scholarly journals Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa

2021 ◽  
Author(s):  
Ruiqi Wang ◽  
Mengxuan Reng ◽  
Shuanghui Tian ◽  
Cong Liu ◽  
He Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Target Genes ◽  
Developmental Stages ◽  
Process Analysis ◽  
Populus Trichocarpa ◽  
Secondary Growth ◽  
Integrated Analysis ◽  
Cell Wall Modification ◽  
Individual Mirnas ◽  
Mirna Species

Abstract We applied miRNA expression profiling method to Populus trichocarpa stems of the three developmental stages, primary stem (PS), transitional stem (TS), and secondary stem (SS), to investigate miRNA species and their regulation on lignocellulosic synthesis and related processes. We obtained 892, 872, and 882 known miRNAs and 1,727, 1,723, and 1,597 novel miRNAs, from PS, TS, and SS, respectively. Comparisons of these miRNA species among different developmental stages led to the identification of 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs), which had 921, 2,639, and 2,042 candidate target genes (CTGs) in the three respective stages of the same order. Corelation analysis revealed 47, 439, and 71 DE-miRNA-CTG pairs of high negative correlation in PS, TS and SS, respectively. Through biological process analysis, we finally identified 34, 6, and 76 miRNA-CTG pairs from PS, TS, and SS, respectively, and the miRNA target genes in these pairs regulate or participate lignocellulosic biosynthesis related biological processes: cell division and differentiation, cell wall modification, secondary cell wall biosynthesis, lignification, and programmed cell death processes. This is the first report on an integrated analysis of genome-wide mRNA and miRNA profilings during multiple phases of poplar stem development. Our analysis results imply that individual miRNAs modulate secondary growth and lignocellulosic biosynthesis through regulating transcription factors and lignocellulosic biosynthetic pathway genes, resulting in more dynamic promotion, suppression, or regulatory circuits. This study advanced our understanding of many individual miRNAs and their essential, diversified roles in dynamic regulation of secondary growth in woody tree species.

scholarly journals Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa

2020 ◽  
Author(s):  
Ruiqi Wang ◽  
Mengxuan Ren ◽  
Shuanghui Tian ◽  
Cong Liu ◽  
He Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Target Genes ◽  
Developmental Stages ◽  
Populus Trichocarpa ◽  
Wood Formation ◽  
Pcr Analysis ◽  
Integrated Analysis ◽  
Cell Wall Modification ◽  
Dynamic Regulation ◽  
Genome Wide

Abstract Background: MicroRNAs (miRNAs) are small, non-coding RNAs that have important regulatory functions in plant growth and development. However, the miRNAs that are involved in different developmental stages of tree stems have not been systemically characterized. In this study, we applied miRNA expression profiling method to the Populus trichocarpa trunks of the three distinct developmental stages defined as the primary stem (PS), transitional stem (TS), and secondary stem (SS) to investigate the miRNA species, their dynamic regulation and functions during the transitions of wood formation in different developmental stages at the genome-wide scale by Solexa sequencing.Results: We obtained 892, 872, and 882 known miRNAs and 1,727, 1,723, and 1,597 novel miRNAs, from PS, TS, and SS, respectively. And identified 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs) with 921, 2,639, and 2,042 candidate target genes (CTGs), which formed 158, 855, and 297 DE-miRNA-CTG pairs in PS vs TS, PS vs SS, and TS vs SS , respectively. Among these, 47, 439, and 71 DE-miRNA-CTG pairs showed a significant negative correlation, respectively. Finally, we identified 39, 9, and 92 miRNA-CTG pairs involved in PS, TS, and SS, respectively. These DE-miRNA-CTG pairs in poplar or whose counterparts in other plant species are known to be transcriptional factors or structural genes involved in cell division and differentiation, cell wall modification, secondary cell wall (SCW) biosynthesis, lignification, and programmed cell death processes of wood formation. Moreover, qRT–PCR analysis confirmed that the results of small RNA-seq were robust and reliable and most miRNA-CTG pairs exhibited an inverse correlation.Conclusions: This is the first report on an integrated analysis of genome-wide mRNA and miRNA profiling of diverse phases of wood formation in poplar trunks. We showed that even though miRNAs involved in diverse developmental phases were not in a considerable number, their roles in the regulatory network that govern wood formation during different developmental stages cannot be negligible or underestimated. The information and data obtained in this paper significantly advanced our understanding of these miRNAs and their essential, dynamic and diversified roles as well as functions in diverse phases of wood formation in tree species.

