Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots

Abstract

Recently, long noncoding RNAs (lncRNAs) have emerged as vital regulators of many biological processes in animals and plants. However, to our knowledge no investigations on plant lncRNAs which respond to arbuscular mycorrhizal (AM) fungi have been reported thus far. In this study, maize roots colonized with AM fungus were analyzed by strand-specific RNA-Seq to identify AM fungi-responsive lncRNAs and construct an associated regulatory network. A total of 1837 differentially expressed protein coding genes (DEGs) were identified from maize roots with Rhizophagus irregularis inoculation. Many AM fungi-responsive genes were homologs to MtPt4, STR, STR2, MtFatM, and enriched pathways such as fatty acid biosynthesis, response to phosphate starvation, and nitrogen metabolism are consistent with previous studies. In total, 5941 lncRNAs were identified, of which more than 3000 were new. Of those, 63 lncRNAs were differentially expressed. The putative target genes of differentially expressed lncRNAs (DELs) were mainly related to phosphate ion transmembrane transport, cellular response to potassium ion starvation, and lipid catabolic processes. Regulatory network analysis showed that DELs might be involved in the regulation of bidirectional nutrient exchange between plant and AM fungi as mimicry of microRNA targets. The results of this study can broaden our knowledge on the interaction between plant and AM fungi.

Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase

“…A point of special interest in this study is the detailed genomic description of thousands (5929) of lncRNA loci that make up over 34 % of the total genes occurring in the S. schenckii genome. A similar number has been reported recently in other fungal genomes [41,42], but their abundance may vary widely among different species with different genome sizes [43]. However, the real occurrence of lncRNAs in fungi is, currently, likely underestimated, because the detection of these regulatory elements largely depends on the type of experimental condition examined and on the sequenced transcripts which, as in our study, are often poly(A) selected; thus, precluding the possibility of capturing the non-polyadenylated lncRNAs [44].…”

Brassinosteroid Priming Improves Peanut Drought Tolerance via Eliminating Inhibition on Genes in Photosynthesis and Hormone Signaling

“…Many known additional regulations in other plants could be also involved in the BR priming, including small RNA regulation [ 43 , 63 , 64 , 65 , 66 ], lncRNA regulation [ 67 ], alternative splicing in transcripts [ 65 , 68 ], and methylation regulation [ 69 ]. These additional regulations may work in a network manner under drought stress after BR-priming and are worth of dissecting in future using omics methods [ 70 , 71 ].…”

Mining endophytic microbiome information from plant and animal transcriptome data

“…In our previous study, the maize ( Zea mays ) roots inoculated with AM fungus Rhizophagus irregularis DAOM-197198 (previously known as Glomus intraradices ) were compared with the control without fungal inoculation (Han, et al, 2019). The maize raw RNA-Seq data (Bioproject accession: PRJNA553580) were used in this study.…”

“…In addition, many endophytes can protect plants from microbial pathogens by the production of ammonia, hydrogen cyanide, and siderophores (Ali, et al, 2021; Carrion, et al, 2019; Lata, et al, 2019). Pathogenic fungi and symbiotic fungi can also penetrate plant cells for absorption or exchange of nutrients (Han, et al, 2019; Han, et al, 2020).…”