Exploring weird Australian genomes

We now know about three billion base pairs of the human genome - at huge cost. But this is very boring information unless we know what it does. One of the questions I am most often asked is: “Well, we’ve got the human sequence now, why do we need other mammals? Particularly, why do we need weird animals from Australia?”

In fact this is going to help us find new genes and discover what they do, so we can understand human genetic disease and how to treat it, and maybe even make money in developing new drugs and a better traits for our domestic animals. It will also tell us how the human genome evolved.

I would like to explain what’s being done and how animals are related to each other. A number of different placental mammal species have been sequenced, including humans whose genome has been sequenced multiple times. We also have the sequences for chimpanzees, mice, rats, dogs, cats, and even the elephants are now lined up for sequencing. But these animals are actually all rather closely related.

They shared a common ancestor only 100 million years ago, and that isn’t enough time for the genome to have changed sufficiently for us to get the maximal information out of it. If we go to the other extreme and look at animals that are very distantly related - that is birds, frogs and even fish - they share a common ancestor with mammals 300 or 400 million years ago and that’s too far because now the sequence is so different, it’s actually hard to line up.

But Australian animals are right in the middle. Marsupials and monotremes last shared a common ancestor with humans about 200 million years ago, so they’re exactly in the right spot to give us maximal information to make comparisons. Right now the genomes of two marsupials and the platypus are being completely sequenced. This gives Australia a fantastic opportunity to make a major contribution to the understanding of the human genome by using our own mammals.

I wish I could tell you that Australia is rising to the challenge, but apart from small contributions to the cow genome project, Australia has hardly participated in the international comparative genomics project. Our one standout is the kangaroo, which is supported, not by the Australian Government, but by the Victorian State Government. The Australian Genome Research Facility is doing half the sequencing of this and the Baylor Genome Centre in Houston is doing the other half.

It is the kangaroo genome project that is saving Australia’s reputation in the genomics community and giving us a seat at the genomics table.

There are 26 species of kangaroo and we chose to sequence the Tammar Wallaby, on which much of the classic biochemistry and physiology was done.

The ARC Centre for Kangaroo Genomics that I direct is doing the mapping and preparing the genome for sequencing. The kangaroo genome is about the same size as the human genome but it’s packaged very differently - into just eight enormously large chromosomes that are a dream to work with. The other good thing about marsupials is their chromosomes have not been rearranged much, so if you’ve seen one genome you’ve seen them all.

The very large kangaroo chromosomes can be cut out of a cell, arranged in a row and assigned numbers according to their size and location of the centromere. There are two copies of each chromosome, one from the mother and one from the father. There are seven pairs of what we call autosomes - that is ordinary chromosomes - and a pair that’s different in males and females; these are the sex chromosomes X and Y. So the Tammar is great because it only has eight pairs and they’re easy to distinguish from one another, compared with humans who have 23 pairs that are all rather small and dull.

The first thing you need to do when sequencing an animal genome is to make a map of it. There are two different kinds of maps you need to make. One is a genetic map made by mating animals with different characteristics - these can be anything, including fur colour, proteins, or sections of DNA. The other kind is a physical map where you’re actually looking at the location of particular bits of DNA on the chromosomes under a microscope. Once you have both maps you need to put them together. We already have a framework genetic map of the Tammar and are rapidly building a physical map.

All these genes exist in humans as well and we know where they are. So we can colour the bits of the kangaroo genome according to what parts of the human genome they represent. This is useful because we can read off one map and onto another. For instance, if we map a milk gene in the Tammar, we know exactly where that gene is going to be in the human genome and we can go in and look for it in the human genome sequence. So this comparative map is already extremely valuable to us.

The platypus is even more distantly related to humans than kangaroos. There is a huge amount of interest in the platypus because it has characteristics that seem rather reptile and bird-like: for example they lay eggs. There is a lot of international interest in how the platypus evolved.

The platypus genome is surprisingly small - somewhere between that of a bird and a placental mammal. The platypus has 26 chromosomes, many of which are small and hard to work with. We are able to clone platypus genes and map them to chromosomes. But when we line the chromosomes up we find something very strange. Most of the chromosomes are perfectly normal - two copies in both males and females - but 10 chromosomes don’t have a partner in males.

These chromosomes that don’t have pairs all turn out to be sex chromosomes, 5X chromosomes and 5 Y chromosomes. At male meiosis they form a big, long, strange-looking chain with alternating Xs and Ys. We have no idea how they make baby platypuses or how baby platypuses know what sex they are supposed to be. But we have some evidence that all five X chromosomes go into one sperm and all five Y chromosomes go into another sperm and that’s how sex is determined.

The chain is also interesting because we find that the X chromosome at one end of the chain is homologous to the mammalian X and Y chromosome, and the X chromosome at the other end is homologous to the bird sex chromosomes. Scientists thought that mammalian and bird sex chromosomes were completely different and evolved separately, but we now think this is wrong. Humans probably started off with the same system that birds and reptiles had and evolved a new system by exchanging our sex chromosomes with other chromosomes. This has been quite a surprise in the sex chromosome world.

There are two reasons why weird Australian mammals are especially important. One is that they’re very distantly related to humans, as I mentioned before, and this gives us a good opportunity to discover genes and the sequences that control them. The other is they’re different enough to have unique traits that might be useful.

