Botanic Gardens Trust, Sydney, Australia

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What can we learn from rainforest genomes?

by Dr Maurizio Rossetto - Principal Research Scientist, Manager Evolutionary Ecology, Science and Conservation 

The evolutionary ecology research team is using advanced molecular techniques (similar to those employed in the medical world to produce ‘personalised’ human genomes) to learn more about the factors that influence the distribution and diversity of Australian rainforests.

The team, lead by Maurizio Rossetto, has taken advantage of recent technical advancements (and the financial support from the Foundation and Friends of the Botanic Gardens) to develop pioneering DNA-based analyses that will help them measure and interpret rainforest dynamics across variable landscapes.

The first step was to gather leaf material from over 100 species of rainforest trees distributed across NSW. A team including Hannah McPherson, Marlien van der Merwe, Robert Kooyman, and a number of external collaborators travelled across the State multiple times during a period spanning over six months. Collection trips sometimes involved the exploration of hot, near-impenetrable rainforest areas that had been rarely visited by our botanists. Indeed, once the relevant specimens were vouchered in the NSW Herbarium, we found that over 80 per cent of the species collected in Nightcap National Park represented new local records for our institution.

Extracting DNA from so many species proved to be more complex and resource intensive than previously imagined. In due course we managed to obtain genetic material of the necessary quality and quantity, and preparation for genome sequencing could finally proceed. After a number of attempts, a pilot study involving the sequencing of samples representing 12 species collected across two different regions was completed.

Next generation sequencing produces enormous quantities of data. A single sequencing run can read well in excess of 200 billion base-pairs, a quantity significantly greater than the three billion base-pairs contained in the human genome. Such an output bonanza comes with its setbacks however, and bio-informatic analyses soon presented the research team with significant analytical hurdles. In order to make sense of the enormous amount of sequence data, a pair of brand new high-end computers was put to the task. With the invaluable help of our home grown bio-informatician Juelian Siow, the use of numerous software applications and support from collaborating research teams, results were finalised and prepared for publication.

The preliminary findings are exciting. For example, we found extremely low genetic diversity in red cedar (Toona ciliata (Meliaceae) a widespread and economically important tree), suggesting recent and rapid expansion throughout Australia. Similar patterns were detected in other easily dispersed species such as Cinnamomun oliveri (Lauraceae), also likely to have recently colonised Australia from northern origins. We also found that genetic diversity is considerably higher in northern than in southern NSW, even for species that are generally associated with cooler rainforest types such as sassafras (Doryphora sassafras - Atherospermataceae). These preliminary findings highlight how the unique landscapes of northern NSW act as critical refugia for biodiversity and evolutionary potential.

Although this pilot project took over two years to complete, it paved the way for further increasingly complex studies. Thanks to the support from Bioplatforms Australia Ltd, we are now analysing similar genomic datasets from 80 rainforest species sampled from a considerably broader distributional range. Our preliminary experience has significantly reduced expected completion time, so more exciting findings soon!

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