Cabrera Javier, Bustos Regla, Favery Bruno, Fenoll Carmen, Escobar Carolina
Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avenida de Carlos III s/n, 45071, Toledo, Spain.
Mol Plant Pathol. 2014 Aug;15(6):627-36. doi: 10.1111/mpp.12114. Epub 2014 Feb 12.
Novel approaches for the control of agriculturally damaging nematodes are sorely needed. Endoparasitic nematodes complete their life cycle within the root vascular cylinder, inducing specialized feeding cells: giant cells for root-knot nematodes and syncytia for cyst nematodes. Both nematodes hijack parts of the transduction cascades involved in developmental processes, or partially mimic the plant responses to other interactions with microorganisms, but molecular evidence of their differences and commonalities is still under investigation. Transcriptomics has been used to describe global expression profiles of their interaction with Arabidopsis, generating vast lists of differentially expressed genes. Although these results are available in public databases and publications, the information is scattered and difficult to handle. Here, we present a rapid, visual, user-friendly and easy to handle spreadsheet tool, called NEMATIC (NEMatode-Arabidopsis Transcriptomic Interaction Compendium; http://www.uclm.es/grupo/gbbmp/english/nematic.asp). It combines existing transcriptomic data for the interaction between Arabidopsis and plant-endoparasitic nematodes with data from different transcriptomic analyses regarding hormone and cell cycle regulation, development, different plant tissues, cell types and various biotic stresses. NEMATIC facilitates efficient in silico studies on plant-nematode biology, allowing rapid cross-comparisons with complex datasets and obtaining customized gene selections through sequential comparative and filtering steps. It includes gene functional classification and links to utilities from several databases. This data-mining spreadsheet will be valuable for the understanding of the molecular bases subjacent to feeding site formation by comparison with other plant systems, and for the selection of genes as potential tools for biotechnological control of nematodes, as demonstrated in the experimentally confirmed examples provided.
目前迫切需要控制对农业造成破坏的线虫的新方法。内寄生线虫在根维管束内完成其生命周期，诱导形成特化的取食细胞：根结线虫的巨型细胞和孢囊线虫的合胞体。这两种线虫都劫持了参与发育过程的部分信号转导级联，或部分模拟植物对与其他微生物相互作用的反应，但其差异和共性的分子证据仍在研究中。转录组学已被用于描述它们与拟南芥相互作用的全局表达谱，产生了大量差异表达基因列表。尽管这些结果可在公共数据库和出版物中获取，但信息分散且难以处理。在这里，我们展示了一个快速、直观、用户友好且易于操作的电子表格工具，名为NEMATIC（线虫 - 拟南芥转录组相互作用纲要；http://www.uclm.es/grupo/gbbmp/english/nematic.asp）。它将拟南芥与植物内寄生线虫相互作用的现有转录组数据与来自不同转录组分析的关于激素和细胞周期调控、发育、不同植物组织、细胞类型以及各种生物胁迫的数据相结合。NEMATIC有助于对植物 - 线虫生物学进行高效的计算机模拟研究，允许与复杂数据集进行快速交叉比较，并通过连续的比较和筛选步骤获得定制的基因选择。它包括基因功能分类以及与多个数据库工具的链接。通过与其他植物系统进行比较，这个数据挖掘电子表格对于理解取食位点形成的分子基础以及选择作为线虫生物技术控制潜在工具的基因将是有价值的，如所提供的实验证实的例子所示。
