Dual RNA Sequencing Reveals the Genome-Wide Expression Profiles During the Compatible and Incompatible Interactions Between Solanum tuberosum and Phytophthora infestans

Abstract

Late blight, caused by Phytophthora infestans (P. infestans), is a devastating plant disease. P. infestans genome encodes hundreds of effectors, complicating the interaction between the pathogen and its host and making it difficult to understand the interaction mechanisms. In this study, the late blight-resistant potato cultivar Ziyun No.1 and the susceptible potato cultivar Favorita were infected with P. infestans isolate SCPZ16-3-1 to investigate the global expression profiles during the compatible and incompatible interactions using dual RNA sequencing (RNA-seq). Most of the expressed Arg-X-Leu-Arg (RXLR) effector genes were suppressed during the first 24 h of infection, but upregulated after 24 h. Moreover, P. infestans induced more specifically expressed genes (SEGs), including RXLR effectors and cell wall-degrading enzymes (CWDEs)-encoding genes, in the compatible interaction. The resistant potato activated a set of biotic stimulus responses and phenylpropanoid biosynthesis SEGs, including kirola-like protein, nucleotide-binding site-leucine-rich repeat (NBS-LRR), disease resistance, and kinase genes. Conversely, the susceptible potato cultivar upregulated more kinase, pathogenesis-related genes than the resistant cultivar. This study is the first study to characterize the compatible and incompatible interactions between P. infestans and different potato cultivars and provides the genome-wide expression profiles for RXLR effector, CWDEs, NBS-LRR protein, and kinase-encoding genes.

Keywords: Phytophthora infestans; compatible interaction; different potato cultivars; dual RNA-seq; incompatible interaction.

FIGURE 1

Infection response and global transcriptomic response of Phytophthora infestans (P. infestans). (A) phenotypic responses of Solanum tuberosum cv. Favorita and Ziyun No.1 to the infection of P. infestans. (B) Principal coordinates analysis (PCoA) of P. infestans genes. (C) Venn diagrams of the P. infestans genes expressed in different samples. Hbi, hours before inoculation; hpi, hours post-inoculation. R1, R2, and R3 present samples collected at 0 hbi, 24 hpi, and 48 hpi in incompatible interaction. S1, S2, and S3 present samples collected at 0 hbi, 24 hpi, and 48 hpi in compatible interaction. P presents zoospore sample of P. infestans.

FIGURE 2

The Gene Ontology (GO) enrichment of the pathogen specifically expressed genes (SEGs) (A) and potato SEGs (B) identified from compatible interaction. Hypergeometric tests were performed with a threshold value of false discovery rate (FDR) < 0.05 based on the GO classification of 224 pathogen (A) and 1,312 potato (B) SEGs.

FIGURE 3

Expression trend of the potato SEGs identified from incompatible interaction. The 1,180 SEGs were identified in Ziyun No.1 when compared with the susceptible cultivar Favorita. Trend analyses were performed based on the expression levels of the 1,180 SEGs at 0 hbi, 24 hpi, and 48 hpi using the OmicShare tools, a free online platform for data analysis (https://www.omicshare.com/tools).

FIGURE 4

Expression patterns of the effector genes in P. infestans during the infection. The log₂FC values were calculated based on the expression levels and used to draw heatmaps by HemI (version 1.0) (Deng et al., 2014). (A) Venn diagram of the 208 Arg-X-Leu-Arg (RXLR) effector genes. (B) Venn diagram of the 146 RXLR effector genes. (C) Heatmap of the 208 RXLR effector genes. (D) Heatmap of the 146 CRN effector genes.

FIGURE 5

Expression patterns of the differentially expressed cell wall-degrading enzyme (CWDE)-encoding genes. Sequences of CWDEs, including AA17, cellulase, pectin lyases, and pectate lyases, were submitted to MEGA 11 to draw a neighbor-joining tree (Tamura et al., 2021). The log₂FC values of the CWDE genes were calculated based on the expression levels and used to draw heatmaps by HemI (version 1.0) (Deng et al., 2014).

FIGURE 6

Expression patterns of nucleotide-binding site-leucine-rich repeat (NBS-LRR) and pathogenesis-related protein-encoding genes. Sequences of NBS-LRR and pathogenesis-related proteins were submitted to MEGA 11 to draw a neighbor-joining tree (Tamura et al., 2021). The log₂FC values of the encoding genes of these proteins were calculated based on the expression levels and used to draw heatmaps by HemI (version 1.0) (Deng et al., 2014). From top to bottom, PGSC0003DMG401015877 to PGSC0003DMG400017086 are NBS-LRR genes and PGSC0003DMG400015388 to PGSC0003DMG400023922 are pathogenesis-related protein-encoding genes.