Integrated Analysis of MicroRNA and Target Genes in Brachypodium distachyon Infected by Magnaporthe oryzae by Small RNA and Degradome Sequencing

Abstract

Rice blast caused by Magnaporthe oryzae is one of the most important diseases that seriously threaten rice production. Brachypodium distachyon is a grass species closely related to grain crops, such as rice, barley, and wheat, and has become a new model plant of Gramineae. In this study, 15 small RNA samples were sequenced to examine the dynamic changes in microRNA (miRNA) expression in B. distachyon infected by M. oryzae at 0, 24, and 48 h after inoculation. We identified 432 conserved miRNAs and 288 predicted candidate miRNAs in B. distachyon. Additionally, there were 7 and 19 differentially expressed miRNAs at 24 and 48 h post-inoculation, respectively. Furthermore, using degradome sequencing, we identified 2,126 genes as targets for 308 miRNAs; using quantitative real-time PCR (qRT-PCR), we validated five miRNA/target regulatory units involved in B. distachyon–M. oryzae interactions. Moreover, using co-transformation technology, we demonstrated that BdNAC21 was negatively regulated by miR164c. This study provides a new approach for identifying resistance genes in B. distachyon by mining the miRNA regulatory network of host–pathogen interactions.

Transcriptome and Metabolome Analyses of Salt Stress Response in Cotton (Gossypium hirsutum) Seed Pretreated with NaCl

“…In the recent decade, bioinformatics tools and next-generation sequencing (NGS) technologies have made significant advancements that aided in identifying and characterization of related differentially expressed genes (DEGs). For example, as shown in previous research investigations, a substantial amount of up-and down-regulated genes were discovered with Solexa sequencing [42], and TFs, unigenes, and miRNAs were identified through Illumina sequencing [43] in cotton accessions grown in the NaCl stressed environments.…”

“…A sum of 1799 transcription factors was found in the discovered DEGs' functional annotations. A significant count of ethyleneresponsive transcription factors ERF (205) was identified with differential expressions, followed by zinc finger CCCH domain (167), WRKY (151), bHLH (101), MYB (92), NAC domain-containing protein and TF (83), GATA (43), scarecrow-like proteins (40), auxinresponsive protein (30), MADs-box (23), bZIP (27), HHO (13), and many others in the pre-treated cotton seedling samples (Table S7).…”

“…The results showed that there was good consistency between expression levels of the eight genes analyzed using qRT-PCR and their levels detected using RNA-seq (Figure 5). 92), NAC domain-containing protein and TF (83), GATA (43), scarecrow-like proteins (40), auxin-responsive protein (30), MADs-box (23), bZIP (27), HHO (13), and many others in the pre-treated cotton seedling samples (Table S7).…”

TALE Transcription Factors in Sweet Orange (Citrus sinensis): Genome-Wide Identification, Characterization, and Expression in Response to Biotic and Abiotic Stresses

“…All qRT-PCR reactions were run and analyzed using a CFX96 Touch Deep Well Real-Time PCR Detection System (Bio-Rad, Munich, Germany) with a SYBR Green PCR Mastermix (Solarbio, Beijing, China). qRT-PCR was conducted following standard procedures and conditions as previously described ( Peng et al, 2021b ). qRT-PCR gene-specific primers were designed using Oligo7 software ( Supplementary Table 7 ).…”

Identification and characterization of pathogenicity-related genes of Rhizoctonia solani AG3 during tobacco infection

“…High-throughput omics technology provides deeper insights into biological system responses to complex perturbations and is an attractive tool for plant–pathogen interaction research ( Peng et al., 2021 ). RNA sequencing (RNA-seq) is a proximity bias–free measure that can be used to objectively and exhaustively investigate fluctuations in the transcript abundance of an organism in a more precise manner than oligonucleotide array hybridization ( Zhang, 2021 ).…”