A Blog by Ed Yong

You Have 46 Chromosomes. This Pond Creature Has 15,600

Remember when encyclopaedias were books, and not just websites? You’d have a shelf full of information, packaged into entries, and then into separate volumes. Your genome is organised in a similar way. Your DNA is packaged into large volumes called chromosomes. There are 23 pairs of them, each of which contains a long string of genes. And just as encyclopaedia books are bound in sturdy covers to prevent the pages within from fraying, so too are your chromosomes capped by protective structures called telomeres.

That’s basically how it works in any animal or plant or fungus. The number of chromosomes might vary a lot—fruit flies have 8 while dogs have 78—but the basic organisation is the same.

But there’s a pond-dwelling creature called Oxytricha trifallax whose DNA is organised in a very… different… way. A team of US scientists has sequenced its genome for the first time and discovered genetic chaos. It’s like someone has taken the encyclopaedias, ripped out all the individual pages, torn some of them, photocopied everything dozens of times, and stuffed the whole lot in a gigantic messy drawer.

Oxytricha trifallax is neither animal nor plant, but protist –part of the kingdoms of life that include amoebas and algae. Composed of just a single cell, it never gets bigger than a quarter of a millimetre in length. It swims around ponds and puddles in search of other microbes to consume, and moves by beating small hairs called cilia. These hairs give it and its relatives their group name—the ciliates.

Within its cell, Oxytricha contains two nuclei, which enclose its DNA. One of these—the micronucleus— contains the complete edition of Oxytricha’s genome, just like the single nucleus within our own cells. That’s the tidy encyclopaedia shelf. But while the material in our nucleus must be constantly decoded and transcribed so that we can live, Oxytricha’s micronucleus is largely inactive. The encyclopaedia’s are barely read.

Instead, it relies on a second structure called the macronucleus. That’s the messy drawer. All of the DNA in the micronucleus is copied thousands of times over, and shunted into the macronucleus. In the process, it is broken up at tens of thousands of places, rearranged, and pruned. What’s left is a collection of thousands of “nanochromosomes” that contain all the information Oxytricha needs to survive. This is the stuff that gets decoded and transcribed, used and reused while the originals gather dust.

Sequencing this almighty mess must have been a devilish task, but Etienne Swart from Princeton University rose to the challenge. Leading a team of US and Swiss scientists, he has sequenced Oxytricha’s complete macronuclear genome. Modern sequencing works by breaking genomes into small fragments, sequencing these, and assembling everything together. The DNA in Oxytricha’s macronucleus is already fragmented and extremely repetitive, make it hard to capture everything and assemble it into a coherent whole. Then again, almost three-quarters of the fragments were already complete chromosomes.

The team found around 15,600 of these nanochromosomes. On average, each is around 3,200 DNA ‘letters’ long, and around 80 percent of them contain just a single gene.

As if that wasn’t complicated enough, the genome is duplicated so extensively that there are around 2,000 copies of each nanochromosome. And around one in ten of them are broken up into even smaller fragments. So, different copies of the same nanochromosomes might just contain a small passage from the full page of information.

Our 46 chromosomes are capped by protective structures called telomeres that stop DNA from fraying, rather like the plastic tags on the end of shoelaces. All of Oxytricha’s nanochromosomes have their own telomeres, so each individual has tens of millions of these protective caps. It has, in Swart’s words, an “inordinate fondness for telomeres”. It’s like every page in its messy drawer is hard-bound.

As the contents of the micronucleus are copied into the macronucleus, anything that doesn’t contain instructions for making proteins—the so-called “non-coding DNA”—is ruthlessly pruned. Around 96 percent of the genome is jettisoned in this way. The remainder—the nanochromosomes—are a small fraction of the full genome, but they contain all the genes that Oxytricha needs for day-to-day existence. The only things missing are a smattering of genes that the creature needs to reproduce.

