Characteristic Dissection of Xanthomonas oryzae pv. oryzae Responsive MicroRNAs in Rice

Abstract

MicroRNAs (miRNAs) are crucial player in plant-pathogen interaction. While the evidence has demonstrated that rice miRNAs mediate immune response to pathogens invasion, the roles of miRNAs on Xanthomonas oryzae pv. oryzae (Xoo) attack remain be in place. Herein, we monitored the responsive changes of rice miRNAs at 0, 8, 24 h across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. The faithfulness of sequencing data was validated through quantitative real-time stem-loop reverse transcription-polymerase chain reaction assay. Bioinformatic analysis showed that the differentially expressed miRNAs could be divided into three immunity-related clusters, and 80 regulatory units were emerged in infection process, which comprises 29 differentially expressed known miRNAs and 38 cleaved targets. Furthermore, the miRNA presumptive function of separate immunity cluster in rice-Xoo interplay was confirmed through overexpressing osa-miR164a, osa-miR167d and osa-miR159b, and the disruption of regulatory units, osa-miR164a/OsNAC60, osa-miR167d-5p/OsWD40-174 and osa-miR159b/OsMYBGA, OsLRR-RLK2, OsMPK20-4, may reset rice defense response to Xoo infestation in a controllable manner. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.

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

“…We found that 24 nt miRNAs were the most frequent form, followed by 21 nt sRNAs. These patterns of length distribution have also been identified in rice and barley (Hackenberg et al, 2015;Jia et al, 2020). Moreover, the first position in 18-25 nt miRNAs was predominantly U.…”

Identification and Characterization of Rice Circular RNAs Responding to Xanthomonas Oryzae pv. Oryzae Invasion

“…To observe whether the transcriptional regulatory events occurred in rice-Xoo interactions, we checked the expression pro les of OsPR1a and OsPR1b by RT-qPCR using speci c primers (Table S6) at different time points post inoculation (hpi) with PXO99 A . The levels of the OsPR1a and OsPR1b transcripts showed a similar induction pro le (Figure S1), which is consistent with the defense-responsive expression in previous report (Jia et al 2020). Their transcript levels slightly induced at 2 hpi and 6 hpi or markedly increased at 12 hpi and decreased drastically at 24 hpi (Figure S1).…”

An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

“…These observations are incompatible with the possibility that xisRNA loci correspond to canonical MIRNA genes. Previous work has identified differentially accumulating rice miRNA during Asian Xoo infection (21, 22), it was therefore surprising that no xisRNA locus corresponded to a MIRNA . This may be due to differences in the way rice responds to Asian versus African Xoo strains or in sRNA-seq data analysis methods.…”

“…xisRNA loci correspond to canonical MIRNA genes. Previous work has identified differentially accumulating rice miRNA during Asian Xoo infection (21,22), it was therefore surprising that no…”

“…With a few exceptions, such as Arabidopsis AtlsiRNA-1 corresponding to a novel class of 30–40 nt long siRNAs and nat-siRNAATGB2 that contribute to the ETI launched after recognition of a bacterial effector (7), the available functional data on the role of endogenous plant sRNAs in regulating the disease process has focused almost exclusively on miRNAs and their role in promoting immunity. For example, in rice, the expression of multiple miRNAs changes in response to the blast fungus Magnaporthe oryzae (20) and Xoo (21, 22). Here, we aimed at examining all sRNAs associated with the disease process at a genome-wide scale and used an unbiased small RNA deep-sequencing data analysis approach on rice inoculated with Xo strains.…”