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Growing up in India, Parwinder Kaur had never seen a black swan. She didn’t even think they were real.
You can imagine her shock when, shortly after arriving in Western Australia, she caught a glimpse of one – the Australian black swan (Cygnus atratus) – while eating her lunch. She didn’t know it at the time, but it would turn out to be a fateful encounter.
“I never thought I’d be the person to find out that the black swan is normal and the white swan is a mutant,” she says.
That discovery, in 2023, came thanks to her work in genomics, the study and mapping of the entire DNA blueprint of an organism. Kaur initially trained as a plant geneticist in India, but today, she studies charismatic Australian species like the swan, the numbat and the extremely scarce Gilbert’s potoroo in her role as founding director of DNA Zoo Australia.
However, she often goes by a much more intriguing title: DNA Zookeeper.
PLAYING FOR KEEPS
To understand what a DNA Zookeeper is, we need a quick crash course in DNA.
Every cell in every living creature on Earth contains DNA, or deoxyribonucleic acid. DNA is composed of four bases: adenine, cytosine, thymine and guanine. They are usually just referred to as A, C, T and G. The way these letters are arranged gives rise to genes – a set of instructions for cells to make molecules like proteins. And genes are wrapped up in chromosomes, bundling them up tightly together.
The full map of every gene in an organism is called a genome. Genomics tries to build this map, taking DNA from organisms, smashing it up into chunks, reading the order of the As, Cs, Ts and Gs and then using a supercomputer to reassemble it.
It’s a giant jigsaw puzzle, Kaur says.
For instance, in humans, DNA contains 3 billion base pairs – so 3 billion As, Cs, Ts and Gs. The first full map of the human genome took a decade of work and some $2.7 billion. As technology has advanced, so has the capability of our tools, bringing the cost to piece together a genome way down.
Improving technology has also enabled DNA Zookeepers to take the assembly one step further. Instead of just reassembling the DNA in 2D, the researchers use a technique that shows how DNA is assembled in 3D. That makes it a more difficult puzzle but one that provides researchers with extra information about how genes function. It was pioneered by DNA Zoo co-founder Erez Lieberman Aiden.
A model of the 3D structure of Mammoth DNA
Kaur says DNA Zookeepers from across the world have helped to decode the genomes of some 400 different species, with 64 iconic Australian species on the list. “It is probably one of the biggest collections on the planet at this moment,” she notes.
MAMMOTH TASK
The DNA Zoo doesn’t contain any living animals you can visit. Everything in the zoo is a genome sequence.
The most recent addition to the DNA Zoo is the woolly mammoth (Mammuthus primigenius). In research recently published in the prestigious journal Cell, DNA Zookeepers including Kaur unravelled the genetic code of Yuka, a juvenile woolly mammoth. Yuka is believed to have been killed by a sabre-toothed tiger some 52,000 years ago but her body was preserved by the extreme cold of the Siberian tundra.
Typically, it would be impossible to find DNA this old. It degrades fairly quickly when exposed to the elements. Sunlight can rip it apart. But Kaur says the DNA of Yuka was freeze-dried so quickly that it was like a “bumper-to-bumper traffic jam”. There was no way for the DNA to degrade – it was frozen in time. Importantly, it also froze the chromosomes in place, allowing them to rebuild the 3D structure.
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This provided a bunch of new insights. The team were able to tell which genes would have been active in the mammoth and compare them with its closest relative, the Asian elephant. As you might expect, the mammoth has specific regions of the genome related to immunity and to the development of hair – a critical element if you’re spending your days in the cold of an ice age.
The genome could also help with an ambitious project to resurrect the woolly mammoth. Ongoing work in the US is attempting to bring the species back from the dead in the future – and having a full genome provides a template for that work.
A DANGEROUS GAME
Kaur’s not so focused on the ability to bring back species. Her attention is on the vulnerable species of today.
For instance, when Kaur and her colleagues at DNA Zoo studied the black swan genome, they discovered that it contained genes that would make it susceptible to various forms of bird flu. As a new form spreads around the globe, affecting birds as far south as Antarctica, those findings take on renewed importance.
Kaur points out the current rate of extinction is extreme. We could be losing up to one species every 20 minutes. In Australia, we’ve lost 37 species to extinction since colonisation and a further 52 are classified as either critically endangered or endangered. The losses put pressure on ecosystems, which Kaur likens to a game of Jenga.
“We can remove one or two blocks and perhaps the tower remains standing, but if we remove a loadbearing piece – a keystone species – then the entire tower collapses.”
With the rate of extinction so high and existential threats like climate change looming over all species, Kaur says the knowledge we gain from understanding the genomes of life on Earth provides vital information about how we can best protect them.