scholarly journals EARLY BUD BREAK 1 triggers bud break in peach trees by regulating hormone metabolism, the cell cycle, and cell wall modifications

2020 ◽  
Vol 71 (12) ◽  
pp. 3512-3523
Author(s):  
Xuehui Zhao ◽  
Xiaolun Han ◽  
Qingjie Wang ◽  
Xuxu Wang ◽  
Xiude Chen ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Wall ◽  
Prunus Persica ◽  
Populus Trichocarpa ◽  
Bimolecular Fluorescence Complementation ◽  
Bud Break ◽  
Hormone Metabolism ◽  
Cell Wall Modification ◽  
Isopentenyl Adenine ◽  
Peach Trees

Abstract In a previous study we identified EARLY BUD BREAK 1 (EBB1), an ERF transcription factor, in peach (Prunus persica var. nectarina cultivar Zhongyou 4); however, little is known of how PpEBB1 may regulate bud break. To verify the function of PpEBB1 in bud break, PpEBB1 was transiently transformed into peach buds, resulting in early bud break. Bud break occurred earlier in PpEBB1-oe poplar (Populus trichocarpa) obtained by heterologous transformation than in wild type (WT), consistent with the peach bud results, indicating that PpEBB1 can promote bud break. To explore how PpEBB1 affects bud break, differentially expressed genes (DEGs) between WT and PpEBB1-oe poplar plants were identified by RNA-sequencing. The expression of DEGs associated with hormone metabolism, cell cycle, and cell wall modifications changed substantially according to qRT-PCR. Auxin, ABA, and total trans-zeatin-type cytokinin levels were higher in the PpEBB1-oe plants than in WT plants, while the total N6-(Δ 2-isopentenyl)-adenine-type cytokinins was lower. Yeast two-hybrid and bimolecular fluorescence complementation assays verified that a cell wall modification-related protein (PpEXBL1) interacted with PpEBB1 suggesting that PpEBB1 could interact with these cell wall modification proteins directly. Overall, our study proposed a multifaceted explanation for how PpEBB1 regulates bud break and showed that PpEBB1 promotes bud break by regulating hormone metabolism, the cell cycle, and cell wall modifications.

scholarly journals Wood Formation under Severe Drought Invokes Adjustment of the Hormonal and Transcriptional Landscape in Poplar

2021 ◽  
Vol 22 (18) ◽  
pp. 9899
Author(s):  
Dade Yu ◽  
Dennis Janz ◽  
Krzysztof Zienkiewicz ◽  
Cornelia Herrfurth ◽  
Ivo Feussner ◽  
...  
Keyword(s):  
Cell Wall ◽  
Secondary Growth ◽  
Wood Formation ◽  
Severe Drought ◽  
Normal Wood ◽  
Aba Signaling ◽  
Negative Effects ◽  
Transcriptional Responses ◽  
Cell Wall Modification ◽  
Induced Changes

Drought is a severe environmental stress that exerts negative effects on plant growth. In trees, drought leads to reduced secondary growth and altered wood anatomy. The mechanisms underlying wood stress adaptation are not well understood. Here, we investigated the physiological, anatomical, hormonal, and transcriptional responses of poplar to strong drought. Drought-stressed xylem was characterized by higher vessel frequencies, smaller vessel lumina, and thicker secondary fiber cell walls. These changes were accompanied by strong increases in abscisic acid (ABA) and antagonistic changes in salicylic acid in wood. Transcriptional evidence supported ABA biosynthesis and signaling in wood. Since ABA signaling activates the fiber-thickening factor NST1, we expected upregulation of the secondary cell wall (SCW) cascade under stress. By contrast, transcription factors and biosynthesis genes for SCW formation were down-regulated, whereas a small set of cellulose synthase-like genes and a huge array of genes involved in cell wall modification were up-regulated in drought-stressed wood. Therefore, we suggest that ABA signaling monitors normal SCW biosynthesis and that drought causes a switch from normal to “stress wood” formation recruiting a dedicated set of genes for cell wall biosynthesis and remodeling. This proposition implies that drought-induced changes in cell wall properties underlie regulatory mechanisms distinct from those of normal wood.

