Genome-Wide Identification of Long Non-Coding RNAs and Their Potential Functions in Poplar Growth and Phenylalanine Biosynthesis

Zhang, Lei; Ge, Xiaolan; Du, Jiujun; Cheng, Xingqi; Peng, Xiaopeng; Hu, Jianjun

doi:10.3389/fgene.2021.762678

Cited by 6 publications

(3 citation statements)

References 62 publications

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“…[ 85 ]—identifies the role of miRNAs in phenylpropanoids, terpenoids, and alkaloids biosynthesis in medicinal plants; ref. [ 86 ]—is focused on lncRNAs regulatory potential in Populus trichocarpa Torr. & Gray phenylpropanoid pathway; ref.…”

Section: The Involvement Of Mirna In Plant Lignan Biosynthesismentioning

confidence: 99%

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Ražná¹,

Harenčár²,

Kučka³

2022

Cells

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Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.

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Section: The Involvement Of Mirna In Plant Lignan Biosynthesismentioning

confidence: 99%

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Ražná¹,

Harenčár²,

Kučka³

2022

Cells

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“…In addition to coding RNA, non-coding RNA also plays an important role in plant transcriptional regulation ( Liu et al, 2015 ; Liaquat et al, 2021 ; Zhang et al, 2021 ). Previous study has shown that transcriptome sequencing on the mature xylem tissues of NW, TW, and OW reveals 1,377 possible lncRNAs, of which 776 are differentially expressed in different tissue samples of poplar ( Chen et al, 2015b ).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata

Wang

Jin

et al. 2022

Front. Genet.

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Compression wood (CW) in gymnosperm brings great difficulties to wood industry using wood as raw materials since CW presents special wood structure and have different physical and chemical properties from those of normal wood (NW). Chinese fir (Cunninghamia lanceolata) is widely distributed in China. However, global transcriptome profiling of coding and long non-coding RNA in response to compression stress has not been reported in the gymnosperm species. In this study, we revealed that CW in Chinese fir exhibited distinct morphology and cytology properties compared with those of NW, including high lignin content, thick and round tracheid cells. Furthermore, we combined both PacBio long-read SMRT sequencing (Iso-Seq) and Illumina short-read RNA-Seq to reveal the transcriptome in stem-differentiating xylem (SDX) under different time points (2, 26, and 74 h) upon compression stress in NW, CW, and OW (opposite wood), respectively. Iso-Seq was successfully assembled into 41,253 de-novo full-length transcriptome reference (average length 2,245 bp). Moreover, there were striking differences in expression upon compression stress, which were involved 13 and 7 key enzyme genes in the lignin and cellulose synthesis, respectively. Especially, we revealed 11 secondary growth-related transcription factors show differential expression under compression stress, which was further validated by qRT-PCR. Finally, the correlation between 6,533 differentially expressed coding genes and 372 differentially expressed long non-coding RNAs (lncRNAs) indicates that these lncRNAs may affect cell wall biogenesis and xyloglucan metabolism. In conclusion, our results provided comprehensive cytology properties and full-length transcriptome profiling of wood species upon compression stress. Especially we explored candidate genes, including both coding and long non-coding genes, and provided a theoretical basis for further research on the formation mechanism of CW in gymnosperm Chinese fir.

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“…Wood formation is a continuous and highly ordered biological process involved in vascular cambium differentiation, vascular tissue division, cell expansion, cell wall thickening, and programmed cell death (S. Li, Zhang et al., 2020), and is controlled by multi‐level regulations, such as transcriptional regulation (Jiang et al., 2022; Y. Liu et al., 2017; Nakano et al., 2015; Ren et al., 2022; Ye & Zhong, 2015), post‐translational regulation (Kawabe et al., 2018; Morse et al., 2009; Sulis & Wang, 2020; Zhong & Ye, 2009), and epigenetic regulation (Mizrachi & Myburg, 2016; L. Zhang, Ge, et al., 2021), which are organized in a sophisticated network that coordinately integrate developmental and environmental cues into wood formation (Taylor‐Teeples et al., 2015). Among these epigenetic regulation model, the miRNA and methylation regulations have been reported to widely participate in wood formation (R. Wang et al., 2021; Y. Zhang et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar

Wang,

Wu,

Zhang

et al. 2024

The Plant Genome

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MicroRNAs (miRNAs) and DNA methylation are both vital regulators of gene expression. DNA methylation can affect the transcription of miRNAs, just like coding genes, through methylating the CpG islands in the gene regions of miRNAs. Although previous studies have shown that DNA methylation and miRNAs can each be involved in the process of wood formation, the relationship between the two has been relatively little studied in plant wood formation. Studies have shown that the second internode (IN2) (from top to bottom) of 3‐month‐old poplar trees can represent the primary stage of poplar stem development and IN8 can represent the secondary stage. There were also significant differences in DNA methylation patterns and miRNA expression patterns obtained from PS and SS. In this study, we first interactively analyzed methylation and miRNA sequencing data to identify 43 differentially expressed miRNAs regulated by differential methylation from the primary stage and secondary stage, which were found to be involved in multiple biological processes related to wood formation by enrichment analysis. In addition, six miRNA/target gene modules were finally identified as potentially involved in secondary xylem development of poplar stems through degradome sequencing and functional analysis. In conclusion, this study provides important reference information on the mechanism of interaction between different regulatory pathways of wood formation.

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Genome-Wide Identification of Long Non-Coding RNAs and Their Potential Functions in Poplar Growth and Phenylalanine Biosynthesis

Cited by 6 publications

References 62 publications

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata

Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar

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