Global Transcriptomic Analysis Reveals Insights into the Response of ‘Etrog’ Citron (Citrus medica L.) to Citrus Exocortis Viroid Infection

Citrus exocortis viroid (CEVd) is the causal agent of citrus exocortis disease. We employed CEVd-infected ‘Etrog’ citron as a system to study the feedback regulation mechanism using transcriptome analysis in this study. Three months after CEVd infection, the transcriptome of fresh leaves was analyzed, and 1530 differentially expressed genes were detected. The replication of CEVd in citron induced upregulation of genes encoding key proteins that were involved in the RNA silencing pathway such as Dicer-like 2, RNA-dependent RNA polymerase 1, argonaute 2, argonaute 7, and silencing defective 3, as well as those genes encoding proteins that are related to basic defense responses. Many genes involved in secondary metabolite biosynthesis and chitinase activity were upregulated, whereas other genes related to cell wall and phytohormone signal transduction were downregulated. Moreover, genes encoding disease resistance proteins, pathogenicity-related proteins, and heat shock cognate 70 kDa proteins were also upregulated in response to CEVd infection. These results suggest that basic defense and RNA silencing mechanisms are activated by CEVd infection, and this information improves our understanding of the pathogenesis of viroids in woody plants.


Introduction
Viroids are small, circular, infectious RNAs that do not encode any protein, and their genomes range from 246 to 433 nucleotides [1,2]. Viroids can replicate autonomously in higher plants, and they can infect important economically significant crops and cause severe diseases [3]. They are the causative agents of various diseases affecting herbaceous and woody plants as well as agronomic and ornamental plants around the world and can cause chlorosis, leaf deformation, stunting, and even plant death on sensitive hosts [4]. RNA silencing is an important defense mechanism for plants to cope with RNA virus and viroid infections. Viroids can function as precursors for small interfering RNAs (siRNAs), and viroid-derived siRNAs involved in post-transcriptional gene silencing (PTGS) cause RNA silencing of the host mRNA to induce disease symptoms in higher plants [5]. Studies have been conducted to detect siRNAs in PSTVd-infected tobacco and tomato plants and demonstrate that viroids are activators and targets for RNA silencing [6,7]. The plant's Dicer-like proteins (DCLs)

Preparation of Infectious CEVd RNAs
CEVd were isolated from Meishan No. 9 [Citrus sinensis (L.) Osb.] in China. Sequence analysis was performed using Clustal W program and secondary structure was obtained via MFOLD web server and RNAviz program. Total RNA of approximately 0.1 g of citrus symptomatic leaves was extracted using EASYspin Plus Complex Plant RNA Kit (Aidlab Biotech, Beijing, China), according to the manufacturer's instructions. Based on the sequences of CEVd (371 bp), one-step RT-PCR analysis using PrimeScript TM One Step RT-PCR Kit Ver.2 (Takara, Beijing, China) was conducted to synthesize full-length cDNA of CEVd-dimer using CEVd-specific primers (CEVd-For: 5'-GGAAACCTGGAGGAAGTCGAG-3' and CEVd-Rev: 5'-CCGGGGATCCCTGAAGGACTT-3') [32]. The dimeric products, which were amplified by one-step RT-PCR, were ligated overnight at 4 • C using the pGEM-T Easy Vector System (Promega, Beijing, China) to obtain pGEM-CEVd-dimers, which were dimeric linker products. All the entire cDNA inserts were transformed into Escherichia coli DH5α competent cells. Then, the expected dimeric recombinant plasmids were identified by sequencing and selected out. The plasmids were extracted using Plasmid DNA Mini Kit I (EZNA, Shanghai, China), linearized with the SpeI enzyme, and then purified by ethanol. The linearized plasmids containing the full-length dimeric cDNA of CEVd were used as templates for in vitro transcription. Infectious CEVd RNAs were generated by in vitro transcription with T7 RNA polymerase (Promega, Madison, WI, USA) according to the manufacturer's instructions.

