Digital Botany New connections bring fresh insights

THE BRAVE NEW WORLD OF DIGITAL BOTANY

DIGITAL CONNECTIVENESS HAS BEEN A GODSEND TO BOTANICAL SCIENTISTS THROUGHOUT COVID. DR BRETT SUMMERELL, CHIEF SCIENTIST AND DIRECTOR RESEARCH, REPORTS.

Like most Australians – and many people around the world – botanical scientists were forced to primarily work from home during the COVID pandemic. This restricted our ability to interact with colleagues face-to-face, hampered efforts to get out in the field, and put a stop to a number of academic conferences and meetings.

There have, however, been upsides from the lockdown. Most notably, in response to COVID, many seminars moved online. This not only freed up time usually required to travel, but also made events more accessible to colleagues all over the world. As a result, our scientists at the Australian Institute of Botanical Science have had the opportunity to connect and participate in seminars and conferences taking place across a more diverse array of countries.

Of course, online engagement is still no substitute for attendance at a face- to-face conference or meeting, where long conversations over refreshments and dinner can often lead to wonderful (and sometimes unexpected) outcomes. But thanks to COVID, it has now become the norm for botanical scientists to use digital resources to communicate and collaborate in a more environmentally sustainable way.

The digital world is not something that is necessarily associated with the botanical sciences – there is the tendency to think of our work as being focused on long field trips and hours looking at specimens down a microscope (which is partly true). In reality, as with much of science, our research increasingly involves digital data – whether it be the manipulation of large datasets, the study of genomic data, or our growing reliance on high-resolution digital images and data.

This digitisation of the botanical world does provide a number of challenges. For instance, it means we need to secure large data storage capacities and powerful computers capable of manipulating the vast amount of information we generate, as well as the pipelines that allow the data to move backwards and forwards efficiently. This is increasingly becoming as significant a piece of critical infrastructure as our laboratories and field vehicles. But the type of information we now collect, and what we have access to, allows us to explore many different attributes about how plants evolve, survive, persist and reproduce, and can allow us to come up with strategies to manipulate these outcomes. Although this may sound a little ‘brave new world’ it is becoming more and more necessary as we humans change the world, and our actions detrimentally impact the survival of plants and other organisms.

Ten or more years ago, the idea that we might be able to map the entire genome of a plant species would have been considered preposterous. This was the time of the human genome project, which took 13 years and more than four billion dollars to complete, and the technology and equipment was

‘It has become the norm for botanical scientists to use digital resources to communicate and collaborate’

As a result of COVID, many seminars and conferences moved online

Genome mapping is focused on threatened species

Digitisation of the Herbarium collection has created a resource for scientists across the world

complex and enormously expensive. Fortunately, the cost and time required has been reduced dramatically and we are now in a time where mapping plant genomes, while not necessarily routine, is achievable by our scientists. And to be honest we are on the cusp of genome mapping becoming a standard tool in our armoury of techniques to understand a particular species.

You might be forgiven for wondering precisely what good is going to come out of these advances – is it just an example of scientists generating esoteric information that has no practical outcome? The answer is a most definitive no! The primary focus for mapping genomes has been on those species that are under real and present danger of extinction at this point of time – plant

‘We are on the cusp of genome mapping becoming a standard tool in our armoury’

species on an extinction trajectory from the impacts of myrtle rust such as Rhodamnia rubescens (Scrub Turpentine) and Rhodomyrtus psidioides (Native Guava), and species under threat from Phytophthora root rot such as the iconic Wollemi Pine. Mapping the genome allows us to determine if there are an artillery of disease-resistance genes present in the genome of these species, whether they can be enhanced in the population, or if the genes need to be ‘turned on’ to be effective. More broadly this information can tell us about how species have evolved and responded to climatic changes in the past, and to help predict their ability to survive in the future. The prospects for use of this information are enormously exciting.

The other big digital advance we completed over the period of the pandemic was of course the digitisation of the National Herbarium of New South Wales collection, undertaken as part the opening of the fabulous new facility at the Australian Botanic Garden Mount Annan.

Digitisation meant two things. Firstly, photographing each individual herbarium specimen in very high resolution so that it is possible with a photograph to zoom into many of the features of the specimen in a manner that is similar to looking through a microscope. Secondly, capturing all of the data and information on the Herbarium label and entering it into the Herbarium database so that it can sit alongside the photograph. This has provided an enormous resource to scientists all around the world and is part of global efforts to digitise natural history collections. It will vastly improve efficiency in interrogating the collection, particularly for scientists who may not have the time or funds to travel to Australia. And it means that there will be less need to send our collections overseas or interstate, thus preserving and protecting them.

One of the very exciting prospects of a fully-digitised collection is the potential to use artificial intelligence and machine learning techniques to develop tools for automated or assisted plant identification. Such techniques, being explored currently by Dr Jason Bragg at AIBS and colleagues at the University of New South Wales, depend on highly sophisticated analysis of many attributes such as leaf shape, arrangement and flower structure which, when the dataset is large enough, might be able predict the identity of an unknown specimen. As more and more collections become digitised – and the dataset becomes larger – the potential for this to happen is greatly enhanced.