Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

Abstract

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

“…Further, expression profiling analysis identified 729 up-regulated and 721 down-regulated lncRNAs under B deficiency stress. Functional validation of selected lncRNAs shed light on the target genes involved in the calcium signaling and plant hormone signal transduction pathways under B deficiency stress in Poncirus trifoliata [98].…”

“…Among the various micronutrients, boron (B) is an essential micronutrient for plant growth and development, membrane integrity, and cell wall synthesis [ 137 – 139 ]. Genome-wide exploration of lncRNA regulating B deficiency response in Poncirus trifoliata through strand-specific deep transcriptome analysis detected 2101 unique lncRNAs [ 98 ]. Further, expression profiling analysis identified 729 up-regulated and 721 down-regulated lncRNAs under B deficiency stress.…”

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

“…The emerging evidence suggests that B’s molecular regulation is complicated, limited to coding genes, and attributed to lncRNAs, a novel regulatory player in the regulation of gene expression. A genome-scale exploration of lncRNAs in response to B toxicity detected ~8000 lncRNAs [ 137 ], whereas under B deficiency conditions in P. trifoliata 2101 lncRNAs were detected, of which 729 were upregulated and 721 were downregulated [ 138 ].…”

LncRNA Landscape of Coronary Atherosclerosis Reveals Differentially Expressed LncRNAs in Proliferation and Migration of Coronary Artery Smooth Muscle Cells

“…Therefore, the Fanconi anemia pathway might regulate the proliferation and apoptosis of coronary endothelial cells and smooth muscle cells that are associated with atherosclerotic pathology ( Wolf and Hunziker, 2020 ). Previous research indicated that lncRNA can cis- or trans-regulate the expression of target genes, which is the main regulation mechanism of lncRNA ( Zhou G. F. et al, 2019 ). The coexpressed target genes in our study are on different chromosomes from the correlated lncRNA, which suggest that these lncRNAs trans-regulate the target genes to affect the occurrence and development of atherosclerosis.…”