Another intron clue

Hey, there is one more clue we can add to the mix when considering introns.  Let me quote from Puzzles of the Human Genome: Why Do We Need Our Introns? By L. Fedorova and A. Fedorov (Current Genomics, 2005, 6, 589-595):

One could argue that, in theory, removing “junk” DNA from the genome would have no negative effects on the organism. This has in fact happened in one vertebrate species, the puffer fish Takifugu rubripes, whose genome shrank several times millions of years ago [1]. The general phenotype is essentially the same as that of closely related genera, even though it has lost vast sections of its genome.

Let’s now add this:

One advantage is that it is much faster to get from one end of a pufferfish gene to the other end and from one gene to the next when determining DNA sequence on continuous stretches of chromosomes. This is because the pufferfish genome is only about an eighth of the size of the human genome—400 million DNA bases. But the pufferfish is not deficient in its total number of genes. Rather, the pufferfish genome contains less of what seems to be irrelevant DNA, sometimes called “junk.” This junk DNA separates genes from one another like the space that separates words in a sentence. It also breaks genes into sections like syllables. The human genome is diluted with so much junk DNA that genes are contained in only three percent of it—compared to fifteen percent in the pufferfish.

So here are two vertebrates that have roughly the same number of genes, but while the human genome is filled with 3 billion nucleotides, the puffer fish genome is only 400 millions nucleotides long.

But here’s the catch.

From the paper by  Fedorova and Fedorov:

An interesting example of fast evolutionary genome shrinkage was observed in Takifugu fish. In this case, the diminution of Takifugu intron lengths and the length of its intergenic regions were highly coordinated. Despite dramatic shortening of the Takifugu genome, the number of introns remains the same as other vertebrates [22]. The process of intron loss is extremely rare in vertebrates.

And here is specific example:

In other experiments, Brenner’s team studied certain large complex human disease genes. For example, in 1995 Elgar and colleagues identified and sequenced the pufferfish counterpart of the human Huntington’s disease gene, which had already been sequenced. The pufferfish gene turned out to be only 23,000 DNA bases long—seven and a half times shorter than the human gene. Although the pufferfish gene has the same sixty-seven interruptions, they are rarely over 1,000 DNA bases—compared to interruptions as long as 12,500 DNA bases in the human gene for Huntington’s. The actual gene, however, is very similar to the human gene and provides no further information about the protein.

The puffer fish has not shed one of the sixty-seven introns in the Huntington’s disease gene.

So here’s the thing.  For whatever reason, the puffer fish genome has shed gobs and gobs of its “junk” DNA.  Yet despite this massive pruning, most, or all, of the introns have been retained.   Apparently, the loss of introns would be deleterious to this fish, which is serving  as a model for all vertebrates. The fact that the puffer fish has not been able to shed its introns fits perfectly with the observation that the “process of intron loss is extremely rare in vertebrates.”  But such intron loss does not appear to be rare in single-celled eukaryotic organisms.  Now why is that?

Add it all up, and it indicates introns are playing some role in metazoan life and this would support my hypothesis that introns facilitate the evolutionary spread of metazoans.

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