Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction

Abstract

The interactions between plants and microorganisms, which are widely present in the microbial-dominated rhizosphere, have been studied. This association is highly beneficial to the organisms involved, as plants benefit soil microorganisms by providing them with metabolites, while microorganisms promote plant growth and development by promoting nutrient uptake and/or protecting the plant from biotic and abiotic stresses. Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, an interaction between barley and the P. indica was established to elucidate microRNA (miRNA)-based regulatory changes in miRNA profiles and gene expression that occurred during the symbiosis. Growth promotion and vigorous root development were confirmed in barley colonized by P. indica. The genome-wide expression profile analysis of miRNAs in barley root showed that 7,798,928, 6,418,039 and 7,136,192 clean reads were obtained from the libraries of mock, 3 dai and 7 dai roots, respectively. Sequencing of the barley genome yielded in 81 novel miRNA and 450 differently expressed genes (DEGs). Additionally, 11, 24, 6 differentially expressed microRNAs (DEMs) in barley were found in the three comparison groups, including 3 dai vs. mock, 7 dai vs. mock and 7 dai vs. 3 dai, respectively. The predicted target genes of these miRNAs are mainly involved in transcription, cell division, auxin signal perception and transduction, photosynthesis and hormone stimulus. Transcriptome analysis of P. indica identified 667 and 594 differentially expressed genes (DEG) at 3 dai and 7 dai. Annotation and GO (Gene Ontology) analysis indicated that the DEGs with the greatest changes were concentrated in oxidoreductase activity, ion transmembrane transporter activity. It implies that reprogramming of fundamental miRNA and gene expression occurs both in barley and P. indica. Analysis of global changes in miRNA profiles of barley colonized with P. indica revealed that several putative endogenous barley miRNAs expressed upon colonization belonging to known micro RNA families involved in growth and developmental regulation.

Identification and Characterization of a Plant Endophytic Fungus Paraphaosphaeria sp. JRF11 and Its Growth-Promoting Effects

“…In addition, oxygen level is involved in many important signaling responses and is beneficial to plants by supporting cellular proliferation, physiological function, and viability [48,49]. Similarly, transcriptome analysis of Piriformospora indica indicated that the DEGs with the greatest changes were concentrated in oxidoreductase activity and ion transmembrane transporter activity [50]. KEGG enrichment analysis was also used to understand the DEGs after JRF11 treatment.…”

Detection of closely linked QTLs and candidate genes controlling germination indices in response to drought and salinity stresses in barley

“…In a study, hvu-miR6214 was predicted to target genes involved in photosynthesis pathway, cell division and hormone activity. Therefore, it is associated with plant development and growth 47 . The results showed that hvu-miR159a and hvu-miR159b were associated with some of target genes.…”

Research Progress of Piriformospora indica in Improving Plant Growth and Stress Resistance to Plant

“…The miRNA profiles involved in the interaction between barley and P. indica have been extensively studied, identifying 42 miRNAs through transcriptome sequencing and annotation analysis. These miRNAs are predominantly associated with the target genes that are implicated in cell division, auxin signal reception, and hormone response, thus exerting a pivotal role in the organism's adaptive response to both biotic and abiotic stressors [105]. Furthermore, the effector molecule PIIN_08944 originating from P. indica has been confirmed to interfere with the salicylic acid (SA)-mediated basal immune responses of the host plant [106].…”