Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes

Zhang, Yue; Li, Hui; Chen, Jin‐Ming; Shi, Tao

doi:10.1016/j.csbj.2022.06.001

Cited by 3 publications

(2 citation statements)

References 65 publications

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“…Transcripts that overlapped with mRNA, rRNA, tRNA, snoRNA, and snRNA were excluded from further analysis. Additionally, transcripts shorter than 200 bp, with fewer than two exons, and showing low expression levels (<3 reads) were also excluded based on the exclusion criteria proposed by previous reports ( Derrien et al, 2012 ; Novikova, Hennelly & Sanbonmatsu, 2012 ; Dou et al, 2021 ; Ren et al, 2022 ; Zhang et al, 2022 ). After filtering transcripts based on sequence length and read count, their coding potential was evaluated using two tools: the coding potential assessment tool (CPAT) ( Wang et al, 2013 ) and the coding potential calculator (CPC) ( Kong et al, 2007 ).…”

Section: Methodsmentioning

confidence: 99%

Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard

Wei,

Li,

Huang

et al. 2024

PeerJ

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Leaf mustard (Brassica juncea L. Czern & Coss), an important vegetable crop, experiences pronounced adversity due to seasonal drought stress, particularly at the seed germination stage. Although there is partial comprehension of drought-responsive genes, the role of long non-coding RNAs (lncRNAs) in adjusting mustard’s drought stress response is largely unexplored. In this study, we showed that the drought-tolerant cultivar ‘Weiliang’ manifested a markedly lower base water potential (−1.073 MPa vs −0.437 MPa) and higher germination percentage (41.2% vs 0%) than the drought-susceptible cultivar ‘Shuidong’ under drought conditions. High throughput RNA sequencing techniques revealed a significant repertoire of lncRNAs from both cultivars during germination under drought stress, resulting in the identification of 2,087 differentially expressed lncRNAs (DELs) and their correspondingly linked 12,433 target genes. It was noted that 84 genes targeted by DEL exhibited enrichment in the photosynthesis pathway. Gene network construction showed that MSTRG.150397, a regulatory lncRNA, was inferred to potentially modulate key photosynthetic genes (Psb27, PetC, PetH, and PsbW), whilst MSTRG.107159 was indicated as an inhibitory regulator of six drought-responsive PIP genes. Further, weighted gene co-expression network analysis (WGCNA) corroborated the involvement of light intensity and stress response genes targeted by the identified DELs. The precision and regulatory impact of lncRNA were verified through qPCR. This study extends our knowledge of the regulatory mechanisms governing drought stress responses in mustard, which will help strategies to augment drought tolerance in this crop.

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Section: Methodsmentioning

confidence: 99%

Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard

Wei,

Li,

Huang

et al. 2024

PeerJ

View full text Add to dashboard Cite

show abstract

“…The transcripts that overlapped with mRNA, rRNA, tRNA, snoRNA, and snRNA were excluded from further analysis. Furthermore, the transcripts shorter than 200 bp, with less than 2 exons, and low expression levels (<3 reads) were also excluded( Derrien et al 2012 , Novikova et al 2012 , Dou et al 2021 , Ren et al 2022 , Zhang et al 2022 ). Transcripts after length and read count filtering were used to calculate the coding potential of the transcripts using the coding potential assessment tool (CPAT) ( Wang et al 2013 ) and the coding potential calculator (CPC) ( Kong et al 2007 ).…”

Section: Methodsmentioning

confidence: 99%

Response patterns of lncRNAs of theSpodoptera frugiperda(Lepidoptera: Noctuidae) larvae under 23 pesticide treatments

Wang

Xiao

et al. 2023

Journal of Insect Science

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The response of Spodoptera frugiperda genes toward insecticides is crucial for guiding insecticide use. The regulation of the S. frugiperda genes via long noncoding RNAs (lncRNAs) under insecticide treatment should be investigated. In this study, 452 differentially expressed lncRNAs were identified by analyzing RNA-sequencing data of S. frugiperda under 23 pesticide treatments. We found 59 and 43 differentially expressed lncRNAs that could regulate detoxification-related cytochrome P450 and UDP-glucuronosyltransferase genes, respectively. Furthermore, the target genes of differentially expressed lncRNAs were enriched in Pfam, including chitin bind 4 and gene ontology terms such as structural constituent of the cuticle, revealing their potential mechanism of action on the growth inhibition of S. frugiperda larvae. Insecticide-specific expression of lncRNAs highlights the properties and commonalities of different insecticide-induced lncRNA regulatory mechanisms. To conclude, the results of this study provide new insights and perspectives on the use of 23 insecticides via lncRNA regulation of mRNAs.

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Divergence in MiRNA targeting of AchAco and its role in citrate accumulation in kiwifruit

Ling,

Hu,

Zhang

2024

BMC Plant Biol

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Background MicroRNA (miRNA) is a crucial post-transcriptional regulatory factor in plant growth and development. Duplicated genes often exhibit functional divergence due to competition for the identical miRNA binding sites. Kiwifruit ( Actinidia spp.) is an economically significant horticultural crop renowned for its distinctive flavor, which is largely attributable to elevated citrate levels during fruit development. However, the mechanisms through which miRNA-targeted modules evolve following duplication events and regulate citrate biosynthesis, thereby influencing the unique flavor profile of kiwifruits, remain poorly understood. Results In this study, we examined the expression patterns of miRNAs and interactions with their targets in kiwifruit fruit samples from various pulp tissues and developmental stages. Our analysis identified 46 miRNAs, comprising 44 known miRNAs and two novel/kiwifruit-specific miRNAs, which targeted a total of 1,474 genes. Correlation analysis revealed weak relationships between the expression levels of miRNAs and their target genes. Among these targets, 27 tandemly duplicated genes, and 782 whole genome duplication (WGD) genes exhibited a loss of miRNA binding sites in one of their duplicated copies. Furthermore, weighted gene co-expression network analysis demonstrated that most duplicated genes clustered into distinct gene modules. These findings suggest that the loss of miRNA targets following duplications contributes to expression divergence among gene duplicates, thereby facilitating stable gene expression within the miRNA-targeted network. For instance, the aconitate hydratase genes AchAco4 and AchAco6 were each targeted by different miRNAs, ach-miR-3774 and ach-miR-10371 , respectively. Notably, these genes exhibited distinct expression patterns compared to their duplicated counterparts. Conclusions This study enhances our understanding of how the miRNA- AchAco module regulates citrate content and provides insights into the molecular network that influences the flavor profile of kiwifruit. Clinical trial number Not applicable. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-024-05877-w.

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Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes

Cited by 3 publications

References 65 publications

Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard

Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard

Response patterns of lncRNAs of theSpodoptera frugiperda(Lepidoptera: Noctuidae) larvae under 23 pesticide treatments

Divergence in MiRNA targeting of AchAco and its role in citrate accumulation in kiwifruit

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