US-AUSTRALIAN ACADEMIES JOINT WORKSHOP
US-AUSTRALIAN ACADEMIES JOINT WORKSHOP ON VERTEBRATE COMPARATIVE GENOMICS
Beckman Conference Centre, Irvine, California, 23-25 May 2007
Efficient generation of a physical map for the tammar wallaby genome
by Janine Deakin
Dr Janine Deakin received her PhD in biology from Macquarie University (Sydney, Australia) in 1998. Currently, she is a postdoctoral fellow working for the ARC Centre for Kangaroo Genomics based at the Australian National University in Canberra, Australia. Her research interests include X chromosome evolution, dosage compensation and immunogenetics in marsupials and monotremes
Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials are being sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor ~80MYA. The opossum genome has been sequenced (6x coverage), and most of the sequence anchored to chromosomes. The tammar genome is being sequenced to a depth of 2x coverage.
To anchor tammar sequences, we are generating a physical map of gene locations on tammar chromosomes. We devised a strategy based on chromosome homology revealed by cross-species chromosome painting, using the opossum assembly to predict which genes will be on each tammar chromosome. By aligning the opossum genome assembly to the human and chicken assemblies, we can identify large blocks of shared synteny that we then locate and orient in the tammar genome. We choose conserved genes at the end and within each block, then use sequence from the tammar genome sequencing project to design specific overgo probes to isolate homologous tammar BACs for cytogenetic mapping. This has proved to be a very rapid and efficient approach.
To date, our efforts have concentrated on the chromosomes harbouring human X chromosome genes but we are now expanding this work to the entire genome. Previous gene mapping studies have shown that orthologues of human X gene lie, not only on the tammar X, but also on tammar chromosome, identifying a region that was recently added to the X chromosome in eutherians. Chromosome painting has shown that wallaby chromosome 5 shares homology with opossum chromosomes 4 and 7. We have intensely mapped this “neo-X” region in the wallaby and determined the extent of conserved synteny between chromosome 5 and the human X. Our mapping has detected rearrangements between opossum and wallaby that were undetectable in chromosome painting experiments. Our data highlights the need for comparative gene mapping and the important role the tammar wallaby plays in comparative
genomics studies.
Contact details:
ARC Centre for Kangaroo Genomics
Research School of Biological Sciences
The Australian National University
Canberra ACT 0200
Tel: +61 2 6125 2101
Email: Janine.Deakin@anu.edu.au
