Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar

Ding, Changjun; Shen, Tengfei; Ran, Na; Zhang, Heng; Pan, Huixin; Su, Xiaohua; Xu, Meng

doi:10.3390/ijms23094537

Cited by 8 publications

(8 citation statements)

References 78 publications

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“…[ 91 ]—introduces miRNA-based regulation of secondary metabolites biosynthesis with pharmaceutical applications in medicinal plants; ref. [ 92 ]—reveals miRNA effects on secondary metabolism in Solanum tuberosum L.; and ref. [ 93 ]—characterizes the role of miRNA858 in phenylpropanoid pathway.…”

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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“… f Validated in numerous dicots (Bao et al., 2014; Bazin et al., 2013; Debernardi et al., 2012; Ding et al., 2022; Shi et al., 2019). …”

Section: Resultsmentioning

confidence: 99%

“…Evidence for targets of miR530 have been varied in the literature; for example, predicted miR530 target ARGONAUTE1 (Shao & Lu, 2013;Sunitha et al, 2019) has not been established experimentally. Yang, Du et al (2015) claimed miR530 targets Knotted-Like1 in poplar, and we previously documented slicing activity for Ribosomal protein L10A and zinc knuckle Plus-3 domain/PL3 in grapevine (Sunitha et al, 2019), where PL3 homologues predicted in poplar and chickpea (Kohli et al, 2014;Lu et al, 2008) have been validated in strawberry, rice, poplar, and Kalanchoë marnieriana (Ding et al, 2022;Hu et al, 2021;Sun et al, 2020;Xia et al, 2015). These convergent evidences support the PL3 gene family as a canonical miR530 target, supporting our finding of four degradome-supported zinc knuckle/Plus3 domain target genes (7CP98C, TEF2FC, YIX0R7, SM0BS0; Supporting Information S4a).…”

Section: Validation Of Mirna Cognate and Novel Noncanonical Targets B...mentioning

confidence: 85%

“…Figure S4 and Supporting Information S4 document the 25 noncanonical protein-coding mRNA targets listed in Table 1 of deeply conserved miRNAs elucidated by our data-driven approach. In general support of these claims are the reports for miR530 targeting of basic helix-loop-helix transcription factors (bHLHs) in strawberry and poplar (Ding et al, 2022;Xia et al, 2015), and miR396 targeting bHLHs affecting flowering (Shi et al, 2019), vascular patterning (Debernardi et al, 2012;Ding et al, 2022), and root growth in various dicot species (Bao et al, 2014;Bazin et al, 2013). Xie, Wang et al (2017) also claimed miR166 can target Ser/Thr kinase SD1-8, associated with ABA and defense responses and AGO10 loading (Afzal et al, 2008;Zhu et al, 2011).…”

Section: Validation Of Mirna Cognate and Novel Noncanonical Targets B...mentioning

confidence: 98%

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The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

et al. 2023

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MicroRNAs (miRNAs) are 21–24 nt small RNAs (sRNAs) that negatively regulate protein‐coding genes and/or trigger phased small‐interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant‐like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA‐producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine‐protein phosphatase7 and miRc20 and ahy‐miR3514 targeting penta‐tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS‐like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought‐ and heat‐regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta‐analysis of an expression atlas and over representation of miRNA target genes in co‐expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome‐wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value‐added traits.

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“…Numerous studies have also revealed the role of lncRNAs in plant secondary metabolites. Lignin is one of the major components of wood and one of the important renewable energy sources on Earth [ 43 , 44 ]. Quan et al found that some lncRNAs may regulate some protein-coding genes in the lignin biosynthesis pathway in a cis or trans manner, providing new insights into wood formation [ 45 ].…”

Section: Discussionmentioning

confidence: 99%

Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

Shen

Zheng

Liu

et al. 2022

IJMS

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Crocins are valuable bioactive components of gardenia fruit, and their biosynthesis and accumulation have attracted widespread interest. Studies have investigated the biosynthesis and accumulation of crocin based on Illumina sequencing, but there is a lack of reports based on full-length transcriptome sequencing. Utilising SMRT sequencing and high-performance liquid chromatography (HPLC), we explored crocin biosynthesis and accumulation in the fruit of Gardenia jasminoides. HPLC analysis showed that crocins specifically exist in fruit and that the content of crocins increases gradually during fruit development. SMRT sequencing generated 46,715 high-quality full-length isoforms, including 5230 novel isoforms that are not present in the G. jasminoides genome. Furthermore, a total of 46 genes and 91 lncRNAs were involved in the biosynthesis and accumulation of crocin. The qRT-PCR indicated that genes involved in crocin biosynthesis reached a peak in the NOV stage. These findings contributed to our understanding of crocin biosynthesis and accumulation.

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Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar

Cited by 8 publications

References 78 publications

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

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