Classification and Clustering of the Eucalyptus grandis NBS-LRR Gene Family

Eucalyptus grandis is a commercially important hardwood species. Since E. grandis is known to be susceptible to a number of pests and pathogens, it is of high importance to determine mechanisms of defence. The published genome has aided the identification of an important class of resistance (R) genes that incorporate nucleotide binding sites and leucine-rich repeat domains (NBS-LRR). Based on an E. grandis specific Hidden Markov Model for the conserved NB-ARC protein domain, 1,215 NBS-LRR gene models were identified. Phylogenetic and MEME motif analyses were used to distinguish between classes derived from Toll or interleukin-1 receptor (TIR) and coiled-coil (CC) NBS-LRR genes, as well as genes lacking these amino-terminal domains (449 TIR and 766 non-TIR). A further 272 putative incomplete resistance genes were also identified. NBS-LRR gene-rich regions were identified with 76% organized in clusters of three or more genes. E. grandis has a higher ratio of TIR to CC classed genes compared to other woody plant species and a smaller percentage of single NBS-LRR genes. Transcriptome profiles of resistant and susceptible plants that were challenged with different biotic stresses, indicated expression hotspots, within physical clusters, including expression of many incomplete genes. This indicates functional relevance for the physical arrangement of this gene family. This analysis of the repertoire and expression of E. grandis putative NBS-LRR genes provides an important resource for the identification of novel and functional R-genes, which is a key objective for strategies to enhance defence.