We’ve cracked the cane toad genome, and that could help put the brakes on its invasion



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Cane toads are on the march, but new genetic research could slow them down.
Michael Linnenbach

Peter White, UNSW; Alice Russo, UNSW, and Rick Shine, University of Sydney

We and our international colleagues have deciphered the genetic code of the cane toad. The complete sequence, published today in the journal GigaScience, will help us understand how the toad can quickly evolve to adapt to new environments, how its infamous toxin works, and hopefully give us new options for halting this invader’s march across Australia.

Since its introduction into Queensland in 1935, the cane toad has spread widely and now occupies more than 1.2 million square kilometres of Australia. It is fatally poisonous to predators such as the northern quoll, freshwater crocodiles, and several species of native lizards and snakes.

Previous attempts to sequence the cane toad, by WA researchers more than 10 years ago, were not successful, largely because the existing technology could not assemble the genetic pieces to create a genome. But thanks to new methods, we have succeeded in piecing together the entire genetic sequence.




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Our team, which also featured researchers from Portugal and Brazil, worked at the Ramaciotti Centre for Genomics at UNSW. This centre played a key role in decoding the genomes of other iconic Australian species, including the koala.

Sequencing, assembling and annotating a genome (working out which genes go where) is a complicated process. The cane toad genome is similar in size to that of humans, at roughly 3 billion DNA “letters”. By using cutting-edge technology, our team sequenced more than 360 billion letters of cane toad DNA code, and then assembled these overlapping pieces to produce one of the best-quality amphibian genomes to date.

We deduced more than 90% of the cane toad’s genes using technology that can sequence very long pieces of DNA. This made the task of putting together the genome jigsaw much easier.

Toxic toads

The cane toad has iconic status in Australia, with many Aussies loving to hate the poisonous invasive amphibian. This is a little unfair. It’s not the cane toad’s fault – it was humans who chose to bring it to Australia.

Our obsession with sugar in the 1800s led to the toad’s introduction to many countries around the world. Wherever sugar cane was planted, the cane toad followed, taken from plantation to plantation by landowners as the warty interlopers travelled from South America to the Caribbean and then on to Hawaii and Australia.

But unlike most other places to which the cane toad was introduced, Australia lacks any native toads of its own. The cane toad’s powerful poisons are deadly to native species that have never before encountered this amphibian’s arsenal.

The cane toad has therefore been subject to detailed evolutionary and ecological research in Australia, revealing not only its impact but also its amazing capacity for rapid evolution. Within 83 years of its introduction, cane toads in Australia have evolved a wide range of modifications that affect their body shape, physiology and behaviour.

For example, cane toads at the invasion front are longer-legged and bolder than those in long-colonised areas and invest less into their immune defences (for a summary, see Cane Toad Wars by Rick Shine).

The new genome will give us insights into how evolution transformed a sedentary amphibian into a formidable invasion machine. And it could give us new weapons to help stop, or at least slow, this invasion.

Cracking the cane toad genome.

Viral control

Current measures such as physical removal have not been successful in preventing cane toads from spreading, so fresh approaches are needed. One option may be to use a virus to help control the toad population.

Viruses such as myxomatosis have been successfully used to control rabbits. But the cane toad viruses studied so far are also infectious to native frogs. The new genome could potentially help scientists hunt for viruses that attack only toads.

In a study published this month, we and other colleagues describe how we sampled genetic sequences from cane toads from different Australian locations, and found three viruses that are genetically similar to viruses that infect frogs, reptiles and fish. These viruses could potentially be used as biocontrol agents, although only after comprehensive testing to check that they pose no danger to any other native species.




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The full cane toad genome will help to accelerate this kind of research, as well as research on the toads’ evolution and its interactions with the wider ecosystem. The published sequence is freely available for anyone to use in their studies. It is one of very few amphibian genomes sequenced so far, so this is also great news for amphibian biologists in general.

As the cane toads continue their march across the Australian landscape, this milestone piece of research should help us put a few more roadblocks in their path.The Conversation

Peter White, Professor in Microbiology and Molecular Biology, UNSW; Alice Russo, PhD candidate, UNSW, and Rick Shine, Professor in Evolutionary Biology, University of Sydney

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Koalas sniff out juicy leaves and break down eucalypt toxins – it’s in their genome


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Koalas spend a large part of the day sleeping – while their digestive enzymes get to work.
emmanueleragne/flickr , CC BY

Jenny Graves, La Trobe University

News is out today that the entire genome of the koala has been sequenced. This means we now have a complete read-out of the genes and other DNA sequences of this iconic marsupial mammal.

Knowing the full set of koala genes deepens our knowledge of koalas (and other Australian mammals) in many ways. Now we can understand how koalas manage to survive on such a toxic diet of gum leaves. Now we can follow the fortunes of historic koala populations and make good decisions about how to keep remaining koala populations healthy. Now we have a new point of comparison that we can use to understand how the mammal genome evolved.

This is important for science – but also economically. Koalas are incredibly well loved, with their baby-faces, shiny noses and big fluffy ears. Millions of visitors line up each year to spot them snoozing in gum trees – indeed, they are worth A$3.2 billion in tourist dollars.

