The Australian Centre for Wildlife Genomics at the Australian Museum has developed DNA collection and extraction protocols that assist vital research on the Crown of Thorns Starfish (COTS) – Acanthaster planci.
The Centre has particular know-how and experience in isolating DNA from the tissues of plants and animals. This can be technically challenging when the samples are collected on a dive or in the presence of potential contaminants. The Centre has developed collection and extraction protocols that ensure DNA samples from COTS are sufficiently free of inhibitors and degradation.
Inhibitors (substances that inhibit the biochemical process used to amplify DNA) present a major technical challenge. The presence of an inhibitor renders DNA inaccessible for downstream steps such as library preparation and sequencing.
The Centre also has an extensive frozen tissue collection and a database of DNA reference markers derived from the Museum’s natural science collections, including a large number of marine species. This facilitates wildlife DNA analysis and species identification.
An organism’s complete set of DNA is called a genome. A collection of physical DNA fragments which together represent a genome is called a genomic library. These vials are part of a library.
The genetic instructions for the development and functioning of all living organisms is encoded in DNA molecules by a sequence of four base nucleotides – Adenine, Guanine, Cytosine and Thymine. The sequence is represented in a notation that can be read by humans and computers using the letters A,G,C and T. Computers are essential. A typical starfish genome is comprised of over 1 billion base pairs (1Gbp). Here is a small fragment of the sequence from a specimen of Acanthaster planci, a.k.a Crown of Thorns Starfish (COTS) found at Lizard Island:
Many technically demanding scientific steps are required to get from a COTS tissue sample to an understanding of its genetic code. There are four main stages in the process: (1) DNA sample preparation; (2) library preparation, (3) DNA sequencing; and (4) interpretation and analysis. Although the Australian Centre for Wildlife Genomics has expertise in all 4 stages, DNA sequencing is done most efficiently on highly expensive and specialized equipment and is accordingly contracted out to service providers.
COTS eat coral. They have a cluster of extraordinary characteristics, including the ability for a single female to produce many millions of eggs each year. When conditions are favourable they multiply rapidly to plague proportions that can kill all the living coral in an entire reef area. When conditions are adverse the COTS population shrinks to just a few surviving specimens…and then the cycle starts again. Scientists are conducting vital research at the Lizard Island Research Station to advance our understanding of the factors involved in these dramatic cycles, where they begin, how they advance along the length and breadth of our Great Barrier Reef, and how to contain them. This work is very important to the conservation of the reef and could be greatly assisted by DNA analysis.