Inoculation of the Viroid-Free Plants
CEVd RNAs diluted to 500 ng/µL with buffer (100 mM Tris-HCl, 10mM EDTA, pH 7.5) were mechanically inoculated onto viroid-free plants. Each of the five 'Etrog' citron (knife cutting for inoculation) or tomato plants (friction used carborundum for inoculation) was inoculated with CEVd RNAs and five other viroid-free plants were used as healthy controls. All plants were stored in a 28-32 • C greenhouse. CEVd systemic infection was verified by one-step RT-PCR as described above. Finally, 'Etrog' citron seedlings were inoculated via bark grafting. Seedlings infected with CEVd were treated groups, while viroid-free seedlings were healthy controls. After 3 months of storage in the 28-32 • C greenhouse, the leaves of the citron plants were collected for transcriptome sequencing.

Northern Blot Hybridization
Northern blot hybridization using DIG-labelled CEVd-specific RNA probes was conducted to verify infection activity. DIG Northern Starter Kit Ver.10 was used for northern blot analysis as instructed by the manufacturer (Roche, Mannheim, Germany). Equal amounts of total RNA from CEVd-infected tomato plants and healthy controls were electrophoresed in an acetaldehyde-containing agarose gel. The RNAs in the agarose gel were then transferred to a Hybond N + nylon membrane using a capillary transfer system. Northern blot hybridization was performed at 68 • C for at least 6 h with the CEVd-dimer full length probe. The hybridized probes were immunodetected with anti-digoxigenin-AP, Fab fragments and then visualized with the colorimetric substrates NBT/BCIP.

Library Construction and Transcriptome Sequencing
Three biological replicates were separately used for the treatment group and healthy controls, and each biological replicate included at least five plants to eliminate differences between individual plants. Equal amounts of total RNA from CEVd-infected and mock-inoculated plants were used for RNA sequencing. Approximately 1 µg of RNA per sample was used to prepare RNA samples. The NEBNext®Ultra™ RNA Library Prep Kit (NEB, Ipswich, USA) was used to construct sequencing libraries, and index codes were added to the attribute sequence for each sample. The library preparations were performed by Beijing Novogene Bioinformation Technology Company and then sequenced on an Illumina HiSeq 2500 platform. The raw RNA-seq datasets are available at NCBI (accession no: PRJNA542205).

Identification and Enrichment Analysis of Differentially Expressed Genes (DEGs)
High-quality citron genome was used for mapping, and high mapping scores were conducive to subsequent data analysis [33]. The DESeq R package was used to perform differential expression analysis between the two groups [34]. The DESeq statistical program uses a model based on a negative binomial distribution to determine differential expression in digital gene expression data. The Benjamini and Hochberg methods were used to adjust the resulting p-values. The adjusted p-value <0.05 genes were designated as differentially expressed.
Gene Ontology (GO) enrichment analysis of DEGs was performed using the GOseq R package [35]. GO terms with corrected p-value < 0.05 were considered significantly enriched. The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). The KOBAS software [36] was used to perform statistical enrichment analysis of DEGs in KEGG pathways. KEGG terms with corrected p-value < 0.05 were considered to be significantly enriched in DEGs.

Validation of DEGs by RT-qPCR
Some DEGs were randomly selected for quantitative real-time PCR (RT-qPCR) analysis using specific primer pairs to validate our transcriptome data (Table S1). Primer 5.0 was used to design suitable primers for qPCR. Template cDNA was synthesized by means of M-MLV reverse transcriptase and random hexamer primers. A IQ5 real-time PCR detection system (Bio-Rad, CA, USA) was used to perform PCR amplification. The amplification system (20 µL) included diluted cDNA, 10 µL SYBR Green Real-Time PCR Master Mix and 10 µM forward and reverse specific primers. The reaction conditions were as follows: 95 • C for 5 min, and then 40 cycles at 95 • C for 15 s, at 58 • C for 30 s, and at 72 • C for 30 s. Ct (2 −DDCt ) was calculated to determine the relative expression levels of the selected genes [37]. The citron actin gene was selected as internal reference to normalize gene expression levels [38]. Three independent biological replicate assays were performed to reduce the error.

