Comparative Transcriptome Analysis Reveals the Transcriptional Alterations in Growth- and Development-Related Genes in Sweet Potato Plants Infected and Non-Infected by SPFMV, SPV2, and SPVG

Abstract

Field co-infection of multiple viruses results in considerable losses in the yield and quality of storage roots in sweet potato. However, little is known about the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses. Here, a comparative transcriptomic analysis was performed to reveal the transcriptional alterations in sweet potato plants infected (VCSP) and non-infected (VFSP) by Sweet potato mild mottle virus (SPFMV), Sweet potato virus Y (SPV2) and Sweet potato virus G (SPVG). A total of 1580 and 12,566 differentially expressed genes (DEGs) were identified in leaves and storage roots of VFSP and VCSP plants, respectively. In leaves, 707 upregulated and 773 downregulated genes were identified, whereas 5653 upregulated and 6913 downregulated genes were identified in storage roots. Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in chloroplast and photosynthesis and brassinosteroid (BR) biosynthesis in leaves and the vitamin biosynthetic process in storage roots was inhibited by co-infection of three viruses: SPFMV, SPV2, and SPVG. This was likely closely related to better photosynthesis and higher contents of Vitamin C (Vc) in storage roots of VFSP than that of VCSP. While some genes involved in ribosome and secondary metabolite-related pathways in leaves and alanine, aspartate, and glutamate metabolism in storage roots displayed higher expression in VCSP than in VFSP. Quantitative real-time PCR analysis demonstrated that the expression patterns of 26 DEGs, including 16 upregulated genes and 10 downregulated genes were consistent with the RNA-seq data from VFSP and VCSP. Taken together, this study integrates the results of morphology, physiology, and comparative transcriptome analyses in leaves and storage roots of VCSP and VFSP to reveal transcriptional alterations in growth- and development-related genes, providing new insight into the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses.

Keywords: SPV2 and SPVG; co-infection; gene ontology; pathway analysis; sweet potato plants infected by SPFMV; sweet potato plants non-infected by SPFMV; transcriptome profiling.

Figure 1

Phenotypes and growth indexes of sweet potato plants infected (VCSP) and non-infected (VFSP) leaves. (A) Phenotypes of VCSP and VFSP leaves. (B) Fluorescence images of VCSP and VFSP leaves. (C) Three virus genes were not detected in leaf and tuber of sweet potato. (D) Length and width of VCSP and VFSP leaves. (E) Content of chlorophyll a, b, and total chlorophyll. (F) Fv/Fm of VCSP and VFSP leaves. Three independent experimental replicates were analyzed for each treatment, and data are indicated as the mean ± SE (n = 3). Independent t-test was performed to check difference between VFSP and VCSP (** p < 0.01; * p < 0.05).

Figure 2

Comparison of yield and quality of VCSP and VFSP storage roots. (A) Content of starch. (B) Content of beta-carotene. (C) Content of vitamin C. (D) Yield of plot. Three independent experimental replicates were analyzed for each treatment, and data are indicated as the mean ± SE (n = 3). Independent t-test was performed to check difference between VFSP and VCSP (** p < 0.01; * p < 0.05).

Figure 3

Gene expression profile of leaves and storage roots in VCSP and VFSP.

Figure 4

Gene Ontology (GO) classification of differentially expressed genes (DEGs) identified. GO classification of differentially up-regulated genes of VFSP/VCSP (A) leaves and (B) storage roots. GO classification of differentially down-regulated genes of VFSP/VCSP (C) leaves and (D) storage roots.

Figure 4

Gene Ontology (GO) classification of differentially expressed genes (DEGs) identified. GO classification of differentially up-regulated genes of VFSP/VCSP (A) leaves and (B) storage roots. GO classification of differentially down-regulated genes of VFSP/VCSP (C) leaves and (D) storage roots.

Figure 4

Gene Ontology (GO) classification of differentially expressed genes (DEGs) identified. GO classification of differentially up-regulated genes of VFSP/VCSP (A) leaves and (B) storage roots. GO classification of differentially down-regulated genes of VFSP/VCSP (C) leaves and (D) storage roots.

Figure 5

Validation of differentially expressed candidate genes. A,B: qRT-PCR analysis of ten upregulated genes (A) and four downregulated genes (B) in VFSP and VCSP leaves. C,D: qRT-PCR analysis of six upregulated genes (C) and six downregulated genes (D) in VFSP and VCSP storage roots. Three independent experimental replicates were analyzed for each sample, and data are indicated as the mean ± SD (n = 3). Independent t-test was performed to check difference between VFSP and VCSP (p < 0.05 or p < 0.01). All differentially expressed genes displayed significant differences between VFSP and VCSP at 0.05 confidence level.

Figure 6

Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis of DEGs identified. KEGG Pathway enrichment analysis based on the differentially up-regulated genes between VFSP and VCSP (A) leaves and (B) storage roots. KEGG Pathway enrichment analysis based on the differentially down-regulated genes between VFSP and VCSP (C) leaves and (D) storage roots.

Figure 6

Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis of DEGs identified. KEGG Pathway enrichment analysis based on the differentially up-regulated genes between VFSP and VCSP (A) leaves and (B) storage roots. KEGG Pathway enrichment analysis based on the differentially down-regulated genes between VFSP and VCSP (C) leaves and (D) storage roots.

Figure 6

Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis of DEGs identified. KEGG Pathway enrichment analysis based on the differentially up-regulated genes between VFSP and VCSP (A) leaves and (B) storage roots. KEGG Pathway enrichment analysis based on the differentially down-regulated genes between VFSP and VCSP (C) leaves and (D) storage roots.

Figure 6

Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis of DEGs identified. KEGG Pathway enrichment analysis based on the differentially up-regulated genes between VFSP and VCSP (A) leaves and (B) storage roots. KEGG Pathway enrichment analysis based on the differentially down-regulated genes between VFSP and VCSP (C) leaves and (D) storage roots.