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 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 Functional Characterisation of the Poplar Atypical Aspartic Protease Gene PtAP66 in Wood Secondary Cell Wall Deposition

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1002
Author(s):  
Shenquan Cao ◽  
Cong Wang ◽  
Huanhuan Ji ◽  
Mengjie Guo ◽  
Jiyao Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Secondary Cell Wall ◽  
Fluorescent Protein ◽  
Secondary Xylem ◽  
Populus Trichocarpa ◽  
Wood Formation ◽  
Protease Gene ◽  
Cellulose Content ◽  
Transcription Analysis ◽  
Functional Characterisation

Secondary cell wall (SCW) deposition is an important process during wood formation. Although aspartic proteases (APs) have been reported to have regulatory roles in herbaceous plants, the involvement of atypical APs in SCW deposition in trees has not been reported. In this study, we characterised the Populus trichocarpa atypical AP gene PtAP66, which is involved in wood SCW deposition. Transcriptome data from the AspWood resource showed that in the secondary xylem of P. trichocarpa, PtAP66 transcripts increased from the vascular cambium to the xylem cell expansion region and maintained high levels in the SCW formation region. Fluorescent signals from transgenic Arabidopsis plant roots and transiently transformed P. trichocarpa leaf protoplasts strongly suggested that the PtAP66-fused fluorescent protein (PtAP66-GFP or PtAP66-YFP) localised in the plasma membrane. Compared with the wild-type plants, the Cas9/gRNA-induced PtAP66 mutants exhibited reduced SCW thickness of secondary xylem fibres, as suggested by the scanning electron microscopy (SEM) data. In addition, wood composition assays revealed that the cellulose content in the mutants decreased by 4.90–5.57%. Transcription analysis further showed that a loss of PtAP66 downregulated the expression of several SCW synthesis-related genes, including cellulose and hemicellulose synthesis enzyme-encoding genes. Altogether, these findings indicate that atypical PtAP66 plays an important role in SCW deposition during wood formation.

Reference gene selection and evaluation for expression analysis using qRT-PCR in Galeruca daurica (Joannis)

2016 ◽  
Vol 107 (3) ◽  
pp. 359-368 ◽  
Author(s):  
Y. Tan ◽  
X.-R. Zhou ◽  
B.-P. Pang
Keyword(s):  
Reference Gene ◽  
Reference Genes ◽  
Target Genes ◽  
Gene Selection ◽  
Developmental Stages ◽  
Pcr Analysis ◽  
Experimental Conditions ◽  
Reference Gene Selection ◽  
Functional Studies ◽  
Qrt Pcr

AbstractQuantitative real-time PCR (qRT-PCR) has been used extensively to analyze gene expression and decipher gene function. To obtain the optimal and stable normalization factors for qRT-PCR, selection and validation of reference genes should be conducted in diverse conditions. In insects, more and more studies confirmed the necessity and importance of reference gene selection. In this study, eight traditionally used reference genes in Galeruca daurica (Joannis) were assessed, using qRT-PCR, for suitability as normalization genes under different experimental conditions using four statistical programs: geNorm, Normfinder, BestKeeper and the comparative ΔCt method. The genes were ranked from the most stable to the least stable using RefFinder. The optimal suite of recommended reference genes was as follows: succinate dehydrogenase (SDHA) and tubulin-alpha (TUB-α) for temperature-treated larvae; ribosomal protein L32, SDHA and glutathione S-transferase were best for all developmental stages; ACT and TUB-α for male and female adults; SDHA and TUB-α were relatively stable and expressed in different tissues, both diapause and non-diapause adults. Reference gene evaluation was validated using expression of two target genes: the P450 CYP6 gene and the heat shock protein gene Hsp70. These results confirm the importance of custom reference gene selection when studies are conducted under diverse experimental conditions. A standardized qRT-PCR analysis procedure for gene functional studies is provided that could be useful in studies on other insect species.

