Comparative Genomics

Since 2003, in collaboration with Prof Arthur Georges, and Prof Janine Deakin and Prof Tariq Ezaz (Institute of Applied Ecology, University of Canberra), we have been studying sex determination in the Australian lizard Pogona vitticeps (the central bearded dragon). We discovered a ZZ male ZW female chromosomal sex determining system with SF1 as the sex determining gene which delivers 50% male and 50% female hatchlings at physiological temperatures. At higher temperatures, all hatchlings are female; half of these are ZW (normal) female and half ZZ sex reversed female. By mating ZZ sex reversed females to normal ZZ males, we can completely swap the sex determining system from genetic to environmental in one generation. We are using this system to discover how environmental sex determination works, by examining transcription in normal and sex reversed animals, finding unique transcripts of epigenetic modifying genes, and upregulation of stress markers at sex reversing temperatures. We aim to explore the pathways by which epigenetic changes modify gonad and germcell development.

An ongoing collaboration with Prof Frank Grutzner (University of Adelaide) includes Dr Paul Waters (UNSW), and scientists in China (Shenzhen and Hangzhou) and Germany (Heidelberg). Building on our demonstration that platypus sex chromosomes share homology with birds, and our high quality platypus genome sequence, we can use new –omics techniques to explore how different autosomes became sex chromosomes in mammals, and examine a rare case of an autosome that is either an ex-sex chromosome, or a “wannabe” proto-sex chromosome. We will discover how different sex chromosome dosages in platypuses are compensated by epigenetic modifications to gene expression, and explore how different systems of dosage compensation evolved independently in monotremes and therian mammals.

Recent collaboration with the University of Canberra and scientists in Japan and Austria compares the DNA sequences of chromosomes of reptiles (including birds) to those of chordates such as Amphioxus. Sequence comparison is identifying extraordinary homology between chordate chromosomes and the gene-dense microchromosomes of birds and reptiles, implying that they, rather than the classical large vertebrate chromosomes, represent the original vertebrate chromosomes. The large, repeat-rich chromosomes of mammals seem to have been puffed up by insertion of transposable elements, and by duplications and amplification, allowing them to be greatly rearranged in evolution.

A large international collaboration costing USD14.6 billion, aims to sequence the genomes of all complex life on earth
(1.5M identified eukaryote species) in ten years. By changing the way biology is done, reducing reliance on a few model species and facilitating studies of any species, it will solve questions of phylogeny, provide new opportunities for agriculture, and inform wildlife conservation and management. EBP is headed by scientists at UC Davis (USA) and the Sanger Centre (UK). As one of the pioneers of comparative genomics, who was involved in the first international vertebrate sequencing consortium (Genome 10K), Prof Jenny Graves has been on the frontline for launching this project, and is on the EBP Advisory Council. At the national level Jenny is involved in the Oz Mammal Genome (OMG) consortium that aims to sequence all Australian mammals, as well as new moves to gain support to sequence all Australian reptiles.