Identification of MicroRNAs and Their Targets Involved in Paeonia rockii Petal Variegation Using High-throughput Sequencing

Shi, Qianqian; Zhang, Xiaoxiao; Li, Xiang; Zhai, Lijuan; Luo, Xiaoning; Luo, Jianrang; He, Li; Zhang, Yanlong; Li, Long

doi:10.21273/jashs04395-18

Cited by 7 publications

(8 citation statements)

References 64 publications

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“…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 ( bHLH s) in strawberry and poplar (Ding et al., 2022; Xia et al., 2015), and miR396 targeting bHLH s 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.…”

Section: Resultsmentioning

confidence: 98%

“… 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%

“…e Validated in strawberry(Xia et al, 2015). 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). g Validated in Arabidopsis(Brousse et al, 2014), Cruciferae(Huen et al, 2018), and grapevine(Sunitha et al, 2019).…”

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confidence: 99%

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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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Section: Resultsmentioning

confidence: 98%

“… 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%

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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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“…Prediction of miRNAs in tree peony have been reported, including miRNAs in response to copper stress ( Jin et al., 2015 ), involved in bud dormancy release ( Zhang et al., 2018 ), seed fatty acid synthesis ( Yin et al., 2018 ), flower spot formation ( Zhao et al., 2019 ), petal variegation ( Shi et al., 2019 ), flower development ( Han et al., 2020 ), and brassinolide treatment on flowering ( Zhang et al., 2022 ). In herbaceous peony, miRNAs involved in response to stress from high temperature ( Hao et al., 2017 ) and Botrytis cinerea infection ( Zhao et al., 2015 ), as well as lateral branch formation ( Liu et al., 2020 ) have been predicted.…”

Section: Introductionmentioning

confidence: 99%

Integrated analysis of miRNAome transcriptome and degradome reveals miRNA-target modules governing floral florescence development and senescence across early- and late-flowering genotypes in tree peony

Guo

Zhang

et al. 2022

Front. Plant Sci.

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As a candidate national flower of China, tree peony has extremely high ornamental, medicinal and oil value. However, the short florescence and rarity of early-flowering and late-flowering varieties restrict further improvement of the economic value of tree peony. Specific miRNAs and their target genes engaged in tree peony floral florescence, development and senescence remain unknown. This report presents the integrated analysis of the miRNAome, transcriptome and degradome of tree peony petals collected from blooming, initial flowering, full blooming and decay stages in early-flowering variety Paeonia ostii ‘Fengdan’, an early-flowering mutant line of Paeonia ostii ‘Fengdan’ and late-flowering variety Paeonia suffruticosa ‘Lianhe’. Transcriptome analysis revealed a transcript (‘psu.G.00014095’) which was annotated as a xyloglucan endotransglycosylase/hydrolase precursor XTH-25 and found to be differentially expressed across flower developmental stages in Paeonia ostii ‘Fengdan’ and Paeonia suffruticosa ‘Lianhe’. The miRNA-mRNA modules were presented significant enrichment in various pathways such as plant hormone signal transduction, indole alkaloid biosynthesis, arachidonic acid metabolism, folate biosynthesis, fatty acid elongation, and the MAPK signaling pathway. Multiple miRNA-mRNA-TF modules demonstrated the potential functions of MYB-related, bHLH, Trihelix, NAC, GRAS and HD-ZIP TF families in floral florescence, development, and senescence of tree peony. Comparative spatio-temporal expression investigation of eight floral-favored miRNA-target modules suggested that transcript ‘psu.T.00024044’ and microRNA mtr-miR166g-5p are involved in the floral florescence, development and senescence associated agronomic traits of tree peony. The results might accelerate the understanding of the potential regulation mechanism in regards to floral florescence, development and abscission, and supply guidance for tree peony breeding of varieties with later and longer florescence characteristics.

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“…The miRNAs comprise %21 to 24 nucleotides and function as negative regulators of gene expression by degrading mRNA or inhibiting translation (Betti et al, 2021). Extensive research has demonstrated critical roles for miRNAs in regulation of various biological processes (Feng et al, 2019;Shi et al, 2019), including organ development and hormone signaling, as well as responses to abiotic stresses (Lin et al, 2020). Plants are more vulnerable to environmental stresses, such as low temperature or high temperature at the reproductive growth stage than during the vegetative growth phase (Tang et al, 2012).…”

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confidence: 99%

Identification and Functional Analysis of MicroRNAs and Their Target Genes in Reverse Thermosensitive Genic Male Sterility of Eggplant

Zhang

XiuRui

et al. 2022

J. Amer. Soc. Hort. Sci.

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Thermosensitive genic male sterile (TGMS) lines are the core of two-line hybrid systems. MicroRNAs (miRNAs) play critical roles in plant growth and development. However, knowledge of regulation of anther development by miRNAs in TGMS eggplant (Solanum melongena) is largely unexplored. To investigate the mechanism underlying miRNA regulation of male sterility, we employed high-throughput small RNA sequencing in anther samples from the reverse TGMS line 05ms and the temperature-insensitive line S63 in eggplant, under high temperature and low temperature conditions. The 05ms line is sterile at low temperature and fertile at high temperature. A total of 166,273,427 raw reads were obtained, 143 known miRNAs from 42 miRNA families and 104 novel miRNAs were detected. Further, six differentially expressed miRNAs (DEMs) were identified, including three known (miR168b-3p, miR397–5p, and miR408) and three novel miRNAs (Novel_116, Novel_119, and Novel_97), which might be related to anther development. Moreover, the six DEMs were validated by quantitative real-time polymerase chain reaction and 892 target genes of which were predicted. Gene Ontology analysis of target genes revealed significant enrichment in the “copper ion binding,” “oxidation-reduction process,” and “oxidoreductase activity” terms. Kyoto Encyclopedia of Genes and Genomes analysis revealed that “plant hormone signal transduction” and “other glycan degradation” were enriched. In addition, we constructed regulatory networks comprising miRNAs, target genes, and important terms/pathways and found the miR397-5p was the most linked miRNA, down-regulated under low temperature. Our findings contribute to understanding of the roles of miRNA during anther development and provide the theoretical foundation for two-line hybrid breeding of eggplant.

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Identification of MicroRNAs and Their Targets Involved in Paeonia rockii Petal Variegation Using High-throughput Sequencing

Cited by 7 publications

References 64 publications

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

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

Integrated analysis of miRNAome transcriptome and degradome reveals miRNA-target modules governing floral florescence development and senescence across early- and late-flowering genotypes in tree peony

Identification and Functional Analysis of MicroRNAs and Their Target Genes in Reverse Thermosensitive Genic Male Sterility of Eggplant

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