If we look at a map showing how animals are related, we see how different Australian mammals are. There are three groups of mammals and Australia has a monopoly on two of them - marsupials and monotremes. The important thing is they shared a common ancestor so long ago that there are lots of differences in gene sequence and arrangement that we can use.

One surprising use for these different genomes is the discovery of new genes. Our laboratory has actually discovered 13 new human genes, mostly by accident, when we were looking for something else. It turns out that looking for a homologue in marsupials is actually a jolly good way of finding new genes.

We first hit the headlines when we were looking at a gene that was supposedly the male-determining gene. Students in my laborstory discovered that this gene was not on the Y chromosome in kangaroos and other marsupials, where it should have been if it’s the correct male determining gene. So it was the wrong gene. That led my student, Andrew Sinclair in London, to isolate the SRY gene on the human Y chromosome - which is also found on the kangaroo Y chromosome - and this is the right gene. That finding led to the isolation of a gene on the X chromosome called SOX3 - the female partner of SRY - and this also turns out to be a very important gene.

Similarly, we were looking for a gene on the human Y chromosome that is important in making sperm. We searched for and found a kangaroo version of it. But unexpectedly we found it had a homologue on the X chromosome and we were able to clone the human version, which we call RBMX. It maps to a very interesting region which is deleted in families with mental retardation. Since then we have cloned this gene in a zebra fish, knocked it down - that is we made it express less - and those zebra fish have a brain that rots away. So we seem to have accidentally discovered yet another gene that is probably required for building a brain and making it work.

Kangaroos do reproduction very well and this is one unique trait we hope to exploit. The female can switch on and off embryonic development and they have a very sophisticated milk system that we can possibly learn from.

At a very early stage the kangaroo embryo can go into a quiescent state and stay there for up to 11 months before the signal is given to resume development. Of course, we would love to know what genes are involved in turning off and then turning on embryonic development because it would mean we could better understand development and possibly manipulate it in domestic animals and maybe even humans.

The kangaroo is born at a very immature stage - about the size of a jellybean and with no back legs or gonads. It crawls up into the pouch, latches onto a teat and develops under the influence of factors in the milk.

Then later on while the young is still in the pouch and still suckling, it receives a completely different constitution of milk. The extraordinary thing is that the two completely different constitutions of milk are delivered by two teats lying next to each other. We want to know what’s in that milk, particularly the growth factors, and how the kangaroo switches from one type of milk to the other - how do the two bowsers deliver different milks?

Researchers have been studying kangaroo milk and saliva for some time because the pouch is a very dirty, grotty sort of place for a poor little pouch young who doesn’t even have an immune system. Something must be killing off the bacteria. As reported in The Age recently, kangaroo milk contains a very powerful new antibiotic. There may be a number of antibiotics in milk that can be harnessed for treating bacterial infections in humans. Kangaroo milk may be a strange place to look for new products but it looks like it has delivered.

My own interest is in genome evolution and I’m particularly interested in the evolution of the sex chromosomes. We can find out a lot about where and how the sex chromosomes originated by comparing sex chromosomes from humans, kangaroos and even platypus.

In humans, as in other mammals, females have two copies of a large gene rich X chromosome (approximately 1,000 genes), while males only have one copy of the x plus a small Y chromosome. The Y chromosome is a very peculiar little chromosome with only 45 genes. It seems to be specialised for a male role, with genes for sex determination and making sperm. The Y has always been known to be very peculiar so there is been a lot of interest in it.

There are two models for the Y chromosome. The model we were all brought up with was the Y as a macho little thing because if you have a Y you’re male and that’s it. But it turns out that’s only because the Y chromosome has the SRY gene on it. The other theory is that the Y is a selfish sort of entity and it grabs genes from other parts of the genome that are handy in males. But our work on comparative mapping says that the Y is merely a wimp, a relic of the X chromosome. It started off being identical to the X but over millions of years it has been losing genes and there are hardly any left.

This, of course, makes men very anxious. Will the Y chromosome disappear? I have predicted that at the rate it’s going the Y chromosome will disappear in something like 15 million years. This doesn’t necessarily mean that males will disappear. It’s possible that we’ll evolve a new sex determining gene somewhere else in the genome.

The other interesting thing about this hypothesis that the Y chromosome is a relic of the X, is that the genes on the Y are all, or mostly, evolved from genes on the X. We’ve done a lot of work on some of the special function genes, like the sex determining gene SRY, and other genes like RBMY which is critical for spermatogenesis, and we found they all evolved from genes on the X and, oddly enough, appear to be involved in brain development and function. So it looks like intelligence genes that find themselves on the Y chromosome have been commandeered to make them into fertility genes.

Will the possession of sex and spermatogenesis genes save the Y? Probably not. We know that some genes needed for making sperm in mice have been lost from the primate Y. If this gene can be lost in other species, why not the SRY gene itself? If it becomes inactive and then gets lost there is no reason to keep a Y chromosome at all - it can just disappear

So I hope I have answered the question of why sequence genomes of Australian mammals (are important). Animal genomes can give depth and meaning to the human genome sequence: our Australian animals, are particularly good for finding new genes and the sequences that control them; they help us understand diseases and possibly lead to new treatments and even cures; they can lead to the development of new antibiotics, new drugs and better breeds of animals; and they also help us discover where our genome came from and how it has changed.

In fact, comparative genomics is giving us information that can help us discover how humans are made and how humans function. It’s been called the greatest scientific adventure of our age. The prestigious journal Science thinks so too - naming evolutionary genomics the “breakthrough of the year” at the end of 2005.