Functional genomics of Eucalyptus defences against pests and pathogens:  Forest trees are a nutrient- and carbon-rich source for pests and pathogens.  Notable pests and pathogens that pose a threat to Eucalyptus in South Africa, and can be used as models for genomic studies, include the Eucalyptus gall wasp, Leptocybe invasa, the stem canker pathogen, Chrysoporthe austroaficana, the oomycete root pathogen, Phytophthora cinnamomi, and recently, Myrtle rust Pucciniapsidii.

Plants are able to defend themselves against pest and pathogen attack by using a sophisticated defence system comprising physical barriers, constitutive resistance, induced resistance and systemic resistance mechanisms. The timing and magnitude of the defences activated dictate the outcome of the interaction. We are employing a functional genomics approach towards understanding the defence responses of Eucalyptus when challenged with L. invasa, C. austroafricana, P. cinnamomi and P. psidii. We are also investigating terpenoid defence responses to the various pathogens at the molecular and metabolic level. Based on the integration of such data, we are now able to identify a core set of defence responses employed in Eucalyptus against various pathogens providing greater insight into specific and general defence mechanisms. This approach greatly aids the discovery of candidate genes to improve defence against pests and pathogens in Eucalyptus in the future.


Functional genomics of Pinus patula defences: In a similar approach to that described above, we are investigating the defence responses of Pinus patula to the pathogen Fusarium circinatum. This fungus causes high mortality in P. patula seedlings in the nursery and is found to persist in the field, affecting older trees. In an exciting recent development, the genome sequence of a related pine species, Pinus taeda, has been completed. This provides a resource for functional genomics of Pinus patula and we have initiated collaboration with the lead bioinformaticists in this area to complete the transcriptome analysis of P. patula. In a related approach, we are investigating the defence response incited by the use of chemical and biologicallyderived elicitors in P. patula. While we are focused on the molecular responses incited by the treatment, the application of the treatments provides a potential solution to reducing the effect of the pathogen in the nursery.


Transcriptome-wide prediction of expressed gene and protein variation in wood-forming tissues of eucalypt hybrids: Deleterious mutations are an inevitable product of DNA sequence evolution. They can persist for many generations, hidden in the heterozygous state, before purifying selection results in their elimination. This ‘baggage’ of deleterious mutations in highly heterozygous organisms such as eucalypts is called genetic load. Deleterious mutations have a range of effects on proteins depending on their location in the gene. They can either eliminate protein function, and are thus denoted loss-of-function (LOF) mutations, or they can truncate the gene, limiting the normal functionality of the protein it encodes. We are using transcriptome-wide sequencing of wood-forming tissues to catalogue LOF mutations and assess their impact on protein-coding genes in Eucalyptus hybrid tree populations. This facilitates the dissection of the genetic variation underlying phenotypic variation of quantitative traits such as wood properties for tree breeding purposes.


Carbohydrate active enzyme (CAZyme) genes involved in wood formation in eucalypts: Using the large amount of available plant genomic data, as well as transciptomic data for Eucalyptus grandis and Populus trichocarpa from our research group and collaborators at the University of British Columbia, this research aims to characterise Carbohydrate Active enZymes encoded in the Eucalyptus genome.  These CAZyme domains are the funtional units of the enymes that synthesise, degrade and modify carbohydrates including complex polysaccharides in fibre cell walls.  We have catalogued and analysed hundreds of genes encoding CAZymes in the E. grandis genome and have identified and prioritised candidate CAZymes that may be used in future bio-techonological applications.