Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 May 17;11(5):453.
doi: 10.3390/v11050453.

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

Yafei Wang  1   2 , Jiaxing Wu  3   4 , Yuanjian Qiu  5   6 , Sagheer Atta  7 , Changyong Zhou  8   9 , Mengji Cao  10   11
Affiliations

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

Yafei Wang et al. Viruses. .

Abstract

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.

Keywords: Citrus exocortis viroid (CEVd); RNA silencing; differentially expressed genes; innate immunity; transcriptome; ‘Etrog’ citron.

PubMed Disclaimer

Conflict of interest statement

The authors have no conflicts of interest to declare.

Figures

Figure 1
Figure 1
Primary and secondary structures of CEVd variant, and disease symptoms of citron plants infected with the CEVd variant. (A) The positions of nucleotides in CEVd variant used in this study that differ from CEVd-Reference (NC_001464). (B) One-step RT-PCR products of CEVd-infected citrus materials. (C) One-step RT-PCR analysis of CEVd-inoculated citron. (D) Northern blot hybridization using specific probes of nucleic acid preparations derived from CEVd-infected tomato leaves and healthy control. (E) Different symptoms between citron plants inoculated with the CEVd variant and healthy control. M, BM2000 DNA marker; 1 and 3, viroid-free samples; 2, CEVd-infected sample; 4, ‘Etrog’ citron inoculated with CEVd RNA transcripts; a, Northern blot; b, RNA control; HC, healthy control.
Figure 2
Figure 2
Disease symptoms of citron plants after grafting for 3 months.
Figure 3
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.
Figure 4
Figure 4
Schematic depiction of the antiviral RNA silencing pathway with differentially expressed genes and their mRNA fold change based on RNA-sequencing (RNA-seq) analysis are shown. DCL2, DICER-LIKE 2; AGO2, ARGONAUTE 2; AGO7, ARGONAUTE 7; RDR1, RNA-DEPENDENT RNA POLYMERASE 1; SDE3, SILENCING DEFECTIVE 3; RISC, RNA-induced silencing complex.
Figure 5
Figure 5
Validation of RNA-seq results by quantitative real-time PCR (RT-qPCR). Expression patterns of 12 representative genes as determined by RT-qPCR and RNA-seq. Normalization for RT-qPCR was performed using expression of the actin gene as an internal reference. CAHC: Carbonic anhydrase, chloroplastic; PAE8: Pectin acetylesterase 8; PLY5: Pectate lyase 5; LECR: Lectin-related protein; DCL2: Endoribonuclease Dicer homolog 2; SDE3: Silencing defective 3; MGL: Methionine gamma-lyase; PCNA: Proliferating cell nuclear antigen; GSTX2: Glutathione S-transferase; SAG12: Senescence-specific cysteine protease SAG12; PR4B: Pathogenesis-related protein PR-4B; GID1B: Gibberellin receptor GID1B.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Flores R., Minoia S., Carbonell A., Gisel A., Delgado S., López-Carrasco A., Navarro B., Serio F.D. Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Res. 2015;209:136–145. doi: 10.1016/j.virusres.2015.02.027. - DOI - PubMed
    1. Serra P., Messmer A., Sanderson D., James D., Flores R. Apple hammerhead viroid-like RNA is a bona fide viroid: autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid. Virus Res. 2018;249:8–15. doi: 10.1016/j.virusres.2018.03.001. - DOI - PubMed
    1. Duranvila N. Viroids as companions of a professional career. Viruses. 2019;11:245. doi: 10.3390/v11030245. - DOI - PMC - PubMed
    1. Flores R., Hernández C., Martínez de Alba A.E., Daròs J.A., Serio F.D. Viroids and viroid-host interactions. Annu. Rev. Phytopathol. 2005;43:117–139. doi: 10.1146/annurev.phyto.43.040204.140243. - DOI - PubMed
    1. Ding S.W. RNA-based antiviral immunity. Nat. Rev. Immunol. 2010;10:632–644. doi: 10.1038/nri2824. - DOI - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources