Genome‐wide identification and characterization of long noncoding RNAs in maize under rice black streaked dwarf virus infection

Cao, Weilin; Wang, Ruolin; Cao, Jiashu; Gao, Jiming; Zhao, Xuan; Gan, Li‐Ming; Zhu, Changxiang

doi:10.1111/ppa.13512

Cited by 3 publications

(1 citation statement)

References 41 publications

(42 reference statements)

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“…All sequencing programs were performed by the OE Biotech Co., Ltd (Shanghai, China) ( Cao et al., 2022 ). The circRNA-, lncRNA-, miRNA-, and mRNA-seq details are summarized in a prior publication ( Shi et al., 2021 ).…”

Section: Methodsmentioning

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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Section: Methodsmentioning

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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Non-coding RNAs and their role in enhancing virus resistance in plants

Majumdar

2024

Eur J Plant Pathol

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Identification and functional analysis of long non-coding RNA (lncRNA) and metabolites response to mowing in hulless barley (Hordeum vulgare L. var. nudum hook. f.)

Bai,

He,

Yao

et al. 2024

BMC Plant Biol

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Background Hulless barley (Hordeum vulgare L. var. nudum Hook. f.) is a significant cereal crop and a substantial source of forage for livestock. Long non-coding RNAs (lncRNAs) and metabolites play crucial roles in the nutrient accumulation and regeneration of hulless barley plants following mowing. The study aimed to identify differentially expressed lncRNAs and metabolites in hulless barley plants by analyzing transcriptomic and metabolomic datasets at 2 h, 24 h, and 72 h following mowing. Results The study revealed that 190, 90, and 438 lncRNA genes were differentially expressed at the 2 h, 24 h, and 72 h time points compared to the non-mowing control. We identified 14 lncRNA genes—11 downregulated and 3 upregulated—showing consistently significant differential expression across all time points after mowing. These differentially expressed lncRNAs target genes involved in critical processes such as cytokinin signaling, cell wall degradation, storage protein accumulation, and biomass increase. In addition, we identified ten differentially expressed metabolites targeting diverse metabolic pathways, including plant hormones, alkaloids, and flavonoids, before and after mowing at various time points. Endogenous hormone analysis revealed that cytokinin most likely played a crucial role in the regeneration of hulless barley after mowing. Conclusions This study created a comprehensive dataset of lncRNAs, metabolites, and hormones in hulless barley after mowing, revealing valuable insights into the functional characteristics of lncRNAs, metabolites, and hormones in regulating plant regeneration. The results indicated that cytokinin plays a significant role in facilitating the regeneration process of hulless barley after mowing. This comprehensive dataset is an invaluable resource for better understanding the complex mechanisms that underlie plant regeneration, with significant implications for crop improvement.

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Genome‐wide identification and characterization of long noncoding RNAs in maize under rice black streaked dwarf virus infection

Cited by 3 publications

References 41 publications

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

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

Non-coding RNAs and their role in enhancing virus resistance in plants

Identification and functional analysis of long non-coding RNA (lncRNA) and metabolites response to mowing in hulless barley (Hordeum vulgare L. var. nudum hook. f.)

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