This isn’t just an academic exercise, targeted at an (admittedly cool) creature. Ciliates have a long history of teaching us about our own genomes. Another of them—Tetrahymena thermophila—taught us about the existence of telomeres in the first place, and these structures are now through to play critical roles in ageing, cancer and other aspects of our lives. Tetrahymena also helped to show that RNA—a genetic molecule that’s related to DNA—can act as an enzyme. That’s crucial to modern theories about the origin of life itself. (And its genome was fully sequenced back in 2006, by the inimitable Jon Eisen)

Meanwhile, Oxytricha, with its bonanza of telomeres, helped scientists to identify the proteins that stick to these caps and help to create, maintain and control them. Perhaps its bizarre genome will tell us even more about how DNA is rearranged and copied—something that happens in our genome to a less dramatic (but still important) extent.

Reference: Swart EC, Bracht JR, Magrini V, Minx P, Chen X, et al. (2013) The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. PLoS Biol 11(1): e1001473. http://dx.doi.org/10.1371/journal.pbio.1001473

31 thoughts on “You Have 46 Chromosomes. This Pond Creature Has 15,600

  1. I wonder if Oxytricha trifallax might be left over from a stage on the way to eukaryotes as we know them. Maybe some creature related to it eventually became more organized and was eventually more successful in other niches.

  2. Knowledge as a legacy of a decade-ago game of Balderdash: The plastic tags on the end of shoelaces are called aglets.

  3. That’s how you would organize the genome if you don’t want to mess with sundry regulative structures. Not as simple to evolve (a 2nd nucleus), but useful if acquired.

  4. @Ralph: We know quite a lot about the evolutionary relationships of Oxytricha and other ciliates. Enough to be sure that their weird genomes aren’t relics of an ancestral eukaryote organization. But not enough to understand the true causes.

  5. @Rosie: Surely the organism described here is a dead end! Where does it go next? With all those copies of everything, I would not want to play the part of a hopefully mutated gene. At best I might be added onto the pile, but to supersede any other version? Not to be dreamt of.

    Seriously… a great puzzle! This little creature is trying to carry around the entire biosphere in its backpack. What a hoarder!

  6. Maybe this little guy IS a genetic repository. Maybe he’s not the only one! When TWAWKI happens something stimulates them into differentiating into several phyla of critters that repopulate Earth!

  7. I was about to retweet this when it occurred to me that not everyone on my Twitter stream DOES have 46 chromosomes and the wording of this post might make those folks uncomfortable. You might want to tweak this post a little.

  8. particle_p, I imagine most of the people on your Twitter actually do have (at least) 46 chromosomes. If not, I hope the few with Turner Syndrome (which Wikipedia describes as “the only full monosomy that is seen in humans”) will fire off sharp comments rather than languishing in arithmetically-challenged dismay. Why not? They have nothing to be ashamed of.

  9. i find it fascinating that such small organisims and tomatoes for example can rival humans or surpass them in their genetic complexity, all life, no matter how “simple” deserves our respect. we should all be humbled and realize we are but a peice in this wonderful puzzle of life!

  10. @RalphD Down Syndrome was what I thought of first. Pretty sure that is more common than Turner Syndrome which I had to look up.

  11. @Joris8pinter, Down Syndrome is certainly more common, but it involves an extra chromosome, not a missing one, as Turner Syndrome does. People with Down Syndrome have all 46 chromosomes. Plus, they have one more. So, except for the rare individuals with Turner Syndrome, we all have (at least) 46.

  12. “and these structures are now through to play critical roles in ageing”: through should be thought.

    Nice article (and organism)!

  13. One must point out that the unusual chromosome structure is only in the macronucleus, while the DNA in the micronucleus is “normal”. And if this critter reproduces like normal ciliates, like the paramecium, IIRC, then it is the micronucleus that is involved in reproduction/conjugation. The unusual DNA in the macronucleus is thus not involved in that process, with macronucleus actually degenerating and disappearing in the early steps (to be rebuilt later).

  14. What would be interesting is to find out what it eats and what eats it. What does it’s environment do for and to it?

    Why would such a molecular machine be structured like this?

    What does it like? What doesn’t it like?

    How long has it been here?

    The DNA in the macronucleus is preserved upon regeneration. What does it do when it’s out and about? What form does it take? Just a cloud of molecules? Is it timing DNA?

  15. Amphiox, are you saying the macronucleus is purely vestigial? If so, it should have disappeared long ago, given the energy and extra food input that must be necessary to create it.

    There has to be something useful the macronucleus is doing. Could it be “merely” an energy repository, almost like a yolk for the adult stage?

