Transtasman scientists sequence entire genome of myrtle rust

Myrtle rust spores on leaf of paperbark tree from Manly Vale, Sydney, NSW. Photo / Peri Tobias

Scientists in Australia and New Zealand have built the entire genetic map of the fungus responsible for myrtle rust.

The result is the world's largest assembled fungal genome, taking up a billion letters of DNA genetic code.

If you printed the genome it would take up more than 400,000 A4 pages.

This discovery marked an important step towards unlocking genetic features of Austropuccinia psidii, which drives the disease threatening myrtle plants in Australia and New Zealand.

Myrtle rust is an invasive disease that had brought at least three native plant species to the brink of extinction since its introduction to Australia a decade ago.

Commonly affected plants in Australia included horticultural staples such as bottlebrush, paperbark trees, lilly pillies, tea-trees and many eucalyptus species.

The research had been published in the journal G3: Genes, Genomes, Genetics.

The genome project was initiated by Professor Robert Park led by Dr Peri Tobias from the School of Life and Environmental Sciences and the Sydney Institute of Agriculture at the University of Sydney.

Assembling the genome was a "huge" collaborative effort, Tobias said.

"We were dealing with the output of new DNA sequence chemistry, new technology and newly developed software."

"This invasive fungus is very problematic for Australian plants of the Myrtaceae family such as eucalypts, paperbark and tea-tree. Some lesser-known species, like the native guava, scrub stringybark and silver malletwood, are now on the verge of extinction."

Tobias said the genome of this fungus, which originated in South America, was so large because it was bloated with transposable elements, genetically unstable regions that can allow the introduction of new mutations.

"We think the transposable elements have been beneficial to the fungus by enabling it to adapt to infect new hosts. We are working to test these ideas experimentally," she said.

The rust was widespread on Australia's east coast from southern New South Wales to far north Queensland. It was also found in nursery production sites around Melbourne.

The NSW Department of Primary Industries said that movement of myrtle plants in Australia was regulated, and Tasmania, Western Australia, Northern Territory and South Australia had quarantine restrictions for the importation of myrtle plant products.

Worldwide there were 5500 plant species potentially affected by myrtle rust disease.

Collaborator on the project and co-author Dr Grant Smith is a principal scientist at Plant & Food Research in New Zealand.

He said: "If you're going to go after a pathogen, it is important to get some understanding of its genome."

At the time myrtle rust arrived in New Zealand in 2017, there was limited understanding of the A. psidii genome.

Lead author Dr Peri Tobias wearing a T-shirt with some of the billion letter genetic code from the myrtle rust fungus. Photo / Supplied

Smith came to Australia to present New Zealand's research intentions, which included sequencing the genome.

While there, he was approached by Tobias from the University of Sydney to work collaboratively on sequencing.

"Instead of us trying to re-sequence what had already been started, we decided to pool our resources and effort to build on what Peri and her colleagues had begun," Smith said.

He said that genome sequencing was like working on a three-dimensional jigsaw puzzle.

The output from a sequencing instrument is millions of small segments. These are then assembled and aligned back to the chromosomes – the building blocks of a genome – from which they originated.

The genome took three months to assemble using the University of Sydney's high-performance computing facility.

Dr Benjamin Schwessinger, a senior lecturer at the Australian National University, and one of the collaborators on the project, put the size of the genome into perspective.

"Other rust fungi have 80 million base pairs. Austropuccinia psidii is more than 10 times as big."

By comparison, the virus causing Covid-19 has about 30,000 bases, about 27,000 times smaller.

Now that the genome has been sequenced, it could be used as a tool to investigate how A. psidii infected plants in the myrtle family and to look for ways to facilitate disease resistance.

The team had started using the genome to get an idea of which pathogen genes and which host genes were interacting at the earliest points in the infection process.

"We are looking at what makes plants resistant to the fungus for better management of the disease," Tobias said.

The research team had received Australian Research Council Linkage Grant funding to further understand the fungus and how to save native plant species in Australia.