The intersection of genomes is empty

From this story in Quanta Magazine:

In fact, there’s no single set of genes that all living things need in order to exist. When scientists first began searching for such a thing 20 years ago, they hoped that simply comparing the genome sequences from a bunch of different species would reveal an essential core shared by all species. But as the number of genome sequences blossomed, that essential core disappeared. In 2010, David Ussery, a biologist at Oak Ridge National Laboratory in Tennessee, and his collaborators compared 1,000 genomes. They found that not a single gene is shared across all of life.

6 thoughts on “The intersection of genomes is empty

  1. On the one hand this doesn’t seem so unlikely given that lifeforms may have evolved at different places and times around the planet, and some may have even been delivered to Earth from outer space on meteors/asteroids. On the other hand, our understanding of “gene” is still so primitive that there might well be building or coding blocks common to all lifeforms that simply don’t come under the current definition of “gene.”

  2. I’m gob-smacked, flabbergasted, gone googly-eyed, mind thoroughly boggled.

    Given the common reliance on DNA/RNA, from an information perspective I’d have thought there would be a few hardy genes representing the best available, most useful , and most durable encodings. Limiting the search to prokaryotes, with their relative simplicity and fewer genes, would seem to be a generous restriction that one would expect to increase the odds of a non-null intersection.

    An empty intersection must then be a meaningful indicator of just how deep diversity goes, despite use of a common encoding/storage mechanism. Only the exclusion of Archaea permits even the tiniest of intersections to exist, which I would think would stretch even the most conservative assumptions.

    Well, there could be genes that slipped through the analysis, perhaps due to an inadequate definition of “gene”. But I doubt that, unless there are encoding/decoding mechanisms yet to be discovered.

    Then again, there *must* be genes encoding for proteins that are “functionally identical” despite having different genetic encodings. That multiple proteins could perform the same job seems much less surprising, if surprising at all.

    For example, there must be proteins that read and replicate DNA, so at least those core functions must be shared, even if the proteins performing them don’t share encodings.

    How many different genes exist that code for fully functional transcription enzymes?

    So, to give this result context, a study of the eukaryotic proteome should follow.

    Time to shove my eyeballs back into their sockets.

  3. Yes, cytochrome-c oxidase, a combination of genes, at least in respiration. Animals inherited the original from a purple bacteria that is/was slightly photosynthetic and became symbiotic with early cells. Respiration is a modified form of photosynthesis and can be accelerated with red and near-infrared light for healing faster. To study this H+ proton mechanical pump in humans, it is usually sufficient to just study the purple bacteria. Linus Pauling correctly dated the approximate age of all respiring animals by the ratio of number of genes that have changed.

  4. I think what this is pointing out is just how long organisms have been evolving under varying selective pressure. As BobC says, there are clearly preserved functionality – synthesis of DNA being the most obvious. I’d imagine that this is a “Grandfather’s Axe” paradox – various parts of the preserved systems are replaced with functional equivalents, until all the parts are replaced, but the system as a whole continues to function the same.

    Under this hypothesis, prokaryotes should show more variability, and be less likely to have a common core, as it where, since they evolve faster, with shorter generation times.

  5. Functions are conserved, but not full length protein sequences. We find about 500 conserved protein functional domains conserved across 60,000 bacterial genomes. These functional domains are for ancient and essential properties for life – like protein synthesis, DNA and RNA replication, and many enzymatic functions.

  6. David Wallace Locke

    Different use cases brought different encodings to the same functionality. I’ve run across group theoretic discussions of these collisions.

    The common genes may have gone extinct. Every niche would have different selection pressures.

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