Combined analysis of mRNA and miRNA transcriptomes reveals the regulatory mechanism of Xanthomonas arboricola pv pruni resistance in Prunus persica

Abstract

Background: Peach bacterial shot hole, caused by Xanthomonas arboricola pv pruni (Xap), is a global bacterial disease that poses a threat to the yield and quality of cultivated peach trees (Prunus persica).

Results: This study compared the mRNA and miRNA profiles of two peach varieties, 'Yanbao' (resistant) and 'Yingzui' (susceptible), after inoculation with Xap to identify miRNAs and target genes associated with peach tree resistance. mRNA sequencing results revealed that in the S0-vs-S3 comparison group, 1574 genes were upregulated and 3975 genes were downregulated. In the R0-vs-R3 comparison group, 1575 genes were upregulated and 3726 genes were downregulated. Through miRNA sequencing, a total of 112 known miRNAs belonging to 70 miRNA families and 111 new miRNAs were identified. Notably, some miRNAs were exclusively expressed in either resistant or susceptible varieties. Additionally, 59 miRNAs were downregulated and 69 miRNAs were upregulated in the R0-vs-R3 comparison group, while 46 miRNAs were downregulated and 52 miRNAs were upregulated in the S0-vs-S3 comparison group. Joint analysis of mRNA and miRNA identified 79 relationship pairs in the S0-vs-S3 comparison group, consisting of 48 miRNAs and 51 target genes. In the R0-vs-R3 comparison group, there were 58 relationship pairs, comprising 28 miRNAs and 20 target genes. Several target genes related to resistance, such as SPL6, TIFY6B, and Prupe.4G041800_v2.0.a1 (PPO), were identified through literature reports and GO/KEGG enrichment analysis.

Conclusion: In conclusion, this study discovered several candidate genes involved in peach tree resistance by analyzing differential expression of mRNA and miRNA. These findings provide valuable insights into the mechanisms underlying resistance to Xap in peach trees.

Keywords: Xanthomonas arboricola pv. pruni; Peach; mRNA; miRNA.

Fig. 1

A Symptoms of peach leaves after 3d and 5d of inoculation. B Statistics of lesion area of different varieties. The error line represents the standard deviation of three biological replicates. The t-test was used to test the significance of the difference in data, and * * * indicated p < 0.001

Fig. 2

A The number of differential genes in the comparison group. B Wayne diagram of differentially expressed genes in the comparison group

Fig. 3

A, B GO Enrichment Bubble Plot. Bubble size represents the number of differentially expressed genes enriched in the GO term. Bubble color represents the significance of enrichment in the GO term, with larger values indicating greater significance. The x-axis represents the Gene Ratio, which is calculated as the number of differentially expressed genes enriched in the GO term divided by the number of differentially expressed genes enriched in the GO term in the background gene set

Fig. 4

A, B KEGG Enrichment Bubble Diagram: To plot, use the top 20 pathways with the smallest Q-value. The pathway names are shown on the y-axis, the enrichment factor is shown on the x-axis, and the size of the bubble represents the number of genes enriched in the pathway. The bubbles are colored from red to blue, with smaller Q-values represented by larger bubbles

Fig. 5

Sequencing verification and qPCR verification. r indicate the correlation coefficient

Fig. 6

Analysis results of differentially expressed miRNAs. A Number of upregulated and downregulated miRNAs in the comparison group. Blue represents upregulated miRNAs, while red represents downregulated miRNAs. B Overlapping regions indicate the number of genes shared between groups or comparison groups, while nonoverlapping regions represent genes that are unique to each group or comparison group. C Heatmap showing the expression of miRNAs that are significantly and differentially expressed

Fig. 7

A, B Enrichment circle plot for differentially expressed miRNA target genes. The first circle shows the top 20 enriched Gene Ontology (GO) terms and the number of genes associated with each term. Different colors represent different GO categories. The second circle displays the number of background genes for each GO term, as well as Q-values. The strip length represents the number of genes, and the color red indicates smaller Q-values. The third circle includes a bar chart displaying the upregulated/downregulated gene ratio, the dark purple bars representing the upregulated gene ratio, and the light purple bars representing the downregulated gene ratio. The values are shown below the chart. The fourth circle shows the Rich Factor values for each GO term

Fig. 8

A, B KEGG enrichment analysis for differentially expressed miRNA target genes. The FDR values indicating the significance of various pathways were plotted, with the x-axis representing gene ratio and the y-axis representing pathway names. Each bubble represents a pathway, with the size of the bubble indicating the number of genes associated with that pathway. The color of the bubble indicates the enrichment significance of the pathway, represented by the size of the FDR value

Fig. 9

The results of miRNA t arget gene analysis (A) and (B) predicted the number of miRNAs and target genes of target genes. The abscissa is the name information, pair represents the relationship between miRNA and target gene, miRNA is the predicted target gene miRNA, and target represents the target gene. The ordinate represents the quantity. The abscissa represents the number of bound miRNAs, and the ordinate represents the number of genes regulated by miRNAs. C and D Negative correlation miRNA‒target gene regulatory network diagram