Infectivity Confirmation of CEVd RNAs
Four nucleotide differences were identified between the CEVd variant used in this study and CEVd-Reference (NC-001464) deposited in NCBI ( Figure 1A). We successfully amplified CEVd-dimers using one-step RT-PCR, and the RT-PCR products of approximately 742 bp in size were observed in CEVd-infected samples ( Figure 1B). Sequencing analysis showed that the genome sequences of CEVd-dimers were truly 742 bp in length. To verify whether infectious clones of CEVd with the cDNA dimers obtained in this study were effective, the viroid-free plants were inoculated with infectious CEVd dimeric RNAs. Infectivity was assayed by RT-PCR and northern blot analysis of leaves that were prepared from the bioassay plants. The presence of CEVd RNAs in the top fresh leaves of the citron plant was determined by RT-PCR three months after inoculation ( Figure 1C). Northern blot analysis of leaf samples from inoculated tomato plants further confirmed that the transcripts of CEVd could systemically infect viroid-free plants ( Figure 1D). The appearance of disease symptoms on citron seedlings was observed within four months after inoculation. The 'Etrog' citron seedlings that were infected with RNA transcripts showed a severe syndrome compared to the uninfected 'Etrog' citron, which was characterized by stunting, leaf curling, and midvein, petiole, and stem necrosis ( Figure 1E). Similar results were observed in all five independent plants, confirming that CEVd appears to be a severe variant in citron.

Transcriptome Sequencing and Gene Expression Analysis
To analyze the interaction of CEVd with citron at the transcriptional level, 10 other CEVdinfected citron plants were obtained by bark grafting, and the parietal leaves of the citron plants at 3 months of healthy control and CEVd infection were collected for transcriptome analysis ( Figure 2). This was a critical stage in the beginning of CEVd symptoms. We constructed and sequenced RNA-Seq libraries of the mock control and CEVd-infected citron leaves with three biological replicates. RNA-seq yielded 73.26-117.80 million raw reads and retained 67.75-112.71 million clean reads after processing the sequencing data (Table 1). Quality control parameters indicated that the data obtained by RNA-seq were reliable, and gene expression pattern correlation analysis between biological replicate samples indicated high reproducibility of sequencing ( Figure S1).

Transcriptome Sequencing and Gene Expression Analysis
To analyze the interaction of CEVd with citron at the transcriptional level, 10 other CEVd-infected citron plants were obtained by bark grafting, and the parietal leaves of the citron plants at 3 months of healthy control and CEVd infection were collected for transcriptome analysis ( Figure 2). This was a critical stage in the beginning of CEVd symptoms. We constructed and sequenced RNA-Seq libraries of the mock control and CEVd-infected citron leaves with three biological replicates. RNA-seq yielded 73.26-117.80 million raw reads and retained 67.75-112.71 million clean reads after processing the sequencing data (Table 1). Quality control parameters indicated that the data obtained by RNA-seq were reliable, and gene expression pattern correlation analysis between biological replicate samples indicated high reproducibility of sequencing ( Figure S1).    FPKM (expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) was used to calculate gene expression levels, and DEGSeq package was used to compare the expression levels of genes identified in different treatments. CEVd infection caused a rich change in gene expression of citron leaves. CEVd induced differential expression of 1530 genes in citron leaves, of which 1249 genes were significantly upregulated, and 281 genes were significantly downregulated ( Figure 3, Tables S2 and S3). The heat cluster map shows the DEG expression patterns between CEVd-infected citron plants and healthy controls ( Figure S2).  . Volcano map of the differential genes. Genes with significant differential expression were indicated by red dots (upregulated) and green dots (downregulated). Genes with no significant differential expression were represented by blue dots.

