Simultaneous RNA-Seq Analysis of a Mixed Transcriptome of Rice and Blast Fungus Interaction

Abstract

A filamentous fungus, Magnaporthe oryzae, is a causal agent of rice blast disease, which is one of the most serious diseases affecting cultivated rice, Oryza sativa. However, the molecular mechanisms underlying both rice defense and fungal attack are not yet fully understood. Extensive past studies have characterized many infection-responsive genes in the pathogen and host plant, separately. To understand the plant-pathogen interaction comprehensively, it is valuable to monitor the gene expression profiles of both interacting organisms simultaneously in the same infected plant tissue. Although the host-pathogen interaction during the initial infection stage is important for the establishment of infection, the detection of fungal gene expression in infected leaves at the stage has been difficult because very few numbers of fungal cells are present. Using the emerging RNA-Seq technique, which has a wide dynamic range for expression analyses, we analyzed the mixed transcriptome of rice and blast fungus in infected leaves at 24 hours post-inoculation, which is the point when the primary infection hyphae penetrate leaf epidermal cells. We demonstrated that our method detected the gene expression of both the host plant and pathogen simultaneously in the same infected leaf blades in natural infection conditions without any artificial treatments. The upregulation of 240 fungal transcripts encoding putative secreted proteins was observed, suggesting that these candidates of fungal effector genes may play important roles in initial infection processes. The upregulation of transcripts encoding glycosyl hydrolases, cutinases and LysM domain-containing proteins were observed in the blast fungus, whereas pathogenesis-related and phytoalexin biosynthetic genes were upregulated in rice. Furthermore, more drastic changes in expression were observed in the incompatible interactions compared with the compatible ones in both rice and blast fungus at this stage. Our mixed transcriptome analysis is useful for the simultaneous elucidation of the tactics of host plant defense and pathogen attack.

Functional Annotation of Cotesia congregata Bracovirus: Identification of Viral Genes Expressed in Parasitized Host Immune Tissues

“…Few studies dedicated to parasite-host or pathogen-host biological systems have evaluated the transcript proportion produced by each protagonist during the course of the interaction. In a plant-fungal pathogen interaction, pathogenic fungal transcripts were estimated to represent 0.5% to 28% of the total transcripts analyzed (60,61). During the course of a baculovirus infection, viral mRNA in host cells increased from 3% to Ͼ80% of the total mRNA within the first 48 h after infection (52).…”

The Impact of Plant-Parasitic Nematodes on Agriculture and Methods of Control

“…Our general understanding of discreet molecular events involved in compatible (susceptible) and incompatible (resistant) plant-nematode interactions is limited in comparison to other signiicant host-pathogen associations. Recently, RNASequencing has been frequently used in plant pathological studies to proile gene expression paterns in host plants and pathogens [93,94]. Diferential genetic expression proiles of many speciic genes involved in plant immune responses has been shown in resistant and susceptible plants challenged by root-knot nematodes [48,95].…”

A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes

“…RNAseq analysis of host-pathogen interactions has already been successfully applied for eukaryotic pathogens [11][12][13][14][15] . Transcripts of eukaryotic pathogens, unlike bacteria, are polyadenylated, and occur with comparable abundance to the hosts.…”