Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae

Abstract

Background: Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection.

Results: Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi.

Conclusions: The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.

Keywords: Biological defense; Biotic stress; Ribosomal proteins; Transcriptional reprogramming; Translational regulation.

Fig. 1

Flow diagram outlining the experimental design and key steps in the process of the de novo transcriptome assembly for V. planifolia plants upon infection by Fov. Total RNA from non-treated (Control; C) and treated (2 and 10 dpi) plants were converted to cDNA and subjected to high- throughput sequencing. For details, see Materials and Methods

Fig. 2

Venn diagrams showing the degree of overlap between DEGs obtained with different methods. a Number of DEGs obtained by DESeq, DESeq2, NOISeq and EdgeR for data set at 2 dpi. b Number of DEGs obtained for data set at 10 dpi with the same methods as shown in a. Results from each method are shown with different colors

Fig. 3

Overall expression patterns of DEGs at 2 and 10 dpi. Heat maps of data sets at 2 (3420 DEGs) and 10 dpi (881 DEGs) are shown. The heat maps were made using the ggplot2 included in R package [36]

Fig. 4

MapMan analysis of DEGs showing their expression profiles at 2 and 10 dpi. a Heat map of DEGs at 2 dpi. b Heat map of DEGs at 10 dpi. The numbers correspond to different MapMan functional categories of gene ontology as described below: 1 PS, 2, major CHO metabolism, 3 minor CHO metabolism, 4 glycolysis, 6 gluconeogenese/glyoxylate cycle, 9 mitochondrial electron transport/ATP synthesis, 10 cell wall, 11 lipid metabolism, 12 N-metabolism, 13 amino acid metabolism, 15 metal handling, 16 secondary metabolism, 17 hormone metabolism, 18 Co-factor and vitamin metabolism, 20 stress, 21 redox, 22 polyamine metabolism, 23 nucleotide metabolism, 24 Biodegradation of Xenobiotics, 25 C1-metabolism, 26 misc., 27 RNA, 28 DNA, 29 protein, 30 signaling, 31 cell, 33 development, 34 transport, 35 not assigned

Fig. 5

Functional association networks among DEGs corresponding to 2 dpi. a Interactions among the up-regulated genes obtained with the STRING software [35]. b Interactions among the down-regulated genes. Colored lines between nodes indicate the various types of interaction: black line, co-expression; light blue line, association in curated databases; purple line, experimental

Fig. 6

Heat map of ribosomal proteins comparing datasets of 2 and 10 dpi. The heat maps were made using the ggplot2 included in R package [36]

Fig. 7

Overview of MapMan RNA-protein synthesis at 2 dpi. Transcript levels of translation-related genes (RPs, tRNAs, initiation factors and elongation factors) are shown. Upon invasion by Fov, induction of RPs leads to changes in ribosome composition, driving to selective translation of certain transcripts