Finding Nemo’s genome

Enabling a sustainable World

In a world-first, Deakin scientists have sequenced the clownfish genome, allowing them to identify and study genes connected to the species’ most intriguing characteristics, including its ability to change sex.

While the Disney Pixar movie ‘Finding Nemo’ catapulted the endearing clownfish into the public imagination, scientists have long been interested in the species’ ability to change sex, its body-colour variations and its symbiotic relationship with sea anemones.

Now a team of researchers led by Deakin University’s Head of School of Life and Environmental Sciences and leader of the University’s new genomics initiative, Professor Chris Austin, have sequenced the clownfish genome, making it the first coral reef fish to be sequenced by scientists from an Australian university.

The clownfish’s genomic information – gathered with the support of the Museum and Art Gallery of the Northern Territory and Monash University – was recently published in the open access journal ‘GigaScience’.

Professor Austin said the work was a major step in furthering knowledge of a high-profile fish species that attracts commercial, conservation and biological interest.

“Having these new genomic resources for clownfish will greatly assist research into the biology and behaviour of this charismatic species, better pinpoint its position in the fish family tree, and contribute resources towards the sustainable management and conservation of natural populations.

 

Since ‘Finding Nemo’, clownfish have also attracted increasing interest from the marine ornamental aquarium industry to the point that local extinctions are occurring in the wild. Comprehensive genetic information can assist in breeding programs and provide accurate species and clownfish population identification, which is crucial for monitoring wild harvesting and trafficking.”

Professor Chris Austin
Professor Chris Austin Head of School of Life and Environmental Sciences

Professor Austin said sequencing the genome of an animal involved reading as many of its DNA molecules as possible, obtained from the cells of one or more individuals.

“Every species has its own distinct molecular patterns to its DNA. These combine to form a large number of genes, which are the units of inheritance passed from parents to their offspring,” he explained.

The genes in turn make up the essential information contained in a species genome.

“Genes differ from one species to the next, as a result of evolution and adaptation, and they determine the distinctive features of each species – for example, their size, shape or colour – as well as how and where the animal grows, lives and reproduces. They also control the day-to-day metabolic activities that occur in all the cells of an animal.”

In the case of the clownfish, the study of its genetic makeup could shed more light on its intriguing body-colour variation. A distinctive black and white clownfish was found near Darwin as part of this study, which contrasts with the more typical orange and white “Nemo” people are familiar with.

Professor Austin said clownfish were also what scientists termed “sequential hermaphrodites,” or in laymen’s terms, “sex changers”.

“They are all born males and the dominant male of a group will turn into a female when the female of that group leaves or dies,” he said.

“While we know that clownfish can change sex, we don’t know exactly how this happens at the genetic level. Access to DNA sequences will now give scientists the fundamental information needed to understand how a male becomes a female in clownfish.”

Professor Austin said another fascinating aspect of the biology of clownfish was its “symbiotic mutualism” with sea anemones.

“In the wild, clownfish and their sea anemone species are almost always found together, a mutually-beneficial relationship that has mostly evolved over millions of years. So we are interested in looking at this at the genetic and evolutionary level.

“What’s special is that anemones have very poisonous stinging tentacles used to capture prey or keep predators away, but clownfish have developed a resistance or tolerance to the anemone toxins. By living among the anemone’s tentacles, the clownfish gets protection, but can also chase away fish that would eat the anemones, as well as clean up algae and help to circulate the water around the anemone.

“There may well be a genetic basis to this resistance to toxins, so it will be of interest to try and find genes that help protect clownfish and to see if they produce proteins with special and useful functions.”

This is the third fish genome published by Professor Austin and his team, with the first being the endangered Asian Arowana in 2015, followed by Australia’s largest freshwater fish the Murray Cod in 2017.

“Like the clownfish, the Murray Cod is one of Australia’s most iconic species, as well as being one of our most important. It can grow to almost two metres in length and live to nearly 50 years old, which makes it of significant biological interest. Scientists want to try and understand why it has these characteristics and how it is able to persist in the sometimes-demanding and variable aquatic environments of inland Australia,” Professor Austin said.

“Genomic information will help us to understand the genetic basis of the fish’s special adaptions, and help determine conservation priorities for different Murray Cod populations, as well as contributing to the selective breeding essential for sustainable aquaculture.”

Professor Austin and his team will continue to build on their world-leading genetic research in a new multimillion-dollar genomics laboratory established by Deakin earlier this year. The centrepiece of the new laboratory is the latest Illumina Novaseq6000 DNA sequencer, which was run for the first time in January. The laboratory will greatly increase Deakin’s capacity to undertake cost effective genomics research, and enhance the University’s teaching and research collaborations, nationally and internationally.
“Our research uses a very new approach to genomics, called hybrid genome assembly, which combines the high accuracy of short Illumina DNA reads – the most common and accurate approach – with a modest amount of long, but less accurate Oxford Nanopore MinION DNA reads,” Professor Austin said.

“This allows us to generate a high-quality fish genome assembly quickly and at low cost that can be applied to almost any species of fish to support research, conservation and the needs of industry.”

Published by Deakin Research on 27 March 2018