Gene families and evolution

[QuarkHead]

25.000 to 30.000 sounds reasonable.

Based on what reasoning? Here's an example of how it might go.....

Human genome = 4 x 10⁹bp

Fraction coding = 0.1

Average processed transcript = 4 x 10³bp

Answer = (4 x 10⁹)(4 x 10^-3)(0.1) = 10⁵

....which is the figure we used to use as an estimate for the number of human genes.

 

[Hercules Rockefeller]

60.000 was the consent before the human genome project.

Consensus opinion before the HGP was more like 80,000 to 100,000 genes. Original estimates coming from the HGP were 30,000 - 35,000 genes, and the count (as far as I am aware) has been climbing ever since as the gene scan algorithims become more sophisticated. As I said, there was one report that the count is more like 20,000 based on a modified gene scan algorithim but I don't think anyone is taking that seriously.

25.000 to 30.000 sounds reasonable.

Not to me it doesn't. That's only a few more thousand genes than <I>C.elegans</I>.<P>

 

[spuriousmonkey]

it doesn't really take that many more genes to make a c. elegans than a human.

Especially since basically the same gene families are used to make every different part in an animal. In humans we might have more than 20 FGFs for instance. But many can be knocked out without any problem for most organs. It is not so much that humans need more FGFs because they are that much more complex. It is a historic result. One that facilitated evolution, by duplication of genes and modification of function, sometimes, in some some organs. Sometimes with major effects in most or all organs.

 

[Hercules Rockefeller]

it doesn't really take that many more genes to make a c. elegans than a human.

That statement is debatable.

But many can be knocked out without any problem for most organs.

There's a lot of subjectivity and generalizations in there. "...many <I>(but not all)</I> can be knocked out without any problem for most <I>(but not all)</I> organs.

But I see where you’re coming from… <P>

 

[CharonZ]

The latest number I read (end of 2004) were around 25k genes, too.

About gene families (or rather paralogues, the term gene families is actually reserved for another classification. I know it is not really important for this discussion, but at least for me it is easier...):
It is indeed known that duplicated genes (or paralogues) present a "playing ground" for modifications and as such, provide a pool for higher variability. I am not quite convinced that block modifications occur more often, though (AlthoughI have no data regarding this). But yes, basically I agree with the notion that duplication is an important factor of evolution.

Now, I am not sure if this has any impact on the basic reasoning above:

It is a fact that, in general, more complex organisms have more DNA that simpler ones. It is also a fact that more complex forms have more genes than simpler ones. Let's assume that these two facts are connected, as seems reasonable.

It appears to me that size of DNA, or the complexity of the organism is not reallly relevant for the occurence of gene duplication. In fact, in bacteria the amount of gene duplication is rather high (despite the fact that in contrast to multicellular organisms there is a stronger selection for maintaining a small chromosome). So the mechanism of gene duplication and its impact on evolutionary change is common for basically all organisms.

 

[QuarkHead]

About gene families (or rather paralogues, the term gene families is actually reserved for another classification. I know it is not really important for this discussion, but at least for me it is easier...):

Paralogies would certainly fit in with my scheme, but these, if we are using the term in the same way, involve massive chromosomal regions. I admit that to call the descendents of an amplification process families now might seem strange, as there isn't much evidence of widespread sequence homology between genes with unrelated functions.
But the point I was trying to make was that, those genes that we have in excess of those posessed by our anscestors, must have been in families at some point in evolution. If their kinship is no longer detectable, that must be due to rather rapid divergence.

I am not quite convinced that block modifications occur more often, though (AlthoughI have no data regarding this).

There is abundant evidence, in Man at least, that genuine gene families participate in sequence exchange, both reciprocal and non-reciprocal. Not only does this often involve many tens of kilobases, but appears to be relatively error-prone. .

It appears to me that size of DNA, or the complexity of the organism is not reallly relevant for the occurence of gene duplication. .

Yes, everybody wants to beat me with that particular stick! I have conceded that it was a rash generalization. As you say, it is not critical to my central point.

 

[invert_nexus]

I don't have time to devote to an in-depth post here, but I would like to make a quick post and hopefully Hercules and QuarkHead have email alerts on their threads.

I'm kinda surprised by the response to the given number of genes. All I can say is that this is the number of genes given by the Human Genome Project site as the latest officially recognized number. The number is still an estimate and is likely to increase some, but apparently not much.

It was while I was doing research for a response to this thread that I came up with the idea that I posted in my new thread in this forum. The Genome as Evolution.

Unfortunately, this was a while ago and the information that I had dug up is now somewhat vague once more as I've been delving into other things in the interim.

I will dig once more and make a more detailed post on this subject.

I'll leave with this.
The question is how can such a surprisingly small number of genes code a human? It's a shock to think it. But, it's even more beautiful in that we make so much more use of the genes we have. The various genes have a variety of configurations to code for different proteins. Epigenetic factors also must be considered in the equation. Methylation and Histone tagging to name just a couple.

The depths of coding to make a complicated organism is so much more than we ever thought it was in the past. Not just genes anymore. Genes are only the tip of the iceberg.

We have a long way to go.

(Crossing fingers on email notification.)

 

[QuarkHead]

I don't have time to devote to an in-depth post here,

Neither do I, hopefully later

I'm kinda surprised by the response to the given number of genes. All I can say is that this is the number of genes given by the Human Genome Project site as the latest officially recognized number. The number is still an estimate and is likely to increase some, but apparently not much.

Yes. The surprise comes from the fact that, the original, higher, estimates were theoretical, and theoroticians seldom like it when nast things like real data prove them wrong!!

However, it is worth remembering that the HGP estimate is also, in its own way a model, worked with an algorithm I think I described before (although they may have changed it since I last looked in detail)

It was while I was doing research for a response to this thread that I came up with the idea that I posted in my new thread in this forum. The Genome as Evolution.

Well, let's take a peek.
Oh - and good to talk to you again

 

[pranks085]

I think you may have a point with these gene repeats. Isn't that how families such as the globin family are thought to have arisen?

 

[valich]

According to the Federal Genome Institue report as of August 31st, 2005, humans have about 25,000 genes, but many animals have a lot more than that. The report stated that they were quite surprised that the number was lower than the original 20-40,000 estimate. Chimps are 95% to almost 99% related to humans and they have currently identified the functional characteristic of the billions of building blocks of their DNA, which will greatly benefit humans in identifying defects and disease. Even though Chimp gene relation is so similar to ours, they state that the physical (phenotype) difference between chimps and humans is ten times as great as the difference between two individual people. Food for thought.