scholarly journals Cell wall O-acetyl and methyl esterification patterns of leaves reflected in atmospheric emission signatures of acetic acid and methanol

2019 ◽  
Author(s):  
Rebecca A. Dewhirst ◽  
Cassandra A. Afseth ◽  
Cristina Castanha ◽  
Jenny C. Mortimer ◽  
Kolby J. Jardine
Keyword(s):  
Cell Wall ◽  
Acetic Acid ◽  
Methyl Ester ◽  
Developmental Stages ◽  
Populus Trichocarpa ◽  
Young Leaves ◽  
Structural Carbohydrate ◽  
Potential Tool ◽  
Methyl Ester Content ◽  
Emission Ratios

AbstractPlants emit high rates of methanol (meOH), generally assumed to derive from pectin demethylation, and this increases during abiotic stress. In contrast, less is known about the emission and source of acetic acid (AA). In this study, Populus trichocarpa (California poplar) leaves in different developmental stages were desiccated and quantified for total meOH and AA emissions together with bulk cell wall acetylation and methylation content. While young leaves showed high emissions of meOH (140 μmol m−2) and AA (42 μmol m−2), emissions were reduced in mature (meOH: 69%, AA: 60%) and old (meOH: 83%, AA: 76%) leaves. In contrast, the ratio of AA/meOH emissions increased with leaf development (young: 35%, mature: 43%, old: 82%), mimicking the pattern of O-acetyl/methyl ester ratios of leaf bulk cell walls (young: 35%, mature: 38%, old: 51%), which is driven by an increase in O-acetyl and decrease in methyl ester content with age. The results are consistent with meOH and AA emission sources from cell wall de-esterification, with young expanding tissues producing highly methylated pectin that is progressively demethyl-esterified. We highlight the quantification of AA/meOH emission ratios as a potential tool for rapid phenotype screening of structural carbohydrate esterification patterns.

scholarly journals Comparative Analyses of Full-Length Transcriptomes Reveal Gnetum luofuense Stem Developmental Dynamics

2021 ◽  
Vol 12 ◽  
Author(s):  
Chen Hou ◽  
Huiming Lian ◽  
Yanling Cai ◽  
Yingli Wang ◽  
Dongcheng Liang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
Developmental Stages ◽  
Secondary Growth ◽  
Alternative Polyadenylation ◽  
Cost Effective ◽  
Developmental Trajectory ◽  
Full Length ◽  
Dynamic Pattern ◽  
Primary Growth

Genus Gnetum, of which the majority species are pantropical liana, have broad industrial uses including for string, nets, and paper production. Although numerous studies have investigated anatomical structures during stem development, the underlying molecular mechanisms that regulate this developmental trajectory in Gnetum species remain poorly understood. A total of 12 full-length transcriptomes were generated from four stem developmental stages of an arborescent representative of this genus, Gnetum luofuense, using Oxford Nanopore Technologies. The results of this analysis reveal a total of 24,151 alternative splicing (AS) and 134,391 alternative polyadenylation events. A remarkably dynamic pattern of AS events, especially in the case of intron retentions, was found across the four developmental stages while no dynamic pattern was found among transcript numbers with varied poly(A) sites. A total of 728 long non-coding RNAs were also detected; the number of cis-regulated target genes dramatically increased while no changes were found among trans-regulated target genes. In addition, a K-means clustering analysis of all full-length transcripts revealed that primary growth is associated with carbohydrate metabolism and fungi defense, while secondary growth is closely linked with photosynthesis, nitrogen transportation, and leaf ontogenesis. The use of weighted gene co-expression network analysis as well as differentially expressed transcripts reveals that bHLH, GRF, and MYB-related transcription factors are involved in primary growth, while AP2/ERF, MYB, NAC, PLAZ, and bZIP participate in G. luofuense stem secondary growth. The results of this study provide further evidence that Nanopore sequencing technology provides a cost-effective method for generating full-length transcriptome data as well as for investigating seed plant organ development.

