scholarly journals Transcriptome Analysis Unravels Metabolic and Molecular Pathways Related to Fruit Sac Granulation in a Late-Ripening Navel Orange (Citrus sinensis Osbeck)

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 95 ◽  
Author(s):  
Li-Ming Wu ◽  
Ce Wang ◽  
Li-Gang He ◽  
Zhi-Jing Wang ◽  
Zhu Tong ◽  
...  
Keyword(s):  
Cell Wall ◽  
Low Temperature ◽  
Citrus Sinensis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Winter Temperature ◽  
Soluble Solid Content ◽  
Navel Orange ◽  
Cell Wall Metabolism ◽  
Qrt Pcr

Lanelate navel orange (Citrus sinensis Osbeck) is a late-ripening citrus cultivar increasingly planted in China. The physiological disorder juice sac granulation often occurs in the fruit before harvest, but the physiological and molecular mechanisms underlying this disorder remain elusive. In this study, we found that fruit granulation of the late-ripening navel orange in the Three Gorges area is mainly caused by the low winter temperature in high altitude areas. Besides, dynamic changes of water content in the fruit after freezing were clarified. The granulation of fruit juice sacs resulted in increases in cell wall cellulose and decreases in soluble solid content, and the cells gradually became shrivelled and hollow. Meanwhile, the contents of pectin, cellulose, and lignin in juice sac increased with increasing degrees of fruit granulation. The activities of pectin methylesterase (PME) and the antioxidant enzymes peroxidase (POD), superoxide dismutase, and catalase increased, while those of polygalacturonase (PG) and cellulose (CL) decreased. Furthermore, a total of 903 differentially expressed genes were identified in the granulated fruit as compared with non-disordered fruit using RNA-sequencing, most of which were enriched in nine metabolic pathways, and qRT-PCR results suggested that the juice sac granulation is closely related to cell wall metabolism. In addition, the expression of PME involved in pectin decomposition was up-regulated, while that of PG was down-regulated. Phenylalanine ammonia lyase (PAL), cinnamol dehydrogenase (CAD), and POD related to lignin synthesis were up-regulated, while CL involved in cellulose decomposition was down-regulated. The expression patterns of these genes were in line with those observed in low-temperature treatment as revealed by qRT-PCR, further confirming that low winter temperature is associated with the fruit granulation of late-ripening citrus. Accordingly, low temperature would aggravate the granulation by affecting cell wall metabolism of late-ripening citrus fruit.

Molecular and physiological mechanisms underlying magnesium-deficiency-induced enlargement, cracking and lignification of Citrus sinensis leaf veins

2020 ◽  
Vol 40 (9) ◽  
pp. 1277-1291 ◽  
Author(s):  
Xin Ye ◽  
Xu-Feng Chen ◽  
Li-Ya Cai ◽  
Ning-Wei Lai ◽  
Chong-Ling Deng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Citrus Sinensis ◽  
Molecular Mechanisms ◽  
Rho Gtpase ◽  
Magnesium Deficiency ◽  
Lignin Biosynthesis ◽  
Starch Accumulation ◽  
Ascorbate Oxidase ◽  
Mg Deficiency ◽  
Leaf Veins

Abstract Little is known about the physiological and molecular mechanisms underlying magnesium (Mg)-deficiency-induced enlargement, cracking and lignification of midribs and main lateral veins of Citrus leaves. Citrus sinensis (L.) Osbeck seedlings were irrigated with nutrient solution at a concentration of 0 (Mg-deficiency) or 2 (Mg-sufficiency) mM Mg(NO3)2 for 16 weeks. Enlargement, cracking and lignification of veins occurred only in lower leaves, but not in upper leaves. Total soluble sugars (glucose + fructose + sucrose), starch and cellulose concentrations were less in Mg-deficiency veins of lower leaves (MDVLL) than those in Mg-sufficiency veins of lower leaves (MSVLL), but lignin concentration was higher in MDVLL than that in MSVLL. However, all four parameters were similar between Mg-deficiency veins of upper leaves (MDVUL) and Mg-sufficiency veins of upper leaves (MSVUL). Using label-free, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, we identified 1229 and 492 differentially abundant proteins (DAPs) in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively. Magnesium-deficiency-induced alterations of Mg, nonstructural carbohydrates, cell wall components, and protein profiles were greater in veins of lower leaves than those in veins of upper leaves. The increased concentration of lignin in MDVLL vs MSVLL might be caused by the following factors: (i) repression of cellulose and starch accumulation promoted lignin biosynthesis; (ii) abundances of proteins involved in phenylpropanoid biosynthesis pathway, hormone biosynthesis and glutathione metabolism were increased; and (iii) the abundances of the other DAPs [viz., copper/zinc-superoxide dismutase, ascorbate oxidase (AO) and ABC transporters] involved in lignin biosynthesis were elevated. Also, the abundances of several proteins involved in cell wall metabolism (viz., expansins, Rho GTPase-activating protein gacA, AO, monocopper oxidase-like protein and xyloglucan endotransglucosylase/hydrolase) were increased in MDVLL vs MSVLL, which might be responsible for the enlargement and cracking of leaf veins.

scholarly journals Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe)

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yuan Li ◽  
Yun Ren ◽  
Ying Zhao ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Mirna Target ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Putative Target ◽  
Genome Wide ◽  
Ginger Rhizome ◽  
Rhizome Development

Abstract Background MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. Results In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. Conclusion This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.

Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq

2020 ◽  
Author(s):  
Xin Ye ◽  
Hui-Yu Huang ◽  
Feng-Lin Wu ◽  
Li-Ya Cai ◽  
Ning-Wei Lai ◽  
...  
Keyword(s):  
Cell Wall ◽  
Citrus Sinensis ◽  
Molecular Mechanisms ◽  
Magnesium Deficiency ◽  
Lignin Biosynthesis ◽  
Common Elements ◽  
Rna Seq ◽  
Transcript Levels ◽  
Mg Deficiency ◽  
Leaf Vein

Abstract Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.

scholarly journals Selection and Validation of Appropriate Reference Genes for qRT-PCR Analysis of Flowering Stages and Different Genotypes of Iris Germanica L.

2021 ◽  
Author(s):  
Yinjie Wang ◽  
Yongxia Zhang ◽  
Qingquan Liu ◽  
Haiying Tong ◽  
Ting Zhang ◽  
...  
Keyword(s):  
Reference Genes ◽  
Molecular Mechanisms ◽  
Gene Selection ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Herbaceous Plant ◽  
Flower Bud ◽  
Perennial Herbaceous Plant ◽  
Qrt Pcr ◽  
Iris Germanica

Abstract Iris germanica L. is a perennial herbaceous plant that has been widely cultivated worldwide and is popular for its elegant and vibrantly colorful flowers. Selection of appropriate reference genes is the prerequisite for accurate normalization of target gene expression by quantitative real-time PCR. However, to date, the most suitable reference genes for flowering stages have not been elucidated in I. germanica. In this study, eight candidate reference genes were examined for the normalization of qRT-PCR in three I. germanica cultivars, and their stability were evaluated by four different algorithms (GeNorm, NormFinder, BestKeeper, and Ref-finder). The results revealed that IgUBC and IgGAPDH were the most stable reference genes in ‘00246’ and ‘Elizabeth’, and IgTUB and IgUBC showed stable expression in ‘2010200’. IgUBC and IgGAPDH were the most stable in all samples, while IgUBQ showed the least stability. Finally, to validate the reliability of the selected reference genes, the expression patterns of IgFT (Flowering Locus T gene) was analyzed and emphasized the importance of appropriate reference gene selection. This work presented the first systematic study of reference genes selection during flower bud development and provided guidance to research of the molecular mechanisms of flowering stages in I. germanica.

scholarly journals Expression Patterns and Gene Analysis of the Cellulose Synthase Gene Superfamily in Eucalyptus grandis

Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1254
Author(s):  
Guo Liu ◽  
Yaojian Xie ◽  
Xiuhua Shang ◽  
Zhihua Wu
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Cellulose Synthase ◽  
Primary Cell Wall ◽  
Regulation Mechanism ◽  
Cellulose Content ◽  
Qrt Pcr ◽  
Different Parts

Cellulose is the world’s most abundant renewable energy resource, and a variety of cellulose synthase genes are involved in the biosynthesis of cellulose. In the process of cellulose synthesis, all cellulose synthases are interrelated and act synergistically. In this study, we analyzed the contents of cellulose, hemicellulose, and lignin in the different parts and tissues of E. grandis. The results showed that the cellulose content had greater differences among three different heights. On this basis, we carried out the transcriptome-wide profiling of gene expression patterns using RNA sequencing. A total of 2066 differentially expressed genes were identified for three pairwise comparisons between three different heights, most of which were related to the programmed photosynthetic membrane and photosystem. A total of 100 transcripts of CSs (58 CesA and 42 Csl) were obtained from transcriptome libraries. The expression pattern of these genes indicated that different CS genes had a wide range of expression profiles. A phylogenetic analysis of 135 reference CS genes showed that the CSs of E. grandis were clustered into six major groups (CesA1-9, CslA, CslB/H, CslD, CslE, and CslG). Based on the weighted gene co-expression network analysis, a dual-directional regulation mechanism between Csl and CesA proteins in the cellulose biosynthesis was identified. The gene expression profile analysis, using qRT-PCR in different tissues of E. grandis, demonstrated that the CSs were highly expressed in xylem, and CesAs had a higher relative expression than Csls. The analysis of sequence similarity combined with the expression pattern indicated that the CesA1, 3, and 6 transcripts were associated with the biosynthesis of the secondary cell wall, and CesA4, 5, and 7 transcripts were more likely to associate with the biosynthesis of the primary cell wall. Finally, the qRT-PCR analysis confirmed the expression of 11 selected CSs in three different parts of E. grandis.

Antioxidant changes of Thomson navel orange (Citrus sinensis) on three rootstocks under low temperature stress

2011 ◽  
Vol 52 (6) ◽  
pp. 576-580 ◽  
Author(s):  
Yahya Tajvar ◽  
Reza Fotouhi Ghazvini ◽  
Yousef Hamidoghli ◽  
Reza Hassan Sajedi
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Citrus Sinensis ