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. 2017 May 10;12(5):e0175391.
doi: 10.1371/journal.pone.0175391. eCollection 2017.

RNA-seq approach to analysis of gene expression profiles in dark green islands and light green tissues of Cucumber mosaic virus-infected Nicotiana tabacum

Lijuan Chen  1 , Chunyan Fei  1 , Lin Zhu  1 , Zhenpeng Xu  1 , Wenshan Zou  1 , Ting Yang  1 , Honghui Lin  1 , Dehui Xi  1
Affiliations

RNA-seq approach to analysis of gene expression profiles in dark green islands and light green tissues of Cucumber mosaic virus-infected Nicotiana tabacum

Lijuan Chen et al. PLoS One. .

Abstract

Dark green islands (DGIs) surrounded by light green tissues (LGTs) are common leaf symptoms of plants that are systemically infected by various viruses that induce leaf mosaic in infected plants. The inoculation of Cucumber mosaic virus (CMV) in Nicotiana tabacum produced a commonly occurring sequence of classic patterns of DGIs and LGTs. Previous studies confirmed that there are significant differences between DGIs and LGTs in terms of physiology, biochemistry and molecular biology, but the mechanisms by which DGIs form remain unclear. To investigate the global gene expression changes that occur in these special tissues, individual differential gene expression tag libraries were constructed from three total RNA samples isolated from DGIs, LGTs and control plants (CK) and were sequenced using an Illumina HiSeqTM 2000. An analysis of differentially expressed genes (DEGs) and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. These analyses revealed the differences between DGIs, LGTs and CK. GO enrichment and KEGG pathway analyses suggested that several pathways related to photosynthesis and chlorophyll metabolism were enriched in DGIs compared to LGTs and CK. Several pathways related to apoptosis were significantly up-regulated in LGTs compared to DGIs. Additionally, we identified sets of DEGs that may be related to the formation or development of DGIs and LGTs. Our systematic analyses provide comprehensive transcriptomic information regarding DGIs and LGTs in CMV-infected N. tabacum. These data will help characterize the detailed mechanisms of DGI and LGT formation.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1
(a) Symptoms of N. tabacum leaves systemically infected with CMV. CK, N. tabacum were mock inoculated with phosphate buffer; DGI, dark green tissues of CMV-infected N. tabacum; LGT, light green tissue of CMV- infected N. tabacum; (b) Venn diagram of DEGs between three comparisons (DGI vs. CK, LGT vs. CK and LGT vs. DGI). The sum of the numbers in each large circle represents total number of differentially expressed genes between combinations, the overlap part of the circles represents common differentially expressed genes between combinations.
Fig 2
Fig 2. Histogram of Gene Ontology classification.
The results are summarized in three main categories: biological process (BP), cellular component (CC), and molecular function (MF). The left Y-axis indicates the percentage of a specific category of genes in that main category. The right Y-axis indicates the number of genes in a category.
Fig 3
Fig 3. Functional classification and pathway assignment of unigenes by KEGG.
Fig 4
Fig 4. Validation of the DGE analysis by quantitative real-time polymerase chain reaction (qRT-PCR).
Error bars represent the standard deviations of qRT-PCR signals (n = 3).
See this image and copyright information in PMC

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