Gene Enrichment Analysis
GO enrichment analysis was performed to analyze the function of DEGs in response to CEVd infection, and the results provided an overview of statistically significant and relevant GO terms. GO terms with a corrected p value < 0.05 were considered to be enriched. Upregulated DEGs were mainly enriched in transcription, RNA biosynthesis, chitin metabolism and protein kinase activity in citron plants (Table 2), while downregulated DEGs were mainly enriched in the terms related to auxin reactions and cell wall ( Table 3). The GO terms related to transcription on biological process and the terms that were related to chitinase activity on molecular function were the most significantly upregulated, whereas the terms related to plant hormone on biological process and the terms related to cell wall on the cellular component were the most significantly downregulated.  Figure 3. Volcano map of the differential genes. Genes with significant differential expression were indicated by red dots (upregulated) and green dots (downregulated). Genes with no significant differential expression were represented by blue dots.

Gene Enrichment Analysis
GO enrichment analysis was performed to analyze the function of DEGs in response to CEVd infection, and the results provided an overview of statistically significant and relevant GO terms. GO terms with a corrected p value < 0.05 were considered to be enriched. Upregulated DEGs were mainly enriched in transcription, RNA biosynthesis, chitin metabolism and protein kinase activity in citron plants (Table 2), while downregulated DEGs were mainly enriched in the terms related to auxin reactions and cell wall ( Table 3). The GO terms related to transcription on biological process and the terms that were related to chitinase activity on molecular function were the most significantly upregulated, whereas the terms related to plant hormone on biological process and the terms related to cell wall on the cellular component were the most significantly downregulated.   KEGG enrichment analysis was performed to identify major metabolic and signal transduction pathways that might be disrupted during CEVd infection. The results showed that four upregulated enrichment KEGG pathways were glutathione metabolism, plant-pathogen interaction, secondary metabolite biosynthesis, and amino sugar and nucleotide sugar metabolism, whereas the downregulated enrichment KEGG pathways were phytohormone signaling, phenylpropanoid biosynthesis and phenylalanine metabolic pathways (Tables 4 and 5). Especially, 52 genes involved in secondary metabolite biosynthesis including flavonoid biosynthesis were found to be significantly upregulated against the CEVd infection in citron plants.

CEVd Infection Induces Expression of Many Genes That Are Related to Basal Defense Responses
Viroid infections can cause disease symptoms, and plants have evolved basic immunity to limit diseases, which are activated at the site of infection and then spread when the plants are attacked by the pathogens [39][40][41]. A central component of signal transduction in the PTI and ETI pathways is the mitogen-activated protein kinase (MAPK) cascade, which activates symptom-related genes including WRKY transcription factors. Our RNA-seq results showed upregulation of genes encoding MAPKs (mitogen-activated protein kinase/mitogen-activated protein kinase kinase/mitogen-activated protein kinase kinase kinase) and WRKY transcription factors. Receptor-like kinase (RLK), a membrane-localized protein, could identify pathogen avirulence determinants, and the LRR-RLK genes were involved in plant innate immunity. CEVd infection induced the expression of the LRR genes in the citron plants. The genes encoding cyclic nucleotide-gated channel (CNGC), respiratory burst oxidase (Rboh), calcium-binding protein CML, heat shock cognate 70 kDa protein, pathogenesis-related protein, and disease resistance protein were also upregulated in CEVd-infected citron plants (Table S4). These genes might play a key role in regulating the innate immune response and revealed potential regulatory elements in citron in response to CEVd infection.

CEVd Infection Impacts Plant Hormone Signaling
Plant hormones regulate plant growth and development, and infection by viruses and viroids can affect a variety of plant hormone signaling pathways and lead to disease symptoms in the infected plants [12,42]. KEGG enrichment analysis was performed to identify DEGs involved in the phytohormone signaling pathway. The result showed that citron plants infected with CEVd had many DEGs associated with phytohormone signal transduction compared to mock-inoculated plants (Table S5). Some DEGs participated in the auxin (IAA), jasmonic acid (JA), brassinosteroid (BR), and gibberellin (GA) signal transduction pathways and downregulation of genes involved in the IAA signal transduction pathway may be associated with the appearance of disease symptoms such as stunting on CEVd-infected citron plants. The DEGs involved in JA, BR, and GA signal transduction pathways were upregulated in CEVd-infected citron leaves.

