Table_2_eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for Eucalyptus Defense Against Biotic Stressors.XLSX

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 down-regulated under resistant interactions. Although previous functional genetics studies in Arabidopsis thaliana support a role in nitrate acquisition and remobilization under long-term 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.

多种害虫与病原菌均对桉树人工林构成严重威胁。针对这一兼具经济价值的木材与纤维作物开展防御响应研究，有助于发掘全新的通路与基因资源，进而应用于作物抗逆性改良。巨桉（Eucalyptus grandis）基因组序列公布后，学界已针对桉树-生物胁迫互作开展了多项功能基因组学研究，但由于缺乏专用比较工具，各研究间的横向对比受到极大限制。为此，本研究开发了eCALIBRATOR（http://ecalibrator.bi.up.ac.za），一款用于桉树生物胁迫互作数据比较的分析工具。该工具并非仅局限于桉树研究场景，可实现多组学数据集的比较分析，并以韦恩图、聚类图等形式生成可视化结果，同时支持提取基因列表用于基因本体（Gene Ontology, GO）富集分析。本研究同时验证了该工具的实用性：其可助力发掘通路与关键基因靶点，为后续功能鉴定提供支撑。本研究针对桉树枝瘿姬小蜂（Leptocybe invasa）、肉桂疫霉菌（Phytophthora cinnamomi）以及非洲壳囊孢菌（Chrysoporthe austroafricana）的胁迫响应进行整合分析，共筛选得到708个巨桉共有差异表达基因。在该基因集合中，富集得到的基因本体术语包含"有机氮化合物响应"，其中硝酸盐转运蛋白2.5（NITRATE TRANSPORTER 2.5, NRT2.5）为关键基因：该基因在感病互作中呈上调表达，在抗病互作中则呈下调表达。尽管此前在拟南芥（Arabidopsis thaliana）中的功能遗传学研究表明，该基因在长期硝酸盐饥饿条件下参与硝酸盐吸收与再转运，但NRT2.5在植物防御中的作用机制仍有待阐明。与野生型拟南芥相比，AtNRT2.5的T-DNA插入突变体对番茄丁香假单胞菌致病变种番茄DC3000（Pseudomonas syringae pv. tomato DC3000）的侵染具有更强抗性，这一结果证实了NRT2.5在植物防御中的直接作用。后续研究将聚焦于桉树NRT2.5同源基因的功能鉴定。