Key points
- We're sequencing the genomes of many Australian species for the first time using next generation long-read DNA sequencing.
- The Australian staghorn coral and the superworm were amongst the first species sequenced.
- Highly accurate long-read sequencing will speed up genomics research and drive innovation.
High quality genetic data is key to projects across the biosecurity, agricultural, medical and environmental sciences.
Long-read sequencing is highly accurate (99.9 per cent) and the machine can read multiple samples quickly and provide high-definition data.
First species sequenced
Amongst the first species to be sequenced with this new machine were the Australian staghorn coral and the superworm.
The Australian staghorn coral, Acropora spathulata, is an iconic coral from the Great Barrier Reef. Having a detailed genome for this species will help to understand its population genetics and how the population is changing as the reef responds to climate change impacts.
The superworm, Zophobas morio, is a key species for biorecycling. Researchers from the University of Queensland found that their larvae can eat plastic thanks to special gut enzymes. This new genomic data could help show how they evolved these specialised gut enzymes.
Another species in line to be sequenced is the short-spined Crown-of-thorns starfish, Acanthaster brevispinus, a subspecies of the infamous, coral-munching Crown-of-thorns starfish. Scientists recently found that it is also a threat to coral reefs, in deeper water. This new genome will be used to expand resources for environmental DNA (eDNA) early detection of all these starfish species, which will help to protect our coral reefs.
What is long-read sequencing?
Mr Leon Court, senior experimental scientist, said the long-read sequencing technique uses long DNA fragments and gives better data outputs.
“Long-read sequencing is like making a jigsaw out of only 100 pieces instead of 1,000 pieces. Using fewer, bigger blocks of information to assemble the data is faster, easier and more accurate,” Leon said.
“The data output doesn’t require additional error correction and can be used immediately, including by partners around the world. It will allow scientists to focus on science, rather than data manipulation and handling.”
Why does long-read sequencing matter?
Dr Rahul Rane, senior research consultant in applied genomics and rapid diagnostics, said that high quality foundational data sets such as the coral and superworm genomes can improve research outcomes and applications in the field.
“Previously it was difficult to accurately and quickly build foundational data assets for complex species,” Rahul said.
“Genomics techniques are evolving rapidly, and genomic data is key to most research projects looking at living organisms as it’s the source code behind all life.
“Some gene anomalies can only be identified using highly accurate long-read technology.”
Looking at whole genomes allows researchers to identify the genetic code behind such things as how a disease infects its host, or how a pest species is able to adapt to the changing climate.
Dr Tom Walsh, principal research scientist, said that accurate genetic reference data informs eDNA, which is a game-changer for monitoring biodiversity and detecting biosecurity pests. This technology allows scientists to analyse eDNA found in samples from the environment, comparing it with reference sequences to see which species are present in a given location.
“My research uses molecular techniques to address questions related to resistance, including bacterial toxins and pesticides,” Tom said.
“Long-read sequencing will allow us to look at whole genomes to identify resistance genes in pest insects. This could lead to applications in managing agricultural and biosecurity pest insects to protect crops, native species and our environment.”
Team work makes the dream work
The new Revio long-read sequencing machine will be housed at the Biomolecular Resource Facility (BRF), based at the John Curtin School of Medical Research, Australian National University (ANU). A key aim is to increase early-career researcher access to this technology to fast-track research outcomes and cross-industry technology development. Collaborators and partners will be able to use this next generation genomics technology across a wide range of scientific research.
The Revio machine was purchased by a consortium of eight research institutes and with the support of the Science and Industry Endowment Fund (SIEF). The collaborators are CSIRO, the Biomolecular Resource Facility (BRF) at the John Curtin School of Medical Research (JCSMR) at the Australian National University (ANU); the Research School of Biology, ANU; the National Centre for Indigenous Genomics, ANU; Canberra Clinical Genomics, ANU and ACT Health; Applied BioSciences, Macquarie University; Research and Innovation, Charles Sturt University; the Centre for Conservation Ecology and Genomics, University of Canberra; the School of Life and Environmental Sciences, University of Sydney; and QUT.