Thursday, July 18, 2013

The Largest Prokaryotic Genomes

Some bacterial genomes are quite large. A few are larger than the smallest eukaryotic genomes.

Many species of cyanobacteria are complex, multicellular organisms [Multicellular Bacteria]. Those species tend to have large genomes.

Recently Degan et al. (2013) sequenced the genomes of six new cyanobacteria species and one of them turns out to have a large genome.1 (see Contradictory Phylogenies for Cyanobacteria for more information on that paper.) The species is Scytonema hofmanni and its genome is 12,073,012 bp in size. It has 12,356 potential protein-coding genes. If all of them are correctly identified then the total, counting non-protein-coding genes, is likely to be 12,500 genes. That's a record for prokaryotes.

Half of these genes are only found in Scytonema and that's very strange.

There are bacteria with larger genomes, notably the soil bacterium Ktedonobacter racemifer with a genome size of 13,661,586 bp.

For comparison, the genome of the yeast, Saccharomyces cerevisiae, is 12,156,677 bp in size and it has 6,200 genes.


Photo Credit: Scytonema hofmanni from cyanobacteria slides.

1. Some of you might be under the impression that I give a shit about Norm Pace and his attempt to banish the word "prokaryote" (Pace, 2009). Don't bother to try and convince me because it requires that I accept the false Three Domain Hypothesis and that ain't gonna happen.

Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., Goremykin, V.V., Rippka, R., de Marsac, N.T., Gugger, M., Lockhart, P.J., Allen, J.F., Brune, I., Maus, I., Pühler, A. and Martin, W.A. (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome biology and evolution 5:31-44.
[doi: 10.1093/gbe/evs117]

Pace, N.R. (2009) Time for a change. Nature 441:289. [doi:10.1038/441289a]

9 comments :

  1. Actually, dislike for "prokaryote" doesn't require the three domain hypothesis. It merely requires that you think 1) only clades deserve names and 2) prokaryotes aren't a clade. And the only way they would be a clade is if Archaea + Eubacteria were the sister group of Eukaryota.

    For the record, I'm a pretty fanatical cladist, and I only require that taxon names refer to clades, not all names in the world. On the other hand, does "prokaryote" give us a false impression of similarity between, say, Thermus aquaticus and Escherischia coli?

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    1. Does "invertebrate" give us a false impression of similarity between, say, tunicates and fruitflies?

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    2. Doesn't it? I mean you hear of people being described as working on "invertebrate zoology" - as if the group was all the same -- bugs, worms, tunicates, whatever. If I worked on such organisms I know I'd be annoyed at the broad classification.

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    3. On the other hand, does "prokaryote" give us a false impression of similarity between, say, Thermus aquaticus and Escherischia coli?

      I dunno. Does "eukaryote" give us a false impression of similarity between, say, diatoms, Paramecium, red algae, and elephants?

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    4. Can I play the rhetorical question game? Is that impression false, at the level of cellular organisation?

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    5. Does "eukaryote" give us a false impression of similarity between, say, diatoms, Paramecium, red algae, and elephants?

      No, it doesn't. They are similar in important ways: they all have nuclei, organelles, big ribosomes, and so on. In short, they have actual shared, derived characteristics.

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    6. As mentioned, there are actual shared and derived characteristics to eukaryotes, so the similarity isn't false at all and actually helpful to people who still think in terms of "higher" and "lower" organisms.

      On the other hand, euks aren't immune to bad terminology. My personal pet peeve is "protist" -- basically a meaningless term for single celled euks that aren't fungi.

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  2. I think the relevant question is whether it's possible to define "prokaryote" other than by the absence of eukaryote features. One can, for example, define "tree" as a perfectly good description of certain plants, even though they don't make a clade. But one can't do the same for "invertebrate", which is just all the animals that aren't vertebrates, some of which are deuterostomes and some of which are even chordates. Useless unless you're a vertebrate chauvinist.

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