Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores

Abstract

Plants experience different abiotic/biotic stresses, which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonateinduced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.

Disentangling transcriptional responses in plant defense against arthropod herbivores

“…A former analysis of 28 Arabidopsis-herbivore transcriptomic experiments reported a group of DEGs in the plant with a correlated expression 23 . To complement the information provided by correlated genes, a gene ontology enrichment analysis of the DEGs of this set of experiments was performed by the Metascape tool.…”

“…Combined species-specific and meta-analysis of transcriptomic responses permitted identify novel relevant processes and specificities in the Arabidopsis response to the spider mite T. urticae 23 . This dataset offers the possibility to increase knowledge on the response of the plant to a variety of arthropod herbivores.…”

“…In a previous work, a set of 28 Arabidopsis-herbivore transcriptomic experiments was collected and analyzed to obtain lists of differential expressed genes (DEGs) 23 . The selected experiments included a broad spectrum of diverse arthropods feeding on Arabidopsis plants of the ecotype Columbia-0 with a preferably vegetative stage of 4 weeks when infested.…”

“…This starting information is compiled in the Supplementary Dataset S1. Processing and normalization of transcriptomic data were previously described in the Methods S1 file of Santamaria et al 23 . Because of the different nature of the data, results of RNA-seq and microarray experiments were compared after extraction of gene expression and filtering by log2FC > 1.5 and p-value adjusted < 0.05, establishing similar thresholds for the different analyses.…”

Spider mite egg extract modifies Arabidopsis response to future infestations

“…However, the lepidopteran models do not represent all plant–herbivore interaction events of this nature, considering that many pests oviposit and feed at the same time. Arthropod species following this pattern belong to diverse and vast groups including hemipterans, coleopterans, and mites 11 – 15 . A transcriptional study exploring such a model has been performed previously 11 .…”