Exploring Tomato Fruit Viromes through Transcriptome Data Analysis

Abstract

This study delves into the complex landscape of viral infections in tomatoes (Solanum lycopersicum) using available transcriptome data. We conducted a virome analysis, revealing 219 viral contigs linked to four distinct viruses: tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato yellow leaf curl virus (TYLCV), and cucumber mosaic virus (CMV). Among these, ToCV predominated in contig count, followed by STV, TYLCV, and CMV. A notable finding was the prevalence of coinfections, emphasizing the concurrent presence of multiple viruses in tomato plants. Despite generally low viral levels in fruit transcriptomes, STV emerged as the primary virus based on viral read count. We delved deeper into viral abundance and the contributions of RNA segments to replication. While initially focused on studying the impact of sound treatment on tomato fruit transcriptomes, the unexpected viral presence underscores the importance of considering viruses in plant research. Geographical variations in virome communities hint at potential forensic applications. Phylogenetic analysis provided insights into viral origins and genetic diversity, enhancing our understanding of the Korean tomato virome. In conclusion, this study advances our knowledge of the tomato virome, stressing the need for robust pest control in greenhouse-grown tomatoes and offering insights into virus management and crop protection.

Keywords: coinfections; high-throughput sequencing; phylogenetic analysis; tomato fruit virome; viral diversity.

Figure 1

Overview of identified viruses based on viral contigs. (A) Distribution of viral contigs among identified viruses across 24 tomato transcriptomes; each virus is represented by a unique color. (B) Number of viral contigs detected in individual samples; the identified viruses are color-coded. (C) Distribution of viral contigs assigned to each identified virus. (D) Occurrence of identified viruses in the samples; for CMV and ToCV, the number of viral contigs assigned to each RNA segment is also displayed.

Figure 2

Overview of identified viruses based on viral reads. (A) Proportion of viral reads in each sample. (B) Distribution of viral reads among identified viruses across 24 tomato transcriptomes, color-coded according to the respective viruses. (C) Number of viral reads assigned to each identified virus in individual samples.

Figure 3

Proportion of identified viruses in each sample based on FPKM values. (A) Proportion of identified viruses in each sample based on FPKM values; different colors represent the identified viruses. (B) Proportion of ToCV RNA1 and RNA2 segments in the infected samples. (C) Pie chart displaying the proportion of three CMV RNA segments.

Figure 4

Viral abundance comparison based on FPKM values. (A) Comparative viral abundance in eight distinct conditions. The FPKM values from replicates were aggregated for each condition. (B) Viral abundance comparison between control and sound-treated samples. We examine the differences in viral abundance between control samples and those subjected to sound treatment. (C) Viral abundance comparison across replicates. We analyze the variation in viral abundance among different replicates to assess result consistency.

Figure 5

Alpha diversity of identified viruses in various conditions. (A,B) Alpha diversity comparison between control and sound-treated samples. The graph presents the alpha diversity of identified viruses in control samples versus those exposed to sound treatment, using both Shannon (A) and Simpson (B) diversity indices. (C,D) Alpha diversity among replicates. The alpha diversity of identified viruses was evaluated among different replicates, employing both Shannon (C) and Simpson (D) diversity indices. (E,F) Alpha diversity at four different time points. The alpha diversity of identified viruses was examined across four distinct time points, utilizing both Shannon (E) and Simpson (F) diversity indices.

Figure 6

Beta diversity of identified viruses across varied conditions. Beta diversity analysis was performed using PERMANOVA to assess the dissimilarity in viral communities under different conditions (A), across four time points (B), and among three replicates (C).

Figure 7

Principal coordinate analysis (PCoA) of viromes for individual samples across replicates.

Figure 8

Phylogenetic analysis of assembled CMV RNA segments and known CMV isolates. The phylogenetic relationship of the assembled CMV RNA segments with known CMV isolates was analyzed. Phylogenetic trees for CMV RNA1 (A), RNA2 (B), and RNA3 (C) were constructed using the maximum likelihood method, with 1000 bootstrap replicates to assess the robustness of the tree topologies. Red dots on the trees represent the assembled CMV RNA fragments obtained in this study. To ensure the accuracy of our analysis, we included only ten known CMV genome segments that exhibited high sequence similarity to the assembled CMV genome segments from this study in the phylogenetic tree construction.

Figure 9

Phylogenetic analysis of assembled ToCV RNA2 segments and known ToCV Isolates. The phylogenetic relationship between two assembled ToCV RNA2 segments in this study and known ToCV isolates was assessed. The phylogenetic tree of ToCV was constructed using the maximum likelihood method with 1000 bootstrap replicates. The assembled ToCV RNA2 fragments in this study are denoted by red dots. For the construction of the phylogenetic tree, ToCV RNA2 segment sequences covering entire ORFs, sourced from GenBank, were utilized. To simplify the phylogenetic tree, certain clades were compressed and represented as triangles. The complete phylogenetic tree can be found in Figure S1.

Figure 10

Phylogenetic analysis of assembled STV genomes and known STV Isolates. The phylogenetic relationship between 14 assembled STV genomes in this study and known STV isolates was examined. The phylogenetic tree of STV was generated using the maximum likelihood method with 1000 bootstrap replicates. The assembled STV genomes in this study are represented by red dots. For the construction of the phylogenetic tree, STV genome sequences covering entire ORFs, sourced from GenBank, were employed.