High-Throughput Sequencing Reveals the Regulatory Networks of Transcriptome and Small RNAs During the Defense Against Marssonina brunnea in Poplar

Abstract

MicroRNAs are implicated in the adjustment of gene expression in plant response to biotic stresses. However, the regulatory networks of transcriptome and miRNAs are still poorly understood. In the present study, we ascertained the induction of genes for small RNA biosynthesis in poplar defense to a hemibiotrophic fungus Marssonina brunnea and afterward investigated the molecular regulatory networks by performing comprehensive sequencing analysis of mRNAs and small RNAs in M. brunnea-inoculated leaves. Differentially expressed genes in M. brunnea-infected poplar are mainly involved in secondary metabolisms, phytohormone pathways, the recognition of pathogens, and MAPK pathway in the plant, with real-time quantitative PCR (qPCR) validating the mRNA-seq results. Furthermore, differentially expressed miRNAs, such as MIR167_1-6, MIR167_1-12, MIR171_2-3, MIR395-13, MIR396-3, MIR396-16, MIR398-8, and MIR477-6, were identified. Through psRobot and TargetFinder programs, MIR167-1-6, MIR395-13, MIR396-3, MIR396-16, and MIR398-8 were annotated to modulate the expression of genes implicated in transportation, signaling, and biological responses of phytohormones and activation of antioxidants for plant immunity. Besides, validated differentially expressed genes involved in lignin generation, which were phenylalanine ammonia-lyase, ferulate-5-hydroxylase, cinnamyl alcohol dehydrogenase, and peroxidase 11, were selected as targets for the identification of novel miRNAs. Correspondingly, novel miRNAs, such as Novel MIR8567, Novel MIR3228, Novel MIR5913, and Novel MIR6493, were identified using the Mireap online program, which functions in the transcriptional regulation of lignin biosynthesis for poplar anti-fungal response. The present study underlines the roles of miRNAs in the regulation of transcriptome in the anti-fungal response of poplar and provides a new idea for molecular breeding of woody plants.

Identification of miRNAs Involving Potato-Phytophthora infestans Interaction

“…Most of known miRNAs and their function were consistent with previous work, such as miR156, miR159, miR171, miR5300, and miR6027 which were involved in plant immunity [ 9 , 34 , 35 , 36 ]. Some miRNAs could regulate R genes in plants directly, the miR482 family (stu-miR482a/d/e-3p and stu-miR482) mainly regulates NBS-LRR genes in eudicots, functioning as an essential component in plant disease resistance [ 37 ]; miR6024-3p regulates NLR genes to facilitate the disease caused by the necrotrophic pathogen [ 38 ].…”

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

“…The psRobot is focused on plant small RNA analysis, which has been widely used for target gene predictions ( Wu et al, 2012 ; Zhao et al, 2020 ; Liao et al, 2021 ). Therefore, we used its online version ( http://omicslab.genetics.ac.cn/psRobot/target_prediction_1.php/ ) to predict the potential target genes of miRNAs, using the default parameters ( Wu et al, 2012 ).…”

Transcriptome Analysis and Reactive Oxygen Species Detection Suggest Contrasting Molecular Mechanisms in Populus canadensis’ Response to Different Formae Speciales of Marssonina brunnea

“…In fact, a few studies have analyzed the interactions between M. brunnea and its poplar host. Through transcriptome sequencing, the gene expression patterns associated with different interaction systems, involving MU with susceptible and resistant Aigeiros hosts and MO with a susceptible Leuce host, were clearly revealed [18][19][20][21]. Using multigene association studies and physiological experiments, photosynthesis was proven to be closely related to the MLSP disease process [22,23].…”