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. 2023 Mar 30:14:1163679.
doi: 10.3389/fpls.2023.1163679. eCollection 2023.

Transcriptomic and functional analyses reveal the molecular mechanisms underlying Fe-mediated tobacco resistance to potato virus Y infection

Chuantao Xu  1   2 , Huiyan Guo  1 , Rui Li  1 , Xinyu Lan  1 , Yonghui Zhang  2 , Qiang Xie  2 , Di Zhu  3 , Qing Mu  3 , Zhiping Wang  1 , Mengnan An  1 , Zihao Xia  1 , Yuanhua Wu  1
Affiliations

Transcriptomic and functional analyses reveal the molecular mechanisms underlying Fe-mediated tobacco resistance to potato virus Y infection

Chuantao Xu et al. Front Plant Sci. .

Abstract

Potato virus Y (PVY) mainly infects Solanaceous crops, resulting in considerable losses in the yield and quality. Iron (Fe) is involved in various biological processes in plants, but its roles in resistance to PVY infection has not been reported. In this study, foliar application of Fe could effectively inhibit early infection of PVY, and a full-length transcriptome and Illumina RNA sequencing was performed to investigate its modes of action in PVY-infected Nicotiana tabacum. The results showed that 18,074 alternative splicing variants, 3,654 fusion transcripts, 3,086 long non-coding RNAs and 14,403 differentially expressed genes (DEGs) were identified. Specifically, Fe application down-regulated the expression levels of the DEGs related to phospholipid hydrolysis, phospholipid signal, cell wall biosynthesis, transcription factors (TFs) and photosystem I composition, while those involved with photosynthetic electron transport chain (PETC) were up-regulated at 1 day post inoculation (dpi). At 3 dpi, these DEGs related to photosystem II composition, PETC, molecular chaperones, protein degradation and some TFs were up-regulated, while those associated with light-harvesting, phospholipid hydrolysis, cell wall biosynthesis were down-regulated. At 9 dpi, Fe application had little effects on resistance to PVY infection and transcript profiles. Functional analysis of these potentially critical DEGs was thereafter performed using virus-induced gene silencing approaches and the results showed that NbCat-6A positively regulates PVY infection, while the reduced expressions of NbWRKY26, NbnsLTP, NbFAD3 and NbHSP90 significantly promote PVY infection in N. benthamiana. Our results elucidated the regulatory network of Fe-mediated resistance to PVY infection in plants, and the functional candidate genes also provide important theoretical bases to further improve host resistance against PVY infection.

Keywords: Fe; Illumina RNA sequencing; PVY; full-length transcriptome; virus-induced gene silencing.

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Conflict of interest statement

