Honeybee Genome Sequenced

mapkinase writes to let us know about articles in Nature on the completed sequencing of the honeybee genome. From the first article: "Two other insects have already been sequenced: the malaria-carrying mosquito Anopheles gambiae, and one of science's great model organisms, the fruitfly Drosophila melanogaster. Like these, the bee is much easier to manipulate and study than, say, the monkey. But unlike the mosquito and the fruitfly, the bee's social behavior is of special interest." Another article in the same issue clarifies why this sequencing is important: "The genome is helping to reveal some of those [such as the bees' dance language and the division of labor in the hive] mechanisms. For instance, there are 65 spots in the genome that seem to code for short RNA molecules called microRNAs (miRNAs), molecular switches that can turn genes on or off. The researchers found that miRNA activity differs between bees doing different jobs."

Re:What about variations?

[valis]

The human genome projects worked from DNA samples pooled from a number of individuals, which were then assembled into a consensus "human genome". However the original sequenced reads can be aligned back to the reference to find differences (such as SNPs -- single nucleotide polymorphisms).

Substantial effort is underway to resequence the human genome in different individuals from different populations. The International Hapmap Project (http://www.hapmap.org/) is among the most high profile.

Re:Purpose?

[valis]

> Am I missing something here?

Yes. There is only so much you can do in a lab to humans. Or for that matter monkeys or mice. However PETA doesn't seem to realize that bees and flys are animals so...

More seriously, we work with model organisms because they are much easier to work with. You can do experiments that would either cost much much more or simply be impossible in a mammal model. Depending on what you are interested in there are lots of popular model organisms: nematodes, flys, bees, zebrafish, xenopus, mouse, rat, macaque... all useful for investigating different aspects of biology, and all relevant to human health at some level.

Re:miRNA?

[MikShapi]

Not exactly. More like:

Make Wings;
Make Thorax;
Make Head;
Size = 10;
if (GrowthStoppingHormonePresent == false){
                Size+=20;
                if (OtherQueenPresent == true){kill it;}
                Spray Growth Stopping Hormone On All Bees Around You;
}
else
{
                Behavior = "Go around gathering honey";
}

Re:softICE, anyone?

[valis]

> Everything DNA related, shares a common encoding scheme

Not so sure about that. The encoding of amino acids in genes is quite well defined (though there are exceptions, such as selenocysteine which is produced when a signal in the 3' UTR changes the meaning of a stop codon).

And protein coding sequences only make up about 1.5% of the genome for humans. Other things in DNA are much less clear, everything in biology is stochastic. Many functional elements are directly involved in protein-DNA interactions where structure is more important than specific sequence. And not everything DNA related is in the genetic code. Positions of histones, DNA methylation, and other signals might be important.

Re:What about variations?

[CharlesEGrant]

So when they sequence the human genome, how do they handle the variations?

For the purposes of creating the reference sequence they essentially ignored them. In the public human genome project the DNA from a handful of individuals was used. The Celera project used mostly the DNA of one individual, Craig Venter, the head of Celera. This does make the reference sequence arbitrary, but so was the block of platinum that was used to define the kilogram. The idea is that you measure differences from the standard.

The rule of thumb is that the sequence of any two individualss differ in about 1 base in 1000. This ignores complications like that fact that women have of two copies of the X chromosome and men have 1 X and 1 Y chromosome, and that whole sections of sequence can sometimes get shifted from one chromosome to another. As the other responder pointed out the variations are a major focus of research, particularly Single Nucleotide Polymorphisms (SNPs) [nih.gov] where 90% of the population have an 'A' in a particulary position and 10% have a 'G'.

Re:honeybees are very cool

[edschurr]

Another cool thing about them is that two genes exist in some groups of honey bee which helps them fight a disease that affects larvae. The first gene causes* them to remove the wax covering the diseased larvae, and the second causes* them to toss the larvae out of the nest to die. Groups of honey bees that only have the first gene will remove the wax and leave it at that. However, it's apparantly more complex than two genes causing behaviour because some honey bees do it without those genes.

Well, that's how I remember it from The Selfish Gene by Dawkins.

* perhaps not completely

Re:What about variations?

[CharlesEGrant]

The definition of the kilogram [nist.gov] was originally made in terms of a particular volume of water, but was later changed to the weight of a particluar ingot of irridium-platinum.