  16. Very interesting article. Additionally, as someone who already uses an awesome scientific name as a username, I have to appreciate how great “trifallax” sounds. Could be the name of a high fantasy character or something… hmmm…

  17. @Ralph – No, I don’t think Amphiox is not saying it’s vestigal, Amphiox is saying that the macronucleus probably isn’t involved in cell division. Only the (relatively normal) micronucleus would be involved in cell reproduction, and the macronucleus is created FROM the micronucleus separately by each daughter cell after a split. . . and the macronucleus would “disappear” before either daughter cell reproduced again.

    1. @Christopher – If it is not vestigial, then it performs some necessary function, right? If it has a necessary function, then the organism would not survive (or at least not thrive) without it? So, can one remove the macronucleus and the ciliate will still survive? One other question: is paramecium a member of this ciliate class (or genus or whatever it is)?

  18. There must be an evolutionary reason for this “messy drawer” that contributes to this organism surviving and procreating in its current environment. Perhaps it is a stupid design and that explains why it has not evolved into something better than pond scum. Any comment on that?

  19. Ralph Dratman, as the article states, the micronucleus is in a dormant state for the majority of the time the cell is undergoing normal metabolism.

    In a typical eukaryote (like us, for example), the nucleus performs two types of functions. One is reproduction and cell division (whether it is mitosis or meiosis), but the other is the day to day work of transcribing genes and producing gene products to keep regular cellular metabolism going. It would appear that in these ciliates, the micronucleus has become specialized for the first function, while the macronucleus is doing the second, and the changes in chromosome structure may be an adaption to do this more efficiently. Splitting the genome into so many chromosomes would potentially create havoc, or at least result in very onerous energy demands, when the time comes, in reproduction, for the chromosomes to line up with their complementary partners for cell division. This is particularly true in sexual reproduction (meiosis), when chromosomes must pair up properly for recombination. These ciliates may get around this problem because the macronucleus doesn’t have to participate in reproduction, which the micronucleus does instead.

  20. @AndrewLohbihler, I don’t think “it has not evolved into something better than pond scum” is a good way of thinking about this.

    Earth’s biosphere needs pond scum. In fact, we need some organism(s) to clean up (eat up) every kind of biomolecule that still has any free energy left. Otherwise the planet would rapidly get congested with chemically unstable bits of dead organisms.

    It is clear that Oxytricha trifallax is wonderfully suited to its niche, a niche that will probably never disappear as long as there is water-dwelling life on Earth.

    1. Sorry, I did not mean to trivialize Oxytricha trifallax (OT) as mere pond-scum as less evolved life forms, especially when compared with higher evolutionary life forms like George Bush. So its nice to think that this organism is the “care-taker” of the earth and consumes dead organism chemicals to feed its life and continued existence. So does that explain this complex genetic structure from an evolutionary point of view? It would seem that this complex genetic structure is an advantage to its evolutionary long term survival, because even if we humans die out as a species, something has to remain to clean up the mess we or others make. I also seems to me that if we are looking for an alien then OT fits the example of an evolutionary organism that survives anything and likely took a ride to earth from asteriods many years ago. Comment?

  21. Thank you for this information. Really fascinating, that “beast”… it’s way to protect seems to be rather fail-safe – with even a complete “back-up”, in case of… This way to do funnily reminds me of Internet, doesn’t that work in a (farthely) similar way ? : Cutting information into small chunks, sending them by different ways, we not really can know how, and at the receiving end put those peaces together, to restore the original information ? If it were so, it might be interesting, to look into those “ends of shoelaces”, the aiglets, perhaps they’d contain some kind of URL ? Something which tells how to assemple them ? I not am biologolist nor informatician, just an old engeneer – Our buildings and machines do not work that way : When one part fails, the whole thing goes to pieces… In some way, it seems to me that this is quite okay so – ashes to ashes… We try to be aeternal, but most of what we humans do neither is of no good for nature around, nor for us ourselves. Trying to understand how life works, is nice. Pardon me.

  22. Just stumbled across this. Have been working hard to get the next weird ciliate story reviewed (in Paramecium)… Thanks for this great writeup! I’m a firm believer that much more interesting biology remains to be discovered, if we only but cast our eyes upon the unfamiliar.

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