Comparative transcriptomic analyses to characterise the core defence gene network in Eucalyptus.
Swanepoel, S.*1, Marchal, K.2, Ployet, R.3, Naidoo, S.1
1 Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lunnon Street, Pretoria, South Africa
2 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
3 Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN37831, USA
Eucalyptus species are a globally important forestry plant widely cultivated for paper, pulp, and biofuel. These trees are threatened by various pests and pathogens that impact the productivity of plantations. Previous studies have investigated single-pest/pathogen interactions of Eucalyptus, with pathogens such as Austropuccinia psidii, Teratosphaeria destructans, Phytophthora cinnamomi and Chrysoporthe austroafricana as well as in the insect pest Leptocybe invasa. While valuable, these studies do not explore the roles of central hubs of defence responses in Eucalyptus. Therefore, this study aimed to characterise the core defence gene network to the abovementioned pest and pathogens to identify key players that contribute to a broad-spectrum defence response. A comprehensive weighted gene co-expression network analysis (WGCNA) consisting of 180 Eucalyptus-biotic stress RNA-sequencing libraries was used to construct a network to identify modules of highly co-expressed genes. A total of 38 modules, consisting of between 40 and 3,328 genes were identified. Gene ontology enrichment revealed genes involved in phytohormone and specialised metabolite biosynthesis and signalling, hypersensitive responses and nitrate transport among the induced defence responses. Transcription factor binding site enrichment analysis revealed module genes to be regulated by a host of transcription factors, including WRKY, NAC and bHLH. Of these, WRKY6, a known contributor to broad-spectrum defence responses, was identified as a hub gene in an induced response module. Additional hub genes included terpene synthase genes, pathogen recognition receptors, and a pathogenesis-related family protein gene. Taken together, this study provides invaluable insights into the broad-spectrum defence responses of Eucalyptus to various biotic stressors. Genes identified through this research are highlighted for future functional studies to gain an understanding of the roles that they play in the Eucalyptus immune response.
Keywords: transcription factors, nitrate transporters, defence hubs, comparative transcriptomics, defence networks
