# Distinct Signatures of Host Defense Suppression by Plant-Feeding Mites
## 2 Results
### Transcriptomic Profiles
#### 2.2.1 General Overview of Mite-Induced Transcriptomic Changes in Tomato  
We annotated our EST-based gene-expression microarray using the ITAG3.2 tomato genome annotation. The probes of our microarray platform represent 16,431 tomato genes, which corresponds to 53.2% of the 30,868 genes annotated in ITAG3.2. Using the C samples as a common reference, a total of 5494 differentially expressed genes (DEGs) were identified across all mite-infestation treatments at a Benjamini-Hochberg (BH) false discovery rate adjusted \(p\leq 0.05\). We found large variation in the number of DEGs in response to the different mite-infestation treatments (Figure 2A, Table S1). Most striking was the extremely low number of DEGs in the Te samples: only 38 were detected (0.1% of the genes annotated in ITAG3.2), from which all but one were up-regulated. In contrast, there were 2460 (8.0%) and 3200 (10.4%) DEGs in the Tu and Al samples, respectively, with an approximately equal number of genes being up- or down-regulated. For the dual-infested plants, we found 2032 DEGs (6.6%) in the Tu+Te samples, which is considerably less than in the Tu samples while leaflets were infested with twice as many mites. The opposite pattern was observed in the Tu+Al samples, which had as many as 5152 DEGs (16.7%). The number of up-regulated and down-regulated genes was similar in dual-infested plants. For the subsequent transcriptomic analyses, we followed a more conservative approach by applying an additional cutoff at an absolute fold change (FC) of 1.5 (i.e., a Log\({}_{2}\)FC of 0.585), resulting in a total of 3570 DEGs across all mite-infestation treatments (Figure 2A, Table S1). As a first step in our functional characterization of the mite-induced tomato transcriptomic responses, we performed a principal component analysis (PCA) based on the 3570 DEGs (absolute FC \(\geq\) 1.5; BH-adjusted \(p\leq\) 0.05). The PCA indicated that nearly half of the variance in differential gene expression could be attributed to the factor \"mite-infestation treatment\" (Figure 2B, PC 1). The Te and C samples clustered together but separated from the other infestation treatments, which is in line with the low number of DEGs between these treatments. Accordingly, the Tu+Al samples clustered furthest away from the controls along PC 1. The transcriptomic profiles of the Tu, Tu+Te, Al and Tu+Al samples did not separate clearly in the PCA plot (Figure 2B), which might be explained by the large overlap of DEGs across these treatments (Figure 2C). Thirty-one out of 35 genes up-regulated in _T. evansi_-infested leaflets were also up-regulated in response to each of the other mite infestation regimes. None of the genes on our microarray were found to be specifically (uniquely) up- or down-regulated by _T. evansi_, and only one (Solyc12g040860; encoding a glucan endo-1,3-\(\beta\)-glucosidase) was significantly up-regulated in the Te and Tu+Te samples but not in the others. With respect to _A. lycopersici_, a very different picture emerged from our transcriptome data analyses. Although the majority of up- and down-regulated Al-DEGs were shared with the other treatments, still 111 genes were specifically expressed in response to the _A. lycopersici_ single infestation. Moreover, a total of 1836 genes (including those 111) were differentially regulated in the Al and/or Tu+Al samples but not in the others (Figure 2C). be significantly overrepresented in the tomato transcriptional responses, with substantial overlap between treatments (Table S2). Among the up-regulated DEGs in the Tu+Te, Tu, Tu+Al and Al samples, genes associated with the BP GO categories \"recognition of pollen\", \"protein phosphorylation\", \"hydrogen peroxide catabolic process\" and \"chitin catabolic process\" were significantly enriched (Table S2A), while down-regulated DEGs were consistently enriched in genes belonging to BP GO category \"photosynthesis\".