RNA Silencing Responses to CEVd Infection
RNA silencing plays a major role in plant defense against RNA and viroid infections [43]. RNA silencing not only participates in plant antiviral responses, but also directly induces viroid diseases in plants [44,45]. Therefore, we screened DEGs related to the RNA silencing pathway, including genes encoding DCLs, AGOs, and RNA-dependent RNA polymerases (RDRs). We found that the expression of DCL2 (Cm146130) was highly upregulated (3.4-fold) in CEVd-infected citrons. Expression of the citron AGO2 gene (Cm196770) was 3.5-fold upregulated and the gene expressing AGO7 (Cm010810) was upregulated 4.3-fold in CEVd-infected citrons. Especially, we also found that the expression of three citron RDR1 gene dramatically increased in CEVd-infected citron plants (Novel01970 by 14.2-fold, Novel01971 by13.9-fold, and Cm225400 by 4.3-fold). In addition, the expression of the PTGS-related gene SILENCING DEFECTIVE 3 (SDE3) (Cm260670) was also upregulated in CEVd-infected citron plants ( Figure 4, Table S6).

Validation of RNA-seq Results by RT-qPCR
To validate the RNA-seq results, 12 DEGs related to responses to CEVd infection were randomly selected and their expression levels were analyzed by RT-qPCR using specific designed gene-specific primers. The expression changes of these genes were similar to those of the RNA-seq data, indicating that the RNA-seq results were reliable ( Figure 5, Table S7).

Validation of RNA-seq Results by RT-qPCR
To validate the RNA-seq results, 12 DEGs related to responses to CEVd infection were randomly selected and their expression levels were analyzed by RT-qPCR using specific designed gene-specific primers. The expression changes of these genes were similar to those of the RNA-seq data, indicating that the RNA-seq results were reliable ( Figure 5, Table S7).

Validation of RNA-seq Results by RT-qPCR
To validate the RNA-seq results, 12 DEGs related to responses to CEVd infection were randomly selected and their expression levels were analyzed by RT-qPCR using specific designed gene-specific primers. The expression changes of these genes were similar to those of the RNA-seq data, indicating that the RNA-seq results were reliable ( Figure 5, Table S7).

