Comparative Plant Transcriptome Profiling of Arabidopsis thaliana Col-0 and Camelina sativa var. Celine Infested with Myzus persicae Aphids Acquiring Circulative and Noncirculative Viruses Reveals Virus- and Plant-Specific Alterations Relevant to Aphid Feeding Behavior and Transmission

Abstract

Evidence is accumulating that plant viruses alter host plant traits in ways that modify their insect vectors' behavior. These alterations often enhance virus transmission, which has led to the hypothesis that these effects are manipulations caused by viral adaptation. However, we lack a mechanistic understanding of the genetic basis of these indirect, plant-mediated effects on vectors, their dependence on the plant host, and their relation to the mode of virus transmission. Transcriptome profiling of Arabidopsis thaliana and Camelina sativa plants infected with turnip yellows virus (TuYV) or cauliflower mosaic virus (CaMV) and infested with the common aphid vector Myzus persicae revealed strong virus- and host-specific differences in gene expression patterns. CaMV infection caused more severe effects on the phenotype of both plant hosts than did TuYV infection, and the severity of symptoms correlated strongly with the proportion of differentially expressed genes, especially photosynthesis genes. Accordingly, CaMV infection modified aphid behavior and fecundity more strongly than did infection with TuYV. Overall, infection with CaMV, relying on the noncirculative transmission mode, tends to have effects on metabolic pathways, with strong potential implications for insect vector-plant host interactions (e.g., photosynthesis, jasmonic acid, ethylene, and glucosinolate biosynthetic processes), while TuYV, using the circulative transmission mode, alters these pathways only weakly. These virus-induced deregulations of genes that are related to plant physiology and defense responses might impact both aphid probing and feeding behavior on infected host plants, with potentially distinct effects on virus transmission. IMPORTANCE Plant viruses change the phenotype of their plant hosts. Some of the changes impact interactions of the plant with insects that feed on the plants and transmit these viruses. These modifications may result in better virus transmission. We examine here the transcriptomes of two plant species infected with two viruses with different transmission modes to work out whether there are plant species-specific and transmission mode-specific transcriptome changes. Our results show that both are the case.

Keywords: RNA-seq; aphid vector; caulimovirus; feeding behavior; insect-plant interactions; plant viruses; polerovirus; transcriptome profiling; transmission.

FIG 1

Phenotypes of CaMV- and TuYV-infected plants and analysis of viral load. (a and b) A. thaliana Col-0 (a) and C. sativa var. Celine (b) plants 21 days after inoculation with the indicated virus or after mock inoculation. The red arrows point to purple-colored leaves in TuYV-infected A. thaliana Col-0 (a) and a yellowed leaf in TuYV-infected C. sativa var. Celine (b), respectively. (c and d) Western blot analysis of TuYV CP coat protein (c) and CaMV coat protein P4 (d). On each lane, a total extract from a different plant was loaded. Ponceau staining of the small ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) subunit is shown as a loading control. M, mock inoculated; T, TuYV infected; C, CaMV infected.

FIG 2

Aphid feeding behavior parameters recorded by EPG on 5-week-old mock-inoculated, TuYV- or CaMV-infected A. thaliana Col-0 (a) and C. sativa var. Celine (b). Different letters indicate significant differences between plants as tested by GLM followed by pairwise comparisons using emmeans (P < 0.05; method, Tukey; n = 20 to 23).

FIG 3

Aphid fecundity 5 days after deposit (one aphid per plant) on 5-week-old mock-inoculated, TuYV- or CaMV-infected A. thaliana Col-0 (a) and C. sativa var. Celine (b). Different letters indicate significant differences between plants as tested by GLM followed by pairwise comparisons using emmeans (P < 0.05; method, Tukey; n = 27 to 33).