scholarly journals Systems-level identification of transcription factors critical for mouse embryonic development

2017 ◽  
Author(s):  
Kai Zhang ◽  
Mengchi Wang ◽  
Ying Zhao ◽  
Wei Wang
Keyword(s):  
Transcription Factors ◽  
Embryonic Development ◽  
Target Genes ◽  
Developmental Stages ◽  
Cell Types ◽  
Integrated Analysis ◽  
Chromatin Interactions ◽  
Regulatory Circuit ◽  
Transcriptional Regulatory ◽  
Comprehensive Survey

AbstractDynamic changes in the transcriptional regulatory circuit can influence the specification of distinct cell types. Numerous transcription factors (TFs) have been shown to function through dynamic rewiring during embryonic development but a comprehensive survey on the global regulatory network is still lacking. Here, we performed an integrated analysis of epigenomic and transcriptomic data to reveal key regulators from 2 cells to postnatal day 0 in mouse embryogenesis. We predicted 3D chromatin interactions including enhancer-promoter interactions in 12 tissues across 8 developmental stages, which facilitates linking TFs to their target genes for constructing genetic networks. To identify driver TFs particularly those not necessarily differentially expressed ones, we developed a new algorithm, dubbed as Taiji, to assess the global importance of TFs in development. Through comparative analysis across tissues and developmental stages, we systematically uncovered TFs that are critical for lineage-specific and stage-dependent tissue specification. Most interestingly, we have identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress and differentiation. Not only does our analysis provide the first comprehensive map of transcriptional regulatory circuits during mouse embryonic development, the identified novel regulators and the predicted 3D chromatin interactions also provide a valuable resource to guide further mechanistic studies.

scholarly journals Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hongyou Li ◽  
Hengling Meng ◽  
Xiaoqian Sun ◽  
Jiao Deng ◽  
Taoxiong Shi ◽  
...  
Keyword(s):  
Seed Development ◽  
Target Genes ◽  
Developmental Stages ◽  
Transcriptome Profiling ◽  
Mineral Elements ◽  
Endosperm Development ◽  
Tartary Buckwheat ◽  
Integrated Analysis ◽  
Fagopyrum Tataricum ◽  
Regulatory Pathways

Abstract Background Tartary buckwheat seed development is an extremely complex process involving many gene regulatory pathways. MicroRNAs (miRNAs) have been identified as the important negative regulators of gene expression and performed crucial regulatory roles in various plant biological processes. However, whether miRNAs participate in Tartary buckwheat seed development remains unexplored. Results In this study, we first identified 26 miRNA biosynthesis genes in the Tartary buckwheat genome and described their phylogeny and expression profiling. Then we performed small RNA (sRNA) sequencing for Tartary buckwheat seeds at three developmental stages to identify the miRNAs associated with seed development. In total, 230 miRNAs, including 101 conserved and 129 novel miRNAs, were first identified in Tartary buckwheat, and 3268 target genes were successfully predicted. Among these miRNAs, 76 exhibited differential expression during seed development, and 1534 target genes which correspond to 74 differentially expressed miRNAs (DEMs) were identified. Based on integrated analysis of DEMs and their targets expression, 65 miRNA-mRNA interaction pairs (25 DEMs corresponding to 65 target genes) were identified that exhibited significantly opposite expression during Tartary buckwheat seed development, and 6 of the miRNA-mRNA pairs were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) and ligase-mediated rapid amplification of 5′ cDNA ends (5′-RLM-RACE). Functional annotation of the 65 target mRNAs showed that 56 miRNA-mRNA interaction pairs major involved in cell differentiation and proliferation, cell elongation, hormones response, organogenesis, embryo and endosperm development, seed size, mineral elements transport, and flavonoid biosynthesis, which indicated that they are the key miRNA-mRNA pairs for Tartary buckwheat seed development. Conclusions Our findings provided insights for the first time into miRNA-mediated regulatory pathways in Tartary buckwheat seed development and suggested that miRNAs play important role in Tartary buckwheat seed development. These findings will be help to study the roles and regulatory mechanism of miRNAs in Tartary buckwheat seed development.

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