Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

Abstract

Background Long non-coding RNAs (lncRNAs) play essential roles in developmental processes and disease development at the transcriptional and post-transcriptional levels across diverse taxa. However, only few studies have profiled fungal lncRNAs in a genome-wide manner during host infection. Results Infection-associated lncRNAs were identified using lncRNA profiling over six stages of host infection (e.g., vegetative growth, pre-penetration, biotrophic, and necrotrophic stages) in the model pathogenic fungus, Magnaporthe oryzae. We identified 2,601 novel lncRNAs, including 1,286 antisense lncRNAs and 980 intergenic lncRNAs. Among the identified lncRNAs, 755 were expressed in a stage-specific manner and 560 were infection-specifically expressed lncRNAs (ISELs). To decipher the potential roles of lncRNAs during infection, we identified 365 protein-coding genes that were associated with 214 ISELs. Analysis of the predicted functions of these associated genes suggested that lncRNAs regulate pathogenesis-related genes, including xylanases and effectors. Conclusions The ISELs and their associated genes provide a comprehensive view of lncRNAs during fungal pathogen-plant interactions. This study expands new insights into the role of lncRNAs in the rice blast fungus, as well as other plant pathogenic fungi.

The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici

“…Although many fungal lncRNAs are intergenic [31, 35, 37], evidence from several fungal pathogens suggests that a large proportion of their lncRNAs could be antisense to protein-coding genes [35, 38, 111]. Surprisingly, only two antisense lncRNAs were identified using our approach.…”

Identification of Long Intergenic Noncoding RNAs in Rhizoctonia cerealis following Inoculation of Wheat

“…lncRNAs have been shown to play critical roles in diverse biological processes in a wide range of species. However, as for plant-pathogenic filamentous fungi, there are only a few studies on lncRNAs, including those of Ustilago maydis ( 27 ), Fusarium graminearum ( 28 ), Ustilaginoidea virens ( 13 ), Verticillium dahlia ( 21 ), and Magnaporthe oryzae ( 29 , 30 ). Naturally, the roles that lncRNAs can play in filamentous pathogenic fungi are less well known.…”

“…It is challenging to confirm the role of lncRNA in RNA-mediated gene regulation ( 31 ). Although thousands of lncRNAs have been identified in phytopathogens ( 13 , 21 , 29 , 32 – 34 ), only a few lncRNAs have been functionally characterized ( 13 , 21 , 33 ). Besides, functional genomics studies have lagged seriously, resulting from the lack of a genetic transformation system, which has hindered the functional verification of R. cerealis genes.…”

Comprehensive transcriptomic analysis of three varieties with different brown planthopper-resistance identifies leaf sheath lncRNAs in rice

“…Evidence is accumulating for a role of lncRNAs in the plant response to biotic stress [ 39 , 41 ]. In rice, lncRNAs response to several pathogens have been identified, such as Maganaporthe oryzae , Xanthomonas oryzae , Meloidogyne graminicola , and rice black-streaked dwarf virus [ 39 , 49 , 59 – 61 ]. In plant-insect interactions, Manduca sexta -elicited and armyworm-elicited lncRNA expression have been studied in wild tobacco and rice, individually [ 41 , 62 ].…”