Expression and localization of SWEETs in Populus and the effect of SWEET7 overexpression in secondary growth

2020 ◽  
Author(s):  
Li Zhang ◽  
Lijuan Wang ◽  
Jin Zhang ◽  
Cai Song ◽  
Yu Li ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Sugar Content ◽  
Expression Patterns ◽  
Secondary Growth ◽  
Wood Formation ◽  
Pcr Analysis ◽  
Sugar Transporters ◽  
Real Time Quantitative Pcr ◽  
Physiological Processes ◽  
Gene Structures

Abstract In trees, wood formation needs carbon import from the photosynthetic source tissues. Sugar transporters play important roles in carbohydrate transport into wood-forming cells. SWEETs (Sugars Will Eventually be Exported Transporters) play essential roles in many physiological processes. However, the roles of this family in the growth and development of woody plants have not been systematically investigated. In this study, 27 SWEET genes were identified in the Populus trichocarpa genome. These SWEET genes were classified into four clades based on their phylogenetic relationships, gene structures, conserved motifs, and chromosomal locations. Representative SWEET members from each clade were selected for further studies. The PagSWEETs were localized to plasma membrane, vacuolar, endoplasmic reticulum (ER) or Golgi. Real-time quantitative PCR analysis showed that PagSWEETs have distinct expression patterns in various tissues, and PagSWEET5, 7, 10b, 10c, 15b, 17a, and 17c exhibited high expression levels in stems. PagSWEET7 is localized to the cytoplasmic membrane and specifically expressed in the phloem as detected by histochemical GUS assays. Xylem production and xylem sugar content were greater in developing wood of SWEET7 overexpression (OX) than Wild-type (WT) lines. Collectively, these results provide valuable information for further investigating functions of PagSWEET genes, and identify PagSWEET7 as a candidate gene for using biotechnology to modify the wood formation in poplar.

scholarly journals Identification of miRNA-eQTLs in maize mature leaf by GWAS

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Shu-Yun Chen ◽  
Mei-Hsiu Su ◽  
Karl A. Kremling ◽  
Nicholas K. Lepak ◽  
M. Cinta Romay ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Developmental Stages ◽  
Mature Leaf ◽  
Plant Genome ◽  
Expression Level ◽  
Genome Wide ◽  
Mirna Expression Level ◽  
Next Generation Sequencing Ngs

Abstract Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.

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 Serotonin and Melatonin Biosynthesis in Plants: Genome-Wide Identification of the Genes and Their Expression Reveal a Conserved Role in Stress and Development

2021 ◽  
Vol 22 (20) ◽  
pp. 11034
Author(s):  
Bidisha Bhowal ◽  
Annapurna Bhattacharjee ◽  
Kavita Goswami ◽  
Neeti Sanan-Mishra ◽  
Sneh L. Singla-Pareek ◽  
...  
Keyword(s):  
Target Genes ◽  
Functional Characterization ◽  
Gene Families ◽  
Pcr Analysis ◽  
Tryptophan Decarboxylase ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Suitable Target

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

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

2021 ◽  
Vol 12 ◽  
Author(s):  
Lei Zhang ◽  
Xiaolan Ge ◽  
Jiujun Du ◽  
Xingqi Cheng ◽  
Xiaopeng Peng ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Wood Quality ◽  
Target Prediction ◽  
Wood Formation ◽  
Sequencing Analysis ◽  
Oxidoreductase Activity ◽  
Regulatory Processes ◽  
Genome Wide ◽  
Phenylpropanoid Biosynthesis

Poplar is an important bioenergy tree species. lncRNAs play important roles in various biological regulatory processes, and their expression pattern is more tissue-specific than mRNAs. In this study, P. deltoides “Danhong” (Pd) and P. simonii “Tongliao1” (Ps) with different growth rates and wood quality were used as experimental materials, and the transcriptomes of their shoot apical meristem, xylem, and phloem were sequenced. Furthermore, high-throughput RNA sequencing analysis revealed that the expression patterns of genes and lncRNAs are different between the two genotypes. 6,355 lncRNAs were identified. Based on target prediction, lncRNAs and target genes were involved in ADP binding, oxidoreductase activity, phenylpropanoid biosynthesis, and cyanoamino acid metabolism. The DElncRNAs in two poplars were co-expressed with transcription factors and structural genes of lignin and flavonoid pathways. In addition, we found the potential target lncRNAs of miRNA. This result provides basic evidence for a better understanding of the regulatory role of lncRNAs in regulating phenylalanine molecular pathways and wood formation.

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.

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