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Thursday 8 May 2008 (Global embargo lifted at 3am AEST on Thu 8 May 2008)

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Platypus genome secrets revealed - Nature

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Ever since its discovery, people have been fascinated by the platypus – an egg-laying mammal with a bill like a duck, producing milk like a cow and with venom like a snake. Today the fascinating platypus genome has been published in Nature as an international team of over 100 researchers, including 26 from Australia, report their findings.

For Australia this is of particular significance, as the platypus is the first Australian animal to be sequenced. However, it is the platypus’s ancient links with birds and reptiles that has generated worldwide interest in the platypus genome and what it reveals about our own genetic origins.

The platypus genome represents a vital missing link, offering the power to discover new genes, to determine how the genomes of humans and other mammals have evolved, and how they function.

Australian authors and experts comment on the significance of the platypus genome below.

ON THE PLATYPUS GENOME

Professor Jenny Graves is Head of the Comparative Genomics Group at ANU and Director of the ARC Centre of Excellence for Kangaroo Genomics. Jenny is a co-author of the Nature paper.

EAGERLY AWAITED
“It’s probably the most eagerly awaited genome since the chimp genome because platypuses are so weird. It was very easy to get the NIH to come up with the money to sequence it because everybody wanted to know what the platypus genome would look like. There’s a lot of excitement, I’m getting calls from all over the world this morning. “

COMPARING HUMANS WITH PLATYPUS
“Comparing us with the platypus means that we can say something about our common ancestor, which was one of the earliest mammals, so that means that we can ask questions about what happened to make us mammals.”

FORK IN THE ROAD
“The platypus of course is not an evolutionary intermediate. The platypus is a platypus. But it’s the comparisons of humans with the platypus that can tell us about the fork in the road, when the platypus went one way and we went another way.”

TRACE CHANGES
“The platypus is a very ancient offshoot of a mammal tree, so it was 166 million years ago that we last shared a common ancestor with platypuses. And that puts them somewhere between mammals and reptiles because they still maintain quite a lot of reptilian characteristics that we’ve lost, for instance they still lay eggs. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having live-born young.”

IMPLICATIONS FOR FURTHER RESEARCH
“It will help existing areas of research and start new areas of research. One thing is that you can line up the sequence of a platypus against the sequence of a human, a mouse and a kangaroo in the same region. And the important bits of the genome really stand out because they haven’t changed much. Everything else changes all the time but the important bits don’t change so you can look at the piece of genome and spot the important bits and say well that looks like a gene we didn’t know about so it’s a good way to discover genes including human genes and a particularly good way of discovering the little signals that turn genes off and on, and that’s probably one of the biggest mysteries of how humans work. “

Dr Sue Forrest is Director of the Australian Genome Research Foundation.

“Features of reptiles as well as mammals have been identified in the sequence that align with the observed biology of the platypus. The mix of origins found within the platypus genome gives us an even better handle on understanding how all mammalian genes evolve and function.

Building such powerful reference genome sequences is the key to unleashing many secrets of the human genome. It will enable better detection of the switches that turn genes on and off in our body, advance our knowledge of how our cells function and open up new avenues for tackling diseases in the human population.

With the latest generation of sequencing technology, projects now take weeks that took many years and cost so much less! This means we are at the crest of a huge wave of genome information that will open many new doors of scientific research. Understanding more about the genetics of cancer, developing crops that cope with the changing environment and identifying the best farm animals for food production will be high on the agenda.”

Dr Frank Grützner is Head of the Genome Organisation, Epigenetics and Sex Determination Laboratory Adelaide University. Frank is a co-author of the Nature paper.

“With the genome sequence we have been handed a key to a mammalian treasure trove. The publication of the platypus genome has already shown the power and potential of the data not only for understanding monotremes but also to get more insights about the evolution of mammals (including humans). Now we need to use these data to build strong links to the general biology of platypus and echidnas also to help protecting these fascinating and iconic creatures.”

Professor Patricia Vickers-Rich, School of Geosciences & Director, Monash Science Centre, Monash University, Clayton, Victoria and Thomas H. Rich, Museum Victoria, Melbourne.

