eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for Eucalyptus Defense Against Biotic Stressors

Abstract

Many pests and pathogens threaten Eucalyptus plantations. The study of defense responses in this economically important wood and fiber crop enables the discovery of novel pathways and genes, which may be adopted to improve resistance. Various functional genomics experiments have been conducted in Eucalyptus-biotic stress interactions following the availability of the Eucalyptus grandis genome, however, comparisons between these studies were limited largely due to a lack of comparative tools. To this end, we developed eCALIBRATOR http://ecalibrator.bi.up.ac.za, a tool for the comparison of Eucalyptus biotic stress interaction. The tool, which is not limited to Eucalyptus, allows the comparison of various datasets, provides a visual output in the form of Venn diagrams and clustering and extraction of lists for gene ontology enrichment analyses. We also demonstrate the usefulness of the tool in revealing pathways and key gene targets to further functionally characterize. We identified 708 differentially expressed E. grandis genes in common among responses to the insect pest Leptocybe invasa, oomycete pathogen Phytophthora cinnamomi and fungus Chrysoporthe austroafricana. Within this set of genes, one of the Gene Ontology terms enriched was "response to organonitrogen compound," with NITRATE TRANSPORTER 2.5 (NRT2.5) being a key gene, up-regulated under susceptible interactions and downregulated under resistant interactions. Although previous functional genetics studies in Arabidopsis thaliana support a role in nitrate acquisition and remobilization under longterm nitrate starvation, the importance of NRT2.5 in plant defense is unclear. The T-DNA mutants of AtNRT2.5 were more resistant to Pseudomonas syringae pv. tomato pv tomato DC3000 inoculation than the wild-type counterpart, supporting a direct role for NRT2.5 in plant defense. Future studies will focus on characterizing the Eucalyptus ortholog of NRT2.5.

To have or not to have: expression of amino acid transporters during pathogen infection

“…Respective references to the included studies can be found in Supplementary Tables 1-3 Type of SA marker genes was strongly increased compared to the wild type, and it was suggested that members of the AtNRT2 family might be important for the plant-pathogen interaction (Camanes et al 2012). More recently it was shown that the nrt2.5 mutant displayed similar responses (du Toit et al 2020). Similarly, also NH 4 + transporters such as AtAMT1.1 seem to play an important role for plant resistance (Pastor et al 2014).…”

Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency

“…Recently, T - DNA mutants of NRT2.5 showed stronger resistance to Pseudomonas syringae pv. tomato DC3000 inoculation compared to its wild-type counterpart, an indication of NRT2.5 role in plant biotic defense ( Du Toit et al., 2020 ; Devanna et al., 2021 ). These research findings have demonstrated the functional roles of transporters in the plant response to biotic stress, while suggesting safe, innovative, and sustainable means of controlling crop pathogens.Mycorrhizal colonization of rice root also appears to promote the expression of a putative nitrate transporter, OsNPF4.5 .…”

Role of transporters in plant disease resistance

“…The Arabidopsis nrt2 double mutant plants ( NRT2.1 and NRT2.2 deficient) grown on reduced N availability displayed reduced susceptibility against the Pseudomonas syringae pv tomato DC3000 ( Pst ) infection (Camañes et al, 2012). Also, the AtNRT2.5 T‐DNA mutant lines exhibit a high level of resistance against P. syringae , indicating the possible role of NRT2.5 in biotic resistance (du Toit et al, 2020). Similarly, Pike et al (2014) reported the inducible nature of VvNPF3.2 gene in V. vinifera and AtNPF3.1 gene in Arabidopsis upon Erysiphe necator attack; these genes code for nitrate and nitrite transporters, respectively.…”