ceRNA Cross-Talk in Paulownia Witches’ Broom Disease

Fan, Guoqiang; Wang, Zhe; Zhai, Xiaoqiao; Cao, Yabing

doi:10.3390/ijms19082463

Cited by 14 publications

(9 citation statements)

References 71 publications

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“…PaWB is a serious disease of Paulownia, which greatly reduces the growth and biomass of P. fortunei . In recent years, some genes related to the occurrence of PaWB have been discovered [ 25 , 41 , 42 , 43 ], including the MADS-box gene, but there is no systematic report on the MADS-box family of P. fortunei. Therefore, the focus of this study was to explore the PfMADS-box gene’s probable molecular functions in the development of PaWB.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection

Deng

Dong

et al. 2023

Genes

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Paulownia witches’ broom (PaWB), caused by phytoplasmas, is the most devastating infectious disease of Paulownia. Although a few MADS-box transcription factors have been reported to be involved in the formation of PaWB, there has been little investigation into all of the MADS-box gene family in Paulownia. The objective of this study is to identify the MADS-box gene family in Paulownia fortunei on a genome-wide scale and explore their response to PaWB infection. Bioinformatics software were used for identification, characterization, subcellular localization, phylogenetic analysis, the prediction of conserved motifs, gene structures, cis-elements, and protein-protein interaction network construction. The tissue expression profiling of PfMADS-box genes was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Transcriptome data and the protein interaction network prediction were combined to screen the genes associated with PaWB formation. We identified 89 MADS-box genes in the P. fortunei genome and categorized them into 14 subfamilies. The comprehensive analysis showed that segment duplication events had significant effects on the evolution of the PfMADS-box gene family; the motif distribution of proteins in the same subfamily are similar; development-related, phytohormone-responsive, and stress-related cis-elements were enriched in the promoter regions. The tissue expression pattern of PfMADS-box genes suggested that they underwent subfunctional differentiation. Three genes, PfMADS3, PfMADS57, and PfMADS87, might be related to the occurrence of PaWB. These results will provide a valuable resource to explore the potential functions of PfMADS-box genes and lay a solid foundation for understanding the roles of PfMADS-box genes in paulownia–phytoplasma interactions.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection

Deng

Dong

et al. 2023

Genes

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“…Associations among mRNAs, miRNAs, lncRNAs, and circRNAs modulate gene expression, and thus, the competitive endogenous RNA (ceRNA) hypothesis was put forth ( Salmena et al., 2011 ). The ceRNA axis was generated and examined in numerous plants, demonstrating crucial functions in plant growth ( Fan et al., 2018 ; Xu et al., 2016 ). Nevertheless, the ceRNAs modulatory network belonging to the vernalization axis remains undetermined.…”

Section: Discussionmentioning

confidence: 99%

Whole-transcriptome analyses of Sorghum leaves identify key mRNAs and ncRNAs associated with GA3-mediated alleviation of salt stress

Liu

Zhou

2022

Front. Plant Sci.

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Sorghum has recently attracted much attention for its tolerance in high salt environment. However, the effect and regulatory mechanism of the gibberellic acid (GA3)-mediated alleviation of salt stress in sorghum remains unclear. Herein, we reported that a GA3 concentration of 50 mg/L is optimal for sorghum (“Jitian 3”) development under salt stress. We conducted a whole-transcriptome analysis between GA3-treated and control sorghum leaves under salt stress, and we identified 1002 differentially expressed (DE)-messenger RNAs (mRNAs), 81 DE-long non-coding RNAs (lncRNAs), 7 DE-circular RNAs (circRNAs), and 26 DE-microRNA (miRNAs) in sorghum following GA3 treatment. We also identified a majority of DE-mRNAs and non-coding RNAs (ncRNAs) targets that serve essential roles in phenylpropanoid biosynthesis and plant hormone networks. In addition, we generated a competitive endogenous RNA (ceRNA)-miRNA-target gene network, and 3 circRNAs (circRNA_2746, circRNA_6515, circRNA_5622), 4 lncRNAs (XR_002450182.1, XR_002452422.1, XR_002448510.1, XR_002448296.1) and 4 genes (LOC8056546, LOC8062245, LOC8061469, LOC8071960) probably act as valuable candidates for the regulation of the GA3-mediated alleviation of salt stress in sorghum. Our findings uncovered potential mRNA and non-coding RNAs that contribute to GA3 regulation, thus offering a basis for the future investigation of underlying mechanisms of salt stress in sorghum.

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“…Additionally, lncRNAs can be targeted by miRNAs and may also serve as an endogenous target mimic (eTM) and/or possible miRNA precursors ( Wu et al., 2013 ; Li et al., 2017 ). By analyzing competing relationships between mRNAs and lncRNAs, genome-scale lncRNA-mediated ceRNAs networks have been inferred in many plants ( Fan et al., 2018 ; He et al., 2020 ; Ren et al., 2022 ). For instance, lncRNA regulates the expression of heat stress response genes (e.g.…”

Section: Introductionmentioning

confidence: 99%

Current perspectives of lncRNAs in abiotic and biotic stress tolerance in plants

Jin,

Wang,

et al. 2024

Front. Plant Sci.

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Abiotic/biotic stresses pose a major threat to agriculture and food security by impacting plant growth, productivity and quality. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long non-coding RNAs (lncRNAs) with sizes larger than 200 nucleotides in length, provides an important new perspective on the centrality of RNA in gene regulation. In plants, lncRNAs are widespread and fulfill multiple biological functions in stress response. In this paper, the research advances on the biological function of lncRNA in plant stress response were summarized, like as Natural Antisense Transcripts (NATs), Competing Endogenous RNAs (ceRNAs) and Chromatin Modification etc. And in plants, lncRNAs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid (ABA), jasmonate (JA), salicylic acid (SA) and redox signaling in response to many abiotic/biotic stresses. Moreover, conserved sequence motifs and structural motifs enriched within stress-responsive lncRNAs may also be responsible for the stress-responsive functions of lncRNAs, it will provide a new focus and strategy for lncRNA research. Taken together, we highlight the unique role of lncRNAs in integrating plant response to adverse environmental conditions with different aspects of plant growth and development. We envisage that an improved understanding of the mechanisms by which lncRNAs regulate plant stress response may further promote the development of unconventional approaches for breeding stress-resistant crops.

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ceRNA Cross-Talk in Paulownia Witches’ Broom Disease

Cited by 14 publications

References 71 publications

Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection

Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection

Whole-transcriptome analyses of Sorghum leaves identify key mRNAs and ncRNAs associated with GA3-mediated alleviation of salt stress

Current perspectives of lncRNAs in abiotic and biotic stress tolerance in plants

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