“This paper is centred around the genetic information now available about the platypus, much of it acquired by its approximately one hundred fifteen authors. While there is reference to an incredible amount of genetic information, the authors go far beyond that. For what they do is to present a smorgasbord of ideas and interpretations relating that genetic information to the known biology of the platypus. One could easily spend months following up the various ideas presented and not come close to exhausting everything in this paper. Students and established scientists interested in the platypus in any aspect would be well advised to not only read but to study in detail this highly stimulating paper for provocative ideas to pursue as research projects.”

ON SEX

Professor Jenny Graves is Head of the Comparative Genomics Group at the Australian National University and Director of the ARC Centre of Excellence for Kangaroo Genomics. Jenny is a co-author of the Nature paper.

“Well the biggest surprise for me was that platypuses do sex like a bird, not like other mammals. We had not expected this - in humans and other mammals we have an X and a Y chromosome and it’s the Y chromosome that has a gene which makes you a male. And we expected that platypus – although they had slightly weird looking sex chromosomes they’d be basically the same. But they’re absolutely not! There’s no copy of this gene - it’s called SRY. Platypuses don’t have it. And the chromosomes that are X and Y – they’re in the platypus genome but they are just ordinary chromosomes and they have nothing to do with sex. So that means we can go right back to the time when our sex chromosomes were just ordinary chromosomes minding their own business and ask well what happened, what made them into sex chromosomes.”

Dr Paul Waters is a Post Doctoral Fellow at the Australian National University and ARC Centre of Excellence for Kangaroo Genomics. Paul is a co-author of the Nature paper.

“Australia’s monotremes (the platypus and echidna) are the last representatives of an ancient mammalian lineage that diverged from other mammals 165 million years ago. In placental (i.e. humans and mice) and marsupial (i.e. kangaroos and possums) mammals females have two X chromosomes; whereas males have only one X chromosome, along with a Y chromosome that determines maleness. Platypus is exceptional in that females have five different pairs of X chromosomes, and males have five X chromosomes and five Y chromosomes. To our surprise we discovered that the platypus X and Y chromosomes are completely unrelated to the X chromosome of all other mammals. Instead, platypus sex chromosomes share extensive similarity to the sex chromosomes of the distantly related birds, suggesting that our ancient mammal-like reptile ancestor might have had sex chromosomes more like those of the current day birds”.

ON CONTROL OF GENES

Professor Marilyn Renfree is a Federation Fellow at the University of Melbourne’s Department of Zoology.

Dr Andrew Pask is Research Fellow at the University of Melbourne’s Department of Zoology.

“Each cell of bodies contains two copies of our genome, one we inherited from our mother and the other from our father. While the gene content of these two copies is identical, they are not functionally equivalent, with some genes switched off in the copies we got from our mothers and others turned off in the copy we got from our fathers. This phenomenon is known as genomic imprinting and occurs in all mammals except the monotremes (platypus and echidnas).

Therefore the platypus genome provides a unique resource in which to investigate the changes that have occurred to the genome with the acquisition of genomic imprinting. Our analysis suggests that the accumulation of repeat sequences and transposable elements within the mammal genome may have sparked the development of this mechanism”.

Dr Janine Deakin is a Post Doctoral Fellow at the Australian National University and ARC Centre of Excellence for Kangaroo Genomics. Janine is a co-author of the Nature paper.

“Dosage compensation equalizes the expression of genes found on sex chromosomes so that they are equally expressed in females and males. Placental and marsupial mammals, achieve this by inactivating one X chromosome in female cells. On the other hand, bird dosage compensation does not seem to be strictly required to balance expression of most genes on the Z chromosome. Whether dosage compensation exists in the platypus is of considerable interest, particularly since they have such fascinating sex chromosomes, possessing five different X and five different Y chromosomes. As part of the platypus genome project, we now know which genes are on the X chromosomes and have been able to study dosage compensation in these animals for the first time. We have shown that there is some evidence for dosage compensation but it is variable between genes and incomplete and is similar to the incomplete and variable dosage compensation of birds”.

ON IMMUNOLOGY

Dr Kathy Belov is a lecturer in genetics in the Faculty of Veterinary Science at the University of Sydney. Kathy is a co-author on the Nature paper.

“Platypuses give birth to immunologically naïve young. Powerful antimicrobial peptides, secreted into the mother’s milk, may protect young from infection. We identified 20 new antimicrobial peptides in the platypus genome and are now testing them to see which bugs they kill. Perhaps they can destroy drug-resistant bacteria?”