Discussion
Citrus is one of the most important fruits in the world, and the research and control of citrus diseases have important economic significance. Specific strains of CEVd can cause pronounced symptoms on sensitive citrus species and can be rapidly spread in commercial orchards by mechanical means. Early studies compared the differences in tomato transcriptomes induced by PSTVd [14], and two studies examined changes of host gene expression in different tomato cultivars following CEVd [13] or PSTVd infection [12]. These studies are all evaluating the response of herbaceous hosts to viroid infection. Here, we used RNA-seq analysis to analyze changes of gene expression associated with CEVd infection in a woody host. A high quality citron genome reported recently was used for mapping analysis and higher mapping rates were conducive to obtain ideal results [33]. The results highlighted the transcriptomic changes in the leaves of citron plants caused by CEVd infection, which showed that CEVd infection affected the expression of several important genes that are involved in the basic defense response, phytohormone signal transduction, RNA silencing pathway, and some other pathways such as secondary production synthesis pathways.
Plants have an innate immune system called the basic defense response that identifies invading pathogens and initiates effective defense [46]. As observed in this study, plants convert the perception of pathogen invasion into signal cascades containing CNGCs, which increase Ca 2+ concentrations and activate CMLs [47]. Rboh genes were upregulated by CEVd in citron leaves, and Rboh was associated with ROS production in Arabidopsis [48]. Expression of the LRR receptor-like kinase FLS2 was also upregulated by CEVd infection, which combines with BAK1 to form a complex [46,49]. The signal was then passed from FLS2 to MEKK1, which had been reported to activate the MAPK cascade in Arabidopsis [46,50]. Pathogen infection usually results in transcriptional changes in the host. A hypersensitive response (HR) leads to significant changes in gene expression patterns and causes large increases of many different proteins, which include members of the PR and disease resistance protein families. We observed a significant upregulation of PR gene expression in CEVd-infected plants, which agreed with the findings of previous studies. Apple stem groove virus (ASGV) infection induces the upregulation of the gene encoding the PR protein in apple [51], and tomato spotted wilt virus (TSWV) and CEVd infections induce PR expression in tomato [52]. CEVd infection also induced the upregulation of genes encoding disease resistance-related proteins in citron plants, suggesting that CEVd infection triggers a plant immune response. HSP family homologs are significantly induced in many plants infected with RNA viruses and viroids [44,53]. It has been suggested that HSP is involved in the regulation of host defense responses in hosts infected by RNA virus [54]. In this study, HSP70 transcripts were found to be induced to higher levels in CEVd-infected citron, suggesting that HSP70 played an important role in the CEVd infection cycle. Transcription factors (TFs) often play an important role against abiotic and biotic stresses in plants [55]. The genes of major TF families (WRKYs, MYBs, and ERFs) were significantly changed in CEVd-infected citron plants, consistent with the findings of previous studies involving PSTVd-infected potatoes [56]. CEVd does not encode any proteins, and how the viroid activates ETI is an interesting and important question. It has been reported that protein kinase viroid-induced (PKV) genes are involved in the development of symptoms during infection with viroids [57]. Numerous PKV genes were upregulated in this study and they might be associated with the actiovation of ETI in citron plants.
Many studies have shown that phytohormones are regulators of many important metabolic pathways associated with abiotic/biotic stress responses and plant growth and development and play important roles in the life cycle of plants [58,59]. Infection by pathogens such as viruses and viroids often alters plant hormone accumulation and signaling, resulting in physiological destruction of the host cells and plant developmental disorders [12,42,57,[60][61][62]. In our study, the expression of multiple genes associated with the plant hormone signal transduction was altered, and some important plant hormone signaling pathways were affected after CEVd infection. We found that CEVd infection induced the upregulation of genes encoding components of the JA signal transduction pathway, and JA may be involved in the interaction between viroids and plants. Some genes involved in GA and BR signal transduction pathways were also upregulated, whereas many genes involved with IAA were downregulated. These results suggest that CEVd infection simultaneously alters several plant hormone signaling pathways, and the relationship between viroids and plant hormones is complex. Recently, salicylic acid (SA) has attracted attention in improving plant basic resistance against viroids [52]. However, no changes in gene expression involved in the SA signal transduction pathway were observed in this study. Similar results were also observed in tomato plants after PSTVd infection, which showed alterations in transcript levels of several genes related to GA and BR signaling, but none of other genes involved in the SA-dependent pathway [12].
