month
|
|The lungfish! All that dna means they’re super wicked smaht
|u/Ffslifee - 1 month
|
|Lookup stop doing math
|u/beefstewie13 - 1 month
|
|Did not disappoint.
|u/Cilad777 - 1 month
|
|It was just a quip. My full meaning. Some guys are out in the field,
|and they likely very specifically chose to research lung fish. That is
|actually the thing I love about science. Find something that has not
|been done, and find out whoa, that is awesome. I didn’t think my
|comment was either negative, or positive. And can’t take
|responsibility for a negative reaction :/
|u/sakredfire - 1 month
|
|Is this part of the reason why their ancestors were able to diversify
|into tetrapods?
|u/LordParsec29 - 1 month
|
|On track to become a 'brainfish'.
|u/microwaffles - 1 month
|
|I was killed by one of these. I cut its head off, then acid melted my
|helmet and he jumped down my throat.  I'm ok now.
|u/Allhailzahn - 1 month
|
|Dang Goa'ulds are already here
|u/Please-Calm-Down - 1 month
|
|“in each cell” — Well, yeah, that’s how DNA works.
|u/masdafarian - 1 month
|
|Put that in your simulation
|u/KingThorongil - 1 month
|
|Darn those programmers became lazy and the software installation size is
|bloated.
|u/Wrexes - 1 month
|
|microsoft ahh fish
|u/Doesanybodylikestuff - 1 month
|
|Sweeet… will this prolong my life somehow ever? Caz that’s uhhh kinda
|what I’m hoping for every day.
|u/42fy - 1 month
|
|There’s a larger one now. A plant. I’m too lazy to find the name, but it
|was fairly recent.
|u/Zaethiel - 1 month
|
|The new guy must have written its genome sequence.
|u/dritmike - 1 month
|
|Yeah but it’s mostly just poorly written code and functions that don’t
|mostly do anything.
|u/fitandgeek - 1 month
|
|when you're paid by lines of code instead of working code
|u/DrGordonFreemanScD - 1 month
|
|I'm not saying it's an alien, but...
|u/retrosenescent - 1 month
|
|Is it good or bad to have DNA that is so complicated?
|u/Silkovapuli - 1 month
|
|Suspicious as heck! Probably all those genethingums will be activated
|when the Stars are Right... ...and then the dragons arrived.
|u/bel2man - 1 month
|
|Lungfish -> facehugger -> xenomorph
|u/Silkovapuli - 1 month
|
|Probably a Goa'uld at some point too!
|u/U_Kitten_Me - 1 month
|
|And humans think they're the crown of creation, heh.
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