AUTHOR=Christie Nanette , Tobias Peri A. , Naidoo Sanushka , Külheim Carsten 

TITLE=The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots

JOURNAL=Frontiers in Plant Science

VOLUME=6

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2015.01238

DOI=10.3389/fpls.2015.01238

ISSN=1664-462X

ABSTRACT=<p><italic>Eucalyptus grandis</italic> is a commercially important hardwood species and is known to be susceptible to a number of pests and pathogens. Determining mechanisms of defense is therefore a research priority. The published genome for <italic>E. grandis</italic> has aided the identification of one important class of resistance (<italic>R</italic>) genes that incorporate nucleotide binding sites and leucine-rich repeat domains (NBS-LRR). Using an iterative search process we identified <italic>NBS-LRR</italic> gene models within the <italic>E. grandis</italic> genome. We characterized the gene models and identified their genomic arrangement. The gene expression patterns were examined in <italic>E. grandis</italic> clones, challenged with a fungal pathogen (<italic>Chrysoporthe austroafricana</italic>) and insect pest (<italic>Leptocybe invasa</italic>). One thousand two hundred and fifteen putative <italic>NBS-LRR</italic> coding sequences were located which aligned into two large classes, Toll or interleukin-1 receptor (<italic>TIR</italic>) and coiled-coil (<italic>CC</italic>) based on NB-ARC domains. <italic>NBS-LRR</italic> gene-rich regions were identified with 76% organized in clusters of three or more genes. A further 272 putative incomplete resistance genes were also identified. We determined that <italic>E. grandis</italic> has a higher ratio of <italic>TIR</italic> to <italic>CC</italic> classed genes compared to other woody plant species as well as a smaller percentage of single <italic>NBS-LRR</italic> genes. Transcriptome profiles indicated expression hotspots, within physical clusters, including expression of many incomplete genes. The clustering of putative <italic>NBS-LRR</italic> genes correlates with differential expression responses in resistant and susceptible plants indicating functional relevance for the physical arrangement of this gene family. This analysis of the repertoire and expression of <italic>E. grandis</italic> putative <italic>NBS-LRR</italic> genes provides an important resource for the identification of novel and functional <italic>R</italic>-genes; a key objective for strategies to enhance resilience.</p>