RNA silencing plays a major role in plant defense mechanisms against RNA viruses and viroids because their genomes can be directly targeted by DCL proteins and RNA-induced silencing complexes (RISCs) [45,63]. In this study, the genes encoding key components such as DCL2, RDR1, AGO2, and AGO7 of the gene silencing pathway were upregulated in CEVd-infected citron plants. RNA silencing begins with the formation of double-stranded RNA (dsRNA) molecules, which are substrates for DCL proteins [64]. There are four DCL proteins that are involved in RNA silencing in Arabidopsis. DCL2 and DCL4 have overlapping functions in antiviral RNA silencing defense, and DCL2 is required to generate secondary small interfering RNA (siRNA) [65,66]. The expression of the DCL2 gene was upregulated in CEVd-infected citron, indicating that DCL2 may play a major role in antiviral defense in woody plants. The AGO proteins in plants are an important component of RISCs. AGO proteins have antiviral functions, and AGO2 has a wide range of effects in antiviral silencing [67][68][69][70]. AGO1 and AGO7 have also been shown to play a role in plant antiviral silencing pathways in Arabidopsis thaliana [71]. The genes encoding AGO2 and AGO7 were significantly upregulated in CEVd-infected citron, whereas the genes encoding AGO1 and other AGO proteins showed no significant changes. The results indicate that AGO7 possibly acts synergistically with AGO2 to suppress CEVd infection to a greater degree than the other AGO proteins in citron plants. RDR1 plays an important role in PTGS immune response [65,[72][73][74]. This study found that CEVd infection induced the upregulated expression of three RDR1 genes in citron plants, consistent with previous findings in PSTVd-infected tomato [75] and HSVd-infected cucumber [22], indicating that RDR1 is involved in viroid-host interactions. Early studies have reported that RNA silencing is an important mediator of host-viroid interactions [76], and RDR1 is one of the major components involved in the RNA silencing pathway [77]. It can lead to basal resistance to some viruses by producing virus-derived siRNA [65,73,78,79]. In Arabidopsis, RDR1 can also confer broad-spectrum antiviral activity by generating viral-activated siRNA (vasiRNA) resulting in extensive silencing of the host genes [80]. These results indicate that RDR1 may be crucial in antiviral and viroid resistance by silencing the RNA of viruses and viroids as well as host immune-related genes. In addition to RDR1, RDR2 and RDR6 are also reported to be involved in viroid-host interactions [73]. No evidence of transcriptional changes in RDR2 or RDR6 was found in this study, but the differences might be due to various viroids and plants. In addition, the upregulated SDE3 gene found in this study is reported to encode RNA helicases in Arabidopsis and is also important for PTGS [81]. Notably, RT-qPCR results further showed that the expression levels of DCL2 and SDE3 was upregulated in response to CEVd infection and they might play important roles in the interaction between CEVd and citron plants.
In addition, we analyzed the GO terminology of DEGs in CEVd-infected citron plants, and found that some enriched GO terms are related to chitinase activity and cell wall, which coincides with the malformation symptoms of citron leaves. Early studies have reported that CEVd infection could change cell wall thickness of the epidermal cells, disorganize spongy and palisade mesophyll, and induce callose deposits in citron plants with the help of confocal laser scanning microscopy, which was confirmed by the enriched GO terms related to cell wall in the present study [13]. KEGG analysis also revealed that CEVd infection caused the differential expression of numerous genes involved in secondary metabolite biosynthesis. Phenylalanine ammonia lyase (PALY) is an important enzyme involved in the biosynthesis of secondary metabolites such as flavonoids [82]. In this study, the expression of the PALY gene increased in the CEVd-infected plants. Flavonoids are components of many phenolic secondary metabolites with a variety of biological functions such as defense against biotic stresses [83]. The observed upregulation of genes in the flavonoid biosynthetic pathway suggested that CEVd infection stimulated the accumulation of defense substances in citron.
In summary, we have studied the transcriptional profile of citron leaves infected with CEVd and healthy controls. Compared to uninfected leaves, CEVd infection triggers basic defense responses, destroys plant hormone homeostasis, induces the expression of key genes involved in RNA silencing, and affects cell wall and secondary metabolism in citron plants. Our findings will help elucidate the response mechanisms of woody plants against viroid infections and facilitate in the development of strategies to combat viroid diseases in fruit trees.
Supplementary Materials: The following are available online at http://www.mdpi.com/1999-4915/11/5/453/s1, Figure S1: Pearson correlation among samples. An R 2 value close to 1 indicates a high degree of correlation among samples. Figure S2: Cluster analysis of differentially expressed genes between CEVd infected citron plants and healthy control. The values of log 10 (FPKM + 1) are normalized (scale number) and clustered; red, high expression genes; blue, low expression genes; the red and blue colors represent the values of log 10 (FPKM + 1) from large to small. Table S1: Oligonucleotide primers used in RT-qPCR analysis.