Koalas are listed as a vulnerable species in some parts of Australia, affected by habitat destruction, disease and other stresses.




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We now have a high quality read-out of the koala genome. Video thanks to the Australian Academy of Science.

The koala genome

Koala DNA was sequenced with new “long-read” technology that delivers a complete and well-assembled genome. As far as quality of the read-out goes, it’s as good as the human genome, with continuous sequences now known over huge (almost chromosome-scale) spans. New technology enabled us to achieve this at a tiny fraction of the $2.7 billion it cost to sequence the first human.

The obtained koala genome sequence is much better quality than that for other sequenced marsupials – opossum, tammar wallaby and Tasmanian devil – and will really help us to assemble and compare genomes from all marsupials.

The koala has a genome a bit bigger than that of humans, with 3.5 billion DNA base-pairs. This amounts to about a metre of DNA, which is divided and packaged into eight large bits that we recognise as chromosomes.




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An animal has a set of chromosomes from mother and a set from father, so koalas have 16 large chromosomes in each cell. This is similar to other marsupials; as a group they seem to have a low chromosome number and a very stable genome arrangement. In placental mammals the number and arrangement of chromosomes is much more varied: for example, humans have 46, and rhinos 82 chromosomes.

The source of junk DNA

New findings from the koala genome help us to understand how mammal genomes evolved and how they work.

A lot (sometimes more than 50%) of animal genomes seem to be “junk DNA” – these are repeated sequences, many deriving from ancient viral infections. The koala, uniquely, seems to be in the middle of one such invasion. A DNA sequence derived from a retrovirus is present in different numbers and sites in different koala populations, testifying to its recent movement and amplification. This helps us learn how the genomes of humans and other mammals got so puffed up with junk DNA.

Like the human genome, the koala genome contains about 26,000 genes. These are stretches of DNA that code for or control proteins. Indeed, most koala genes are present in humans and other mammals – these are the same genes doing the same basic jobs in different animals.

So why is it important to sequence different species if their genomes are so similar? Well, it’s the special genes that have evolved to adapt the koala to its unique lifestyle that give us new and valuable information.




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How to survive on gum leaves

How koalas exist on an exclusive low-calorie and toxin-laced diet of eucalyptus leaves has been somewhat of a science mystery.

The genome provides answers. The koala has multiplied a family of genes that code for enzymes (members of the cytochrome P450 family) that break down the toxins of gum leaves. Evolution of these additional gene copies has enabled the koala to outstrip its competition, even at the cost of sleeping most of the day.

The genome also gives us clues to the koala’s picky eating habits. The koala genome contains many additional copies of genes that enable them to taste and avoid bitter flavours and even to “smell” water and choose juicy leaves (they don’t drink water).

Koalas have 16 chromosomes per cell.
chrisfithall/flickr, CC BY

The genome also gives us new information about how koalas develop. Like other marsupials, they are born about the size of a pea, and complete most of their growth and differentiation in the pouch. Developing koalas are nurtured by milk with a complex composition that changes with the stage of development.




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Saving an iconic Australian

Managing koala populations is very fraught, and there has long been a need for a holistic, scientifically-grounded approach to koala conservation.

Today’s koalas are the “last stand” of the marsupial family Phascolarctidae – and the koala genome contains new information about this evolutionary history. It also tells us that koala populations peaked about 100,000 years ago, then plunged to about 10% of their numbers 30-40,000 years ago, at the same time that the megafauna became extinct. This population was fairly stable until European settlement, when it plunged again to its present numbers (about 300,000).

Koalas once occupied a swathe of timbered habitat from Queensland to South Australia; now, only fragmented populations survive in the south. These are intensively managed, and small numbers of koalas are translocated to other sites, producing dangerously inbred populations. Bizarrely, one of the greatest problems is overbreeding in isolated populations – for example, on South Australia’s Kangaroo Island – which leads to animals eating themselves out of house and home.

The enemies of koalas in the north are habitat destruction and fragmentation by urbanisation and climate change.




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The koala genome paper reports sequence comparisons of different populations and identifies barriers to gene flow. With the information from the koala genome, we can now monitor genetic diversity in the surviving populations, and maximise gene flow between connected populations.

Koalas are the sole surviving member of the Phascolarctidae marsupial family group.
Photo by Holger Link on Unsplash, CC BY

Maintaining genetic diversity is important because different animals can mount different responses to environmental threats and diseases such as chlamydia, a bacteria that affects koala reproduction and eye health.

The koala genome provides us with information about the immune genes of the koala, and the changes in activity of these genes in infected animals. This will help us understand the different responses of animals, vital for developing vaccines and treatments.

The koala genome also identifies powerful anti-bacterials in milk that protect the baby koala from disease – and may provide humans with the next generation of antibiotics.

So sequencing the koala genome is good for science and good for koalas, an iconic species at the top of the tree for conservation efforts.


The Conversation


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Jenny Graves, Distinguished Professor of Genetics, La Trobe University

This article was originally published on The Conversation. Read the original article.