Genomic Sequence Analysis
The platypus genome project and the convergent evolution of platypus and reptile venom
AT Papenfuss, MJ Wakefield, TP Speed in collaboration with K Belov, C Whittington, P Kuchel (University of Sydney), W Warren (Washington University at St Louis, MO USA), (Platypus Genome Sequencing Consortium) Pub ref: 150,153
The platypus, Ornithorhynchus anatinus, exhibits a curious mix of mammalian and reptilian features: it lays eggs, suckles its young, uses electro-reception to target prey underwater, and male platypuses are venomous. The genome of a single female platypus was recently sequenced to draft quality (6×). The 2 gigabase genome of the platypus has an extremely high GC content and about half of the genome consists of transposable elements. The most abundant of these are the LINE2 and SINE elements, which are still active. Despite the high coverage of sequencing, the genome sequence did not assemble well and only 20% of the sequence was mapped to chromosomes.
We used the platypus genome sequence to identify antimicrobial genes involved in innate immunity. This was done by searching with profile hidden Markov models representing key domains and performing gene prediction around the matches. In this way, we predicted 6 beta defensin genes, 4 alpha defensins and 8 cathelicidins. The beta defensins were located on two fragments of the platypus X-chromosome chain (X1 and X2). The alpha defensins were also located on chrX2. Previously, the alpha defensins have been identified only in therians. These results suggest that they were present in the ancestral mammal. The fragmented nature of the genome assembly meant we could not determine the number of gene clusters, but FISH mapping, phylogenetic analysis and synteny suggest that they are split between two defensin gene clusters.
Adjacent to one of the alpha defensins, we identified four defensin-like genes. Three of these were similar to short peptide fragments previously sequenced from the most abundant fractions of platypus venom and called Defensin-Like Peptides (DLPs). The fourth appeared to be intermediate between the DLPs and the beta defensins. This suggests that a major component of platypus venom evolved from genes involved in innate immunity, and is analogous to, but independent of the evolution of some components of snake venom such as the crotasins. The antimicrobial activity and expression of these genes in a range of tissues was also examined. We also identified other genes involved in platypus venom that had previously been partially characterised and found similar signs of convergent evolution with snake venom proteins.
Research into snake venom has revealed or inspired many useful compounds and therapeutics. Platypus venom may also provide a new source of unique compounds for medical research. We are now analysing Next Generation transcriptomic data obtained from a platypus venom gland to look for novel toxins.
Gene organisations of the platypus chrX2 defensin cluster: alpha and beta defensins, platypus venom DLPs and a putative intermediate between the beta defensins and the DLPs.
Pathogenesis gene networks
M Wakefield in collaboration with R Robins-Browne, M Tauschek (University of Melbourne)
Citrobacter rodentium, which causes transmissible colonic hyperplasia in mice, is used as an in vivo model system for the clinically significant pathogens enterohemorrhagic and enteropathogenic Escherichia coli. We have designed custom microarrays that have enabled a systems biology approach to discover a global regulator and a network of genes involved in pathogenesis. This work has allowed the identification of novel virulence determinants and will be the first report to describe the molecular mechanism by which an environmental chemical stimulates transcription of a network of virulence-associated genes of an enteric pathogen through an AraC/XlyS-like activator.
Basecalling for resequencing chips
M O’Hely, TP Speed in collaboration with W Wang (University of California at Berkeley and Stanford Gene Technology Center, CA USA)
Custom resequencing chips are flexible, cost-effective tools for scanning targeted genomic sequence, in tens to hundreds of samples, for variation relative to a reference sequence. The reference might be the human mitochondrial genome, all exons of a collection of genes implicated in a disease, or from microbial pathogens. We are working with colleagues from the Howard Florey Institute, who have a custom resequencing chip with Parkinson’s disease genes, and collaborators from the Stanford Gene Technology Center, who study inherited optic nerve degeneration genes in the same way. Our aim is to reduce the error rate, and improve the call rate for these chips.
Phylogenomics illuminates the evolution of the apicomplexan phylum
TJ Sargeant, GK Smyth, TP Speed
We have developed two new methods for the inference of species trees from genome and EST sequence databases utilising protein domains. The methods we have developed are computationally feasible given modest computing resources. These methods are able to reconstruct deep phyogenies and are ideally suited to inferring species trees for organisms with unannotated genomes and from the results of new sequencing technologies. Application of these methods to the genomes of Apicomplexan parasites has suggested a new model of Plasmodium evolution in which parasites that initially infected mammalian hosts were the subject of a species switch from early primates to reptiles and birds.