The FMG Bioinformatics Platform is hosted in the Centre for Bioinformatics and Computational Biology at the
University of Pretoria. Our team consists of a full-time bioinformatics programmer, Ms Karen van der Merwe, and a
postdoctoral fellow, Dr Nanette Christie. Working alongside biologists and geneticists in the FMG Programme, we are able
to support and build capacity for the analysis, management and interpretation of large amounts of genomics and
transcriptomics data for hundreds to thousands of individual trees. Web services, novel and commercial software, as well
as a Galaxy workflow environment have been implemented to facilitate modular development of data processing and
visualization pipelines. These pipelines can be accessed remotely by group members for high-throughput genomics analysis
and enable quality control, processing of raw data and downstream analyses such as gene and genome annotation, gene
expression analysis, detection of genomic variants, and discovery of genetics associations with phenotypic traits.
Currently, a major focus is working with colleagues at the Umea Plant Science Centre in Sweden on the integration of the
Eucalyptus Genome Integrative Explorer (EucGenIE) into PlantGenIE (plantgenie.org), a dedicated web portal for genome
and transcriptome exploration in plants (also including poplar, Norway spruce, and Arabidopsis). In parallel, Bioinformatics Platform we focus on the development
of a web resource to query and visualize Eucalyptus systems genetics data, such as expression quantitative trait locus (eQTL) networks. We envision our
genetic variation tool (qtlXplorer) to be a significant building block towards a population genomics module in PlantGenIE. We are also hosting a genomic
breeding database (BioPlasm) providing data access and analysis tools for tree breeders of our industry partners.