Pufferfish and ancestral genomes

Posted by PZ Myers on October 22, 2004 06:33 PM

green spotted pufferfish

The fugu is a famous fish, at least as a Japanese sushi dish containing a potentially lethal neurotoxin that was featured on an episode of The Simpsons. Fugu is a member of the pufferfish group, which have another claim to fame: an extremely small genome, roughly a tenth the size of that of other vertebrates. The genome of several species of pufferfish is being sequenced, and the latest issue of Nature announces the completion of a draft sequence for the green spotted pufferfish, Tetraodon nigroviridis, a small freshwater species.

Tetraodon has about the same number of genes as we do, 20,000-25,000, but they are contained in a total genome length of 340Mb vs. our huge 3.1Gb. One major difference is that in Tetraodon, transposable elements are rare: they have 73 types, present in less than 4000 copies, but humans have about 20 different types present in millions of copies. Transposable elements may be reverse transcriptases that blindly copy RNA sequences back into the DNA (called LINES) or shorter sequences that are processed by LINES, called SINES. These really are parasitic bits of selfish DNA, and somehow, pufferfish seem to be largely free of them.

One of the interesting things one can do with a pair of genome sequences is to start mapping synteny. Synteny represents the preservation of small regions of order within a chromosome; while the overall organization may have been scrambled by millions of years of chromosome breaks and fusions and duplications and deletions, we can still identify smaller blocks that maintain the same series of genes within them. For example, if we look on a chromosome of one organism and we see the series of genes A-B-C-D-E-F, and we look in another organism and find a chromosome with the genes W-X-C-D-E-Y-Z, we can see that the C-D-E chunk can be mapped directly to one region of that second organism's chromosome.

Continue reading "Pufferfish and ancestral genomes" (on Pharyngula)

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Comment #9099

Posted by charlie wagner on October 25, 2004 08:33 PM (e) (s)

Paul wrote:

Synteny represents the preservation of small regions of order within a chromosome; while the overall organization may have been scrambled by millions of years of chromosome breaks and fusions and duplications and deletions, we can still identify smaller blocks that maintain the same series of genes within them.

  Yes, indeed. And it is hard to escape an analogy between a genome and the hard drive on your computer. When you use your new computer for the first time, you were probably amazed by its blazing speed. But now it may seem to have slowed down.
  When you add a file or a new program to a brand new computer, the hard disk is relatively empty so new data is written to the hard disk in one contiguous block.  When you need to use that information, the computer can quickly access it because it is all in one place.
As you use your computer adding files and programs, the hard disk begins to fill up. Deleting files or removing programs creates small empty areas among the other data that the computer will reuse.  After a while, the computer is no longer saving information in large blocks. Instead, it stores information in the many little empty nooks and crannies of your hard disk.  The result is that one program or file is broken up, or fragmented, into little pieces and stored in many different areas of the hard disk.  The computer ingeniously keeps track of the addresses of each piece of data and puts it all together when it is needed. Yet, obviously, the more broken up the information is, the longer it takes to access the data and the slower the computer becomes. So you run a defrag utility to restore the file integrity.
  Whether the genome finds it necessary to occassionally “defrag” it’s contents is unknown, but the obvious conclusion is that there is nothing static about the genome. Information is being moved around, rewritten, inserted and deleted, as you point out. But I see that as an ongoing, dynamic process, rather than the result of random, accidental occurrences. While it may be the result of “evolution”, it is  likely that what we interpret as evolution is the unfolding of programs that were either in the genome from the very beginning, or were added to it at subsequent points in it’s evolution.

Comment #9111

Posted by PvM on October 26, 2004 09:28 AM (e) (s)

Charlie wrote:

While it may be the result of “evolution”, it is  likely that what we interpret as evolution is the unfolding of programs that were either in the genome from the very beginning, or were added to it at subsequent points in it’s evolution.

Once self replication arose it seems reasonable to assume that the ‘program’ in the genome was added at subsequent times. The question is, how was this ‘program’ added. Science has some exciting and plausible explanations which seem to be supported by the evidence.
It is the confusion of what is meant by ‘random’ which leads Charlie to pose an ‘ongoing dynamic program’ as an alternative. Evolvability is a fascinating topic and it seems that neutrality plays an essential role. Yet the process of gene duplication and divergence seems to be sufficient in understanding such concepts as modularity, robustness, evolvability, degeneracy, scale free properties, stasic and punctuated equilibria.

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