A new 3D koala genome will aid efforts to defend the threatened species

Parwinder Kaur, University of Western Australia

Koalas are unique in the animal kingdom, living on a eucalyptus diet that would kill other creatures and drinking so little their name comes from the Dharug word gula, meaning “no water”. Today, many koala populations across Australia are in decline, due to habitat destruction caused by agriculture, urbanisation, droughts and bushfires intensified by climate change, and diseases such as chlamydia and koala retrovirus.

Genetic information can play a key role in the effort to conserve koalas and other species. A detailed map of the koala genome is vital to understanding their susceptibility to disease, their genetic diversity, and how they may respond to new environmental pressures.

We have created a new “chromosome-length” sequence of the koala genome, which will allow researchers to study its three-dimensional structure and understand its evolution.

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A unique creature under threat

The modern koala is the only living representative of the marsupial family Phascolarctidae, a family that once included several genera and species. During the Oligocene and Miocene epochs (from 34 to 5 million years ago), the ancestors of modern koalas lived in rainforests and didn’t eat only leaves.

During the Miocene, the Australian continent began drying out, leading to the decline of rainforests and the spread of open eucalyptus woodlands. Koalas evolved several adaptations that allowed them to live on a specialised eucalyptus diet. This specialisation makes them picky eaters, so they’re very prone to habitat loss.

Koalas are listed as a vulnerable species by the International Union for Conservation of Nature. It was hunted heavily in the early 20th century for its fur, and large-scale cullings in Queensland resulted in public outcry, initiating a movement to protect the species. Sanctuaries were established, and koalas whose habitat was disappearing were relocated.

Koalas are particularly vulnerable to bushfires; they are slow moving and eucalypt trees are very flammable. They instinctively seeks refuge in higher branches, exposing them to intense heat and flames. Bushfires also fragment the animal’s habitat, which restricts their movement and leads to population decline and loss of genetic diversity.

Piecing together the puzzle

The koala genome was first sequenced in 2013. This was only the first step in understanding koala genetics — akin to finding all the pieces of the puzzle, but being unsure how to put them all together into the meaningful patterns of genes and chromosomes.

Our new chromosome-length assembly follows the work of others, especially the Koala Genome Consortium and the Koala Genome Project led by Australian geneticist Rebecca Johnson. It is based on a draft by the Earlham Institute in the UK.

We used big-data sequencing methods such as Hi-C, 3D-DNA and Juicebox Assembly Tools courtesy of DNA Zoo labs to create our chromosome-length assembly.

We organised the genome into 8 chromosomes, a great improvement on the draft of 1,907 fragments we began with.

Vital for conservation

A high-quality genome sequence is essential if we want to bring genetic insights to conservation management initiatives. Some 200 Australian vertebrate species currently have species recovery plans, and 80% of those plans include genome-based actions. However, only 15% of those species have any genomic data available.

Our chromosome-length koala genome assembly enables a highly detailed 3D view of the genome architecture for koala. It is easier to use than earlier genomes, and means conservation management initiatives will have fast, cost-effective and reliable analysis options available.

This will give us insights into koalas’ genetic susceptibility to diseases like koala retrovirus (KoRV) and chlamydia. It may also form a basis for innovative vaccines. What’s more, it can be used in new conservation management strategies that aim to diversify the koala gene pool.

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Parwinder Kaur, Associate Professor | Director, DNA Zoo Australia, University of Western Australia

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

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Genome and satellite technology reveal recovery rates and impacts of climate change on southern right whales

University of Auckland tohorā research team, Department of Conservation permit DJI

Emma Carroll

After close to a decade of globe-spanning effort, the genome of the southern right whale has been released this week, giving us deeper insights into the histories and recovery of whale populations across the southern hemisphere.

Up to 150,000 southern right whales were killed between 1790 and 1980. This whaling drove the global population from perhaps 100,000 to as few as 500 whales in 1920. A century on, we estimate there are 12,000 southern right whales globally. It’s a remarkable conservation success story, but one facing new challenges.

A southern right whale calf breaches in the subantarctic Auckland Islands.
University of Auckland tohorā research team, Author provided

The genome represents a record of the different impacts a species has faced. With statistical models we can use genomic information to reconstruct historical population trajectories and patterns of how species interacted and diverged.

