Sequencing rapidly reveals nature’s surprises

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A Sleepy Lizard, Tiliqua rugosa, with an attached tick.

The next generation techniques now used for sequencing DNA are creating data sets on an unprecedented scale. Next generation techniques have applications in an incredibly diverse range of research. It’s the job of Dr Terry Bertozzi, bioinformatician from the Museum’s Evolutionary Biology Unit, to help researchers wade through a sea of sequences to find answers to the genetic questions they’re asking.

Terry’s skills are sought after by researchers within the Museum as well as universities and other research institutes locally, interstate and internationally. Terry recently collaborated with a team of researchers including Ali Morton Walsh, an Honours student in the School of Molecular and Biomedical Science at the University of Adelaide. Ali’s project examined retrotransposons; transposable elements of DNA that are able to ‘copy and paste’ themselves within genomes. One of these elements found in cows, BovB, appeared to have a very strange distribution within animal groups. In fact, vastly different than what could be expected if it had been passed down by evolutionary means from parent to offspring. Amidst widespread public concern about genetically-modified organisms, the research suggests that genetic material has been transferred between different organisms for generations in nature.

Using next generation sequencing and bioinformatics, the team were able to find BovB in sheep and horses — perhaps not a surprisingly evolutionary leap. However, they also found BovB in elephants, reptiles, many marsupials and even a monotreme – the platypus. It was not found in birds, frogs or most mammals. A phylogenetic tree of BovB shows that the presence of BovB in such a diverse range of species could not be explained by traditional means of inheritance.

The researchers also sequenced ticks and found BovB in reptile ticks. They hypothesise that ticks may have been the means of horizontal transfer of these elements; not from parent to offspring but across species. The transfer is not a single event in evolutionary history  there have been at least nine different transfers.

Terry’s role sees him collaborating with researchers looking at everything from black rats and subterranean beetles to gobies: the fish group with the most species worldwide. Older molecular techniques, like polymerase chain reaction (PCR), would typically generate hundreds of sequences for a project. Nowadays, researchers are able to generate tens of millions of sequences for a single project. Terry’s task is made somewhat easier since the Museum purchased a high-end large memory computer server that enables them to run long and complex analyses.

For Terry and the researchers he collaborates with, the bioinformatics research area is a fast-paced but exciting world where putting together the pieces of a puzzle means the next discovery is always just around the corner.

Terry Bertozzi is also planning a research project on marine parasites with Ian Whittington.