2. How do ancient retrovirus-like elements survive in marine animals?

Retroviruses are remarkable for their ability to enter cells and integrate their genetic material into host genomes. Some transposable elements, known as retrovirus-like retrotransposons, share many features with retroviruses, including genes encoding proteins involved in their replication and, in some cases, an envelope (Env) protein that may enable transmission between cells.

Our recent research has revealed that retrovirus-like elements have an unexpectedly deep evolutionary history, with related lineages found across distantly related animal groups. This raises a fascinating question: how have these elements survived for hundreds of millions of years despite the evolution of host defence mechanisms that recognise and suppress them?

To investigate this question, we study two evolutionarily distant groups of marine animals: reef-building corals of the genus Acropora (cnidarians) and Oikopleura dioica, a small, planktonic tunicate. These animals provide complementary opportunities to examine where retrovirus-like elements are active, how their hosts control them, and how they persist within natural populations.

One focus of this project is to determine when and where retrovirus-like elements are expressed during animal development. Using RNA sequencing and RNA fluorescence in situ hybridisation (RNA-FISH), we will investigate their expression across different tissues and developmental stages, including whether they are active in reproductive cells or surrounding somatic tissues. We will also examine the host mechanisms that may restrict their activity, focusing on piRNA-mediated silencing, DNA methylation and repressive histone modifications.

A second focus is the ongoing evolution of retrovirus-like elements in natural populations. We aim to collect O. dioica from Australian coastal waters and generate genomic resources for previously uncharacterised Southern Hemisphere populations. By comparing retroelement sequences, genomic insertion sites and patterns of variation among individuals and populations, we will investigate how these elements spread, diversify and persist over relatively short evolutionary timescales.

Together, these studies will connect molecular mechanisms of retroelement regulation with their evolutionary dynamics in natural populations. Ultimately, we hope to understand how retrovirus-like elements maintain their capacity for propagation, how they interact with host defence systems, and what allows some lineages to survive across extraordinary evolutionary timescales.

Techniques: Marine organism collection and culture, microscopy, DNA and RNA extraction, genome sequencing, RNA sequencing, RNA fluorescence in situ hybridisation (RNA-FISH), small RNA sequencing, and comparative genomic and bioinformatic analyses.