FIG 4

Principal-component (PC) analysis of the transcriptome data sets on A. thaliana Col-0 (a) and C. sativa var. Celine (b). Three dots of the same color correspond to the three biological replicates. (c and d) Venn diagrams presenting the number of differentially expressed genes (DEGs) in TuYV and CaMV-infected A. thaliana Col-0 (c) and C. sativa var. Celine (d). Magenta arrows, number of upregulated genes; cyan arrows, number of downregulated genes; two-color circles, inversely regulated genes (upregulated genes in one virus-infected modality and downregulated in the other virus-infected modality). (e) Comparison of the number of DEGs and enriched GO terms in TuYV- and CaMV-infected A. thaliana Col-0 and C. sativa var. Celine plants.

FIG 5

Gene ontology (GO) analysis showing the top 25 GO terms of deregulated processes in TuYV- and CaMV-infected A. thaliana Col-0 and C. sativa var. Celine. (a) TuYV-infected versus mock-inoculated A. thaliana Col-0; (b) CaMV-infected versus mock-inoculated A. thaliana Col-0, (c) TuYV-infected versus mock-inoculated C. sativa var. Celine; (d) CaMV-infected versus mock-inoculated C. sativa var. Celine. GO IDs and corresponding GO terms are specified in the vertical axis. For each category (BP, biological process; CC, cellular component; MF, molecular function), GOs are sorted according to increasing log₂ P values, also indicated by the color of each spot (magenta representing the most significant P values; see color scale bar) to place the most significantly enriched GOs on top of the graph. The absolute number of DEGs that matched the GO term is indicated by the size of each spot, whereas the horizontal axis shows the ratio of DEGs to all genes belonging to the GO term.

FIG 6

Hierarchical clustering of differentially expressed genes (DEGs) related to photosynthesis (GO:0015979) in CaMV- and TuYV-infected A. thaliana Col-0 and C. sativa var. Celine compared to their mock-inoculated control plants (Data Set S2). The color key scale displays the log₂ fold changes from −10 to +10 as a gradient from cyan to magenta.

FIG 7

Hierarchical clustering of differentially expressed genes (DEGs) related to gluconeogenesis (GO:0006094) (a), sucrose biosynthetic process (GO:0005986) (b), starch biosynthetic process (GO:0019252) (c), and trehalose biosynthetic process (GO:0005992) (d) in CaMV- and TuYV-infected A. thaliana Col-0 and C. sativa var. Celine compared to mock-inoculated controls (Data Set S2). The color key scales display the log₂ fold changes as color gradients from cyan to magenta.

FIG 8

Hierarchical clustering of differentially expressed genes (DEGs) related to production of siRNA involved in RNA interference and gene silencing by RNA (GO:0030422 and GO:0031047) (a), defense response to virus (GO:0051607) (b), and salicylic acid biosynthetic process (GO:0009697) (c) in CaMV- and TuYV-infected A. thaliana Col-0 and C. sativa var. Celine compared to their mock-inoculated controls (Data Set S2). The color key scales display the log₂ fold changes as gradients from cyan to magenta.

FIG 9

Hierarchical clustering of differentially expressed genes (DEGs) related to jasmonic acid biosynthetic process (GO:0009695) (a), ethylene biosynthetic process (GO:0009693) (b), glucosinolate biosynthetic process (GO:0019761) (c), and camalexin biosynthetic process (GO:0010120) (d) in CaMV- and TuYV-infected A. thaliana Col-0 and C. sativa var. Celine compared to mock-inoculated controls (Data Set S2). The color key scales display the log₂ fold changes as gradients from cyan to magenta.

FIG 10

Hierarchical clustering of differentially expressed genes (DEGs) related to phloem proteins (PP2 and PP1) and callose deposition in phloem sieve plates (GO:0080165) (a) and defense response to insect and response to insect (GO:0002213 and GO:0009625) (b) in CaMV- and TuYV-infected A. thaliana Col-0 and C. sativa var. Celine compared to mock-inoculated controls (Data Set S2). The color key scales display the log₂ fold changes as gradients from cyan to magenta.