Authors CX, YZ and QX were employed by company Luzhou City Company of Sichuan Province Tobacco Company. Authors DZ and QM were employed by company Guizhou Qianxinan Prefectural Tobacco Company. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Foliar application of exogenous Fe alleviated PVY infection in tobacco plants. (A) Symptoms of the whole plant, leaves and stems at 7 dpi in four treatments. (B) Symptoms of the whole plant, leaves and stems at 9 dpi in four treatments. (C) The accumulation of PVY genomic RNA in tobacco leaves of PVY + H and PVY + Fe groups determined by RT-qPCR at 1, 3, 5, 7, and 9 dpi. Asterisks indicate statistically significant differences compared to control (Student’s t-test): *P < 0.05, **P < 0.01. (D) The accumulation of PVY CP protein in tobacco leaves of PVY + H and PVY + Fe groups determined by western blot assays at 1, 3, 5, 7, and 9 dpi.
Figure 2
Figure 2
Characterization of tobacco full-length transcripts by PacBio SMRT sequencing. (A) The number of CCS reads in different lengths. (B) The number of FLNC reads in different lengths. (C) The number of consensus reads in different lengths. (D) Number and categories of isoforms based on the PacBio platform.
Figure 3
Figure 3
Identification of alternative splicing (AS) events, alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) based on full-length transcriptome analyses. (A) Number and categories of AS events. (B) Number of genes with different APA sites. (C) Number of lncRNAs based on four analysis methods. (D) Number of various lncRNAs.
Figure 4
Figure 4
Comparative analyses of DEGs in different treatments at 1, 3, and 9 dpi. (A) The number of DEGs in five pairwise comparisons at 1, 3, and 9 dpi. (B) The overlapping DEGs in five pairwise comparisons at 1, 3, and 9 dpi showed by Venn diagram.
Figure 5
Figure 5
GO and KEGG enrichment analyses of DEGs. (A) GO analyses of DEGs in PVY + H vs. P + H at 3 and 9 dpi. (B) KEGG enrichment analyses of DEGs in PVY + H vs. P + H at 3 and 9 dpi. (C) GO analyses of DEGs in PVY + Fe vs. PVY + H at 1 and 3 dpi. (D) KEGG enrichment analyses of DEGs in PVY + Fe vs. PVY + H at 1 and 3 dpi.
Figure 6
Figure 6
Weighted correlation network analysis (WGCNA) of DEGs. (A) Hierarchical cluster tree and heatmap of all DEGs. The hierarchical cluster tree shows co-expression modules identified through WGCNA. Each leaf in the tree represents one DEG. The major tree branches constitute eight modules labeled with different colors. The heatmap shows the relative expressions of the whole DEGs in different modules. (B) Eigengene adjacency heatmap of the eight modules shows the correlations among different modules. The darker red represents a higher correlation. The numbers in individual cells represent the correlations. (C) Associations between modules and traits. The colors of the modules are the same as that shown in (A, B).
Figure 7
Figure 7
Heat map of the expression levels of DEGs involved in different pathways in tobacco. (A) DEGs in transcription factors. (B) DEGs in photosynthesis. (C) DEGs in lipid metabolism. (D) DEGs in protein processing in endoplasmic reticulum. (E) DEGs in cell wall biogenesis.
Figure 8
Figure 8
The expression levels of four genes determined by RT-qPCR under different treatments. Different lowercase letters indicate statistical difference between treatments. The statistical significances were determined using one-way analysis of variance followed by Duncan’s multiple comparison test (P value < 0.05).
Figure 9
Figure 9
Functional analyses of five homologous genes in resistance to PVY infection through TRV-based VIGS assays in N. benthamiana. (A) Disease symptoms on different gene-silenced N. benthamiana plants after PVY infection. (B) Close-up views of upper leaves indicated by white dash boxes in (A). (C) The accumulations of PVY genomic RNAs determined by RT-qPCR in different gene-silenced N. benthamiana. Asterisks indicate statistical difference between treatments, determined by the two-tailed t test (*, P < 0.05; **, P < 0.01). (D) The expression levels of PVY CP proteins in upper leaves of N. benthamiana. CP, coat protein; CBB, Coomassie brilliant blue. (E) Silencing efficiencies of target genes determined through RT-qPCR. Asterisks indicate statistical difference between treatments, determined by the two-tailed t test (*, P < 0.05; **, P < 0.01).
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References

    1. Abdel-Ghany S. E., Hamilton M., Jacobi J. L., Ngam P., Devitt N., Schilkey F., et al. . (2016). A survey of the sorghum transcriptome using single-molecule long reads. Nat. Commun. 7, 11706. doi: 10.1038/ncomms11706 - DOI - PMC - PubMed
    1. Al-Saharin R., Hellmann H., Mooney S. (2022). Plant E3 ligases and their role in abiotic stress response. Cells. 11, 890. doi: 10.3390/cells11050890 - DOI - PMC - PubMed
    1. Amorim L. L. B., da Fonseca Dos Santos R., Neto J. P. B., Guida-Santos M., Crovella S., Benko-Iseppon A. M. (2017). Transcription factors involved in plant resistance to pathogens. Curr. Protein Pept. Sci. 18, 335–351. doi: 10.2174/1389203717666160619185308 - DOI - PubMed
    1. Arnaud N., Murgia I., Boucherez J., Briat J. F., Cellier F., Gaymard F. (2006). An iron-induced nitric oxide burst precedes ubiquitin-dependent protein degradation for Arabidopsis AtFer1 ferritin gene expression. J. Biol. Chem. 281, 23579–23588. doi: 10.1074/jbc.M602135200 - DOI - PubMed
    1. Bacete L., Melida H., Miedes E., Molina A. (2018). Plant cell wall-mediated immunity: Cell wall changes trigger disease resistance responses. Plant J. 93, 614–636. doi: 10.1111/tpj.13807 - DOI - PubMed

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