Koala genome offers important insights into vulnerable icon – 3rd July 2018
The most complete and contiguous marsupial reference genome has been sequenced in the Ramaciotti Centre lab at the University of NSW – an important step in protecting our koalas.
They’re the cuddly, dozy tree-hugging marsupials that are instantly recognisable the world-over – and yet Australia’s koalas face myriad threats, from disease to habitat loss, and their numbers are in decline.
Now, experts at the Ramaciotti Centre at UNSW have played an important role in helping shed light on this complex conservation challenge by sequencing the first-ever complete reference genome for the koala, enabling unprecedented biological insights into this unique marsupial.
The project came about after the Australian Museum and the Ramaciotti Centre – along with renowned conservation scientists from around the world – formed the Koala Genome Consortium, recognising the value of a complete reference genome for ensuring koalas’ future health.
The Ramaciotti Centre had at the time added PacBio long-read sequencing technology to its next-generation sequencing portfolio, offering capability that would be particularly useful for this study. Due to its ability to sequence through much longer fragments of DNA, the PacBio allows researchers a more complete genome, including regions that had previously been inaccessible through short-read technology. “Think of a book that has been shredded. A book that has been shredded into 100 large pieces will be re-assembled easier than 10,000 smaller pieces,” explained the Ramaciotti Centre’s Pacbio Next Generation Sequencing Manager, Tonia Russell.
The PacBio data generated from the koala DNA was then assembled by a team of expert bioinformatics led by Dr Marc Wilkins, Director of the Ramaciotti Centre, before being handed over to biologists. Lead researchers Professor Rebecca Johnson (Australian Museum), Prof. Kathy Belov (University of Sydney) and Prof. Peter Timms (University of the Sunshine Coast), then interpreted the genome with others in the Consortium. The results were ultimately published in the prestigious journal, Nature Genetics.
Transforming our understanding of koalas
“This genome is already transforming our understanding of this iconic species,” said Prof. Wilkins. Among other findings, researchers were able to pinpoint a genetic basis for the koala’s ability to digest toxic eucalyptus leaves. The genetic data collated in the study will also help to identify genetically diverse populations which can be used in translocation programs. This will be “key to the koala’s survival in the wild,” the scientists wrote in the paper.
Already, the koala genome is also being used as a valuable reference for scientists. In a spin-off paper published in Scientific Reports, scientists used Bilbo’s genome sequence to find new genetic insights into Koala Retrovirus (KoRV), a group of viruses specific to koalas.
KoRV is very widespread among koala populations, particularly in Queensland and NSW, and is implicated in a number of diseases and immunodeficiency disorders that may be linked to the species’ decline. The PacBio technology used to sequence Bilbo’s DNA at the Ramaciotti Centre is particularly important for research into KoRV thanks to its ability (over short-read technology) to include the insertion sites of the KoRV infection in the koala genome.
Ms Russell pointed out that since the completion of this koala genome, the Ramaciotti Centre now also has access to the new PacBio Sequel, a higher data throughput PacBio system that enables the sequencing of genomes from microbial through to large mammalian genomes.
Winner Announced – NovaSeq Mini Grant – How would you use 3 billion reads? – 27th September 2017
We are excited to announce that scientists from CSIRO’s Synthetic Biology Future Science Platform, the Australian Institute of Marine Science with the National Sea Simulator, and the University of Melbourne are the winners of the NovaSeq Mini Grant – “What would you do with 3 billion reads.” The group will receive sequencing data from an Illumina NovaSeq 6000 S2 sequencing run valued at $24,300. Congratulations!
The project aims to engineer microbial symbionts to increase corals temperature resilience:
Coral reefs worldwide, including two thirds of the Great Barrier Reef, have suffered extreme bleaching events and mass mortality from high seawater temperatures over the last decades. Current efforts to reduce such climate change associated impacts might be too little to prevent severe long-term impacts on reefs. Therefore, it is essential to consider alternative mitigation strategies, such as genetic technologies to improve the thermal tolerance of corals and their symbiotic algae (Symbiodinium).
Our group is working towards engineering microbial symbionts to increase coral temperature resilience. This project is an interdisciplinary collaboration of scientists from CSIRO’s Synthetic Biology Future Science Platform, the Australian Institute of Marine Science and the University of Melbourne (Dr. Patrick Buerger, Prof. Madeleine van Oppen, Dr. John Oakeshott and Dr. Owain Edwards). We use single cell transcriptomics and gene expression profiles to investigate the genetic mechanisms underpinning the algal symbiont’s thermal tolerance. This information will be used to identify target genes and cellular pathways that are suitable for engineering increased temperature resilience into these symbiotic microalgae.
New Technology and a New Facility – 26th July 2017
In April of this year the Ramaciotti Centre for Genomics moved to UNSW’s new $165M Biosciences South Building and in June commissioned $2M of new genomic sequencing technology. This brings outstanding new capabilities in genomics to Australia. The Centre was formally opened by the NSW Chief Scientists Professor Mary O’Kane read more….
Short Read Sequencing – Illumina NovaSeq
In June the Ramaciotti Centre installed and validated an Illumina NovaSeq 6000 system. The NovaSeq has scalable throughput and flexibility for virtually any sequencing method or genome and brings unprecedented short read sequencing capacity to Australia. The Centre now has the ability to facilitate any size or type of sequencing project using our suite of Illumina instruments. The Centre has Illumina Certified Service Provider (CSPro) status.
Long Read Sequencing – PacBio Sequel
The Ramaciotti Centre also installed a PacBio Sequel system in June adding additional long read sequencing capacity to our portfolio. The Centre was one of the first sites in Australia to install the PacBio RSII system and since then we have completed many successful SMRT sequencing projects for researchers around Australia and overseas. The placement of the Sequel means that Ramaciotti Centre is the only site in Australia with both the RSII and Sequel systems and thus able to offer researchers the flexibility of PacBio SMRT sequencing on either platform. The Centre has PacBio Certified Service Provider (CSP) status.
Linked Read & High Throughput Single Cell – 10x Genomics Chromium
The 10X Genomics Chromium system provides long range genomic or cell-by-cell gene expression information, thereby unlocking further utility on our existing short-read sequencers. The system supports single cell 3’ transcript profiling within complex cell populations and provides long-range information on a genome-wide scale, including variant calling, phasing and extensive characterization of genomic structure.
Please contact us for further information on services provided on the above technology platforms.