ON VENOM

Camilla Whittington is a PhD student at the Faculty of Veterinary Science at the University of Sydney. Camilla is a co-author on the Nature paper.

“Venom in a mammal is extremely unusual, and platypus envenomation of humans causes an interesting range of symptoms such as extreme swelling and terrible pain which normal painkillers can’t relieve. This makes us think that there must be some interesting and potentially useful chemical compounds in the venom. We hope that our research into platypus venom will lead eventually to the development of human medicines such as painkillers and potent antibiotics.”

ON EVOLUTION

Professor Mike Archer AM is Dean of Science at the University of New South Wales and a vertebrate palaeontologist.

“The exciting paper provides significant new understanding about the relationships of the platypus to other animals. Global interest in clarifying these relationships is indicated by the fact that only 26 of the 100 authors are Australian. While the palaeontological record has been rapidly improving, providing information about the minimal age of monotremes (at least 115 million years) and probable ancestor-descendant/sister-group relationships to extinct taxa (Jurassic and Cretaceous ausktribosphenids at 160-115 million years), it has provided much less clarity than this genomic study about the relationships of monotremes to the other crown groups of mammals (marsupials and placentals) as well as other extant vertebrates. As often concluded, the best way to maximise clarity about phylogenetic relationships is to combine the most up-to-date understanding from as many different research areas as possible, which is precisely what this new study enables.”

Dr Sarah Munks is from the School of Zoology at the University of Tasmania. Her main research areas are the ecology and conservation management of hollow dependent fauna and the platypus.

“The platypus is well known as an animal with both reptilian and mammalian features. This exciting piece of work has confirmed this and has also revealed features that are unique to the platypus. These unique features are reflected in its ecology and behaviour enabling the platypus to have survived for millions of years in its freshwater habitat on our dry continent.

This platypus genome study confirms eminent platypus biologist, Merv Griffiths belief that the platypus may be ‘the animal of all time’. Its unique evolutionary status confirmed by this recent work makes it not only an Australian icon but also a species of international importance”.

Professor Des Cooper is an evolutionary biologist at the University of NSW.

“The sequencing of the platypus genome is a major step forward in our knowledge of mammals. Platypuses are often thought of as primitive because they lay eggs. As this paper demonstrates, there is a mixture of characters which they share with other mammals and of highly specialised attributes. They have mammary glands which produce milk, they have hair and one bone in the lower jaw, all of which are shared with other mammals.

Their highly specialised attributes include the ability to detect weak electric currents using their bills as an antenna and in males they have a spur on the hind legs which is attached to a poison gland. They have a complicated sex chromosome system and the way in which this determines sex is yet to be fully understood.

It appears that they share some sex linked genes with birds. It can be expected that the sequencing of the genome will lead to a deeper understanding of these specialised characters.”

Associate Professor Stewart Nicol is from the School of Zoology at the University of Tasmania. Monotremes are his major research interest.

“This paper contains a wonderful mixture of the expected and the unexpected. Given the evolutionary position of the monotremes the genome would be expected to contain a mixture of ancestral reptilian and derived mammalian characteristics, which it clearly does. One of the surprises was the genes involved in chemoreception, with a very large number of genes for type 1 vomeronasal receptors, which may be involved in pheromonal communication, or in underwater food detection. Another unexpected feature was the large number of genes (241) within the natural killer cell complex. One of the intriguing aspects of monotremes is that they possess multiple small sex chromosomes which form translocation chains, rather than pairing, during meiosis. The sequence data shows homology of these with bird Z chromosomes, and no alignment with human X, indicating that the platypus X chromosome evolved directly from a bird-like reptilian ancestor, although the autosomes show no such relationship. The monotremes are an enormously significant group in terms of our understanding of mammalian evolution, and I have no doubt this work will stimulate many more detailed studies.”

ON PLATYPUS CONSERVATION

Dr Melody Serena is a conservation biologist with the Australian Platypus Conservancy. She is a leading authority on the conservation status and ecology of the platypus.

“Our understanding of the platypus’s status is very much hampered by how difficult these animals are to census accurately. However, the past decade of drought in south eastern Australia has certainly reduced platypus numbers in many areas. The species is also under pressure from widespread habitat degradation, water pollution, and mortality due to animals becoming entangled in litter or drowning in illegal fishing nets. It is essential that effective conservation measures for the platypus be initiated now, before numbers are reduced to critical levels.”