We can then link that information with historical habitat and climate patterns. This look back into the past provides insights into how species might respond to future changes. Work on penguins and polar bears has already shown this.

But we also have a new and surprising short-term perspective on the population of whales breeding in the subantarctic Auckland Islands group — Maungahuka, 450km south of New Zealand.

Spying on whales via satellite

Known as tohorā in New Zealand, southern right whales once wintered in the bays and inlets of the North and South Islands of Aotearoa, where they gave birth and socialised. Today, the main nursery ground for this population is Port Ross, in the subantarctic Auckland Islands.

Adult whales socialise at both the Auckland and Campbell Islands during the austral winter. Together these subantarctic islands are internationally recognised as an important marine mammal area.

In August 2020, I led a University of Auckland and Cawthron Institute expedition to the Auckland Islands. We collected small skin samples for genetic and chemical analysis and placed satellite tags on six tohorā. These tags allowed us to follow their migrations to offshore feeding grounds.

It matters where tohorā feed and how their populations recover from whaling because the species is recognised as a sentinel for climate change throughout the Southern Hemisphere. They are what we describe as “capital” breeders — they fast during the breeding season in wintering grounds like the Auckland Islands, living off fat reserves gained in offshore feeding grounds.

Females need a lot in the “bank” because their calves need a lot of energy. At 4-5m at birth, these calves can grow up to a metre a month. This investment costs the mother 25% of her size over the first few months of her calf’s life. It’s no surprise that calf growth depends on the mother being in good condition.

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Females can only breed again once they’ve regained their fat capital. Studies in the South Atlantic show wintering grounds in Brazil and Argentina produce more calves when prey is more abundant, or environmental conditions suggest it should be.

The first step in understanding the relationship between recovery and prey in New Zealand is to identify where and on what tohorā feed. The potential feeding areas for our New Zealand population could cover roughly a third of the Southern Ocean. That’s why we turn to technologies like satellite tags to help us understand where the whales are going and how they get there.

Where tohorā go

So far, all tracked whales have migrated west; away from the historical whaling grounds to the east near the Chatham Islands. As they left the Auckland Islands, two whales visited other oceanic islands — skirting around Macquarie Island and visiting Campbell Island.

It also seems one whale (Bill or Wiremu, identified as male using genetic analysis of his skin sample) may have reached his feeding grounds, likely at the subtropical convergence. The clue is in the pattern of his tracks: rather than the continuous straight line of a whale migrating, it shows the doughnuts of a whale that has found a prey patch.

Migratory track of southern right whale Bill/Wiremu, where the convoluted track could indicate foraging behaviour.

The subtropical convergence is an area of the ocean where temperature and salinity can change rapidly, and this can aggregate whale prey. Two whales we tracked offshore from the Auckland Islands in 2009 visited the subtropical convergence, but hundreds of kilometres to the east of Bill’s current location.

As Bill and his compatriots migrate, we’ve begun analysing data that will tell us about the recovery of tohorā in the past decade. The most recent population size estimate we have is from 2009, when there were about 2,000 whales.

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I am using genomic markers to learn about the kin relationships and, in doing so, the population’s size and growth rate. Think of it like this. Everybody has two parents and if you have a small population, say a small town, you are more likely to find those parents than if you have a big population, say a city.

This nifty statistical trick is known as the “close kin” approach to estimating population size. It relies on detailed understanding of the kin relationships of the whales — something we have only really been able to do recently using new genomic sequencing technology.

Global effort to understand climate change impacts

Globally, southern right whales in South Africa and Argentina have bred less often over the past decade, leading to a lower population growth rate in Argentina.

Concern over this slowdown in recovery has prompted researchers from around the world to work together to understand the relationship between climate change, foraging ecology and recovery of southern right whales as part of the International Whaling Commission Southern Ocean Research Partnership.

The genome helps by giving us that long view of how the whales responded to climate fluctuations in the past, while satellite tracking gives us the short view of how they are responding on a day-to-day basis. Both will help us understand the future of these amazing creatures.

Emma Carroll, Rutherford Discovery Fellow

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

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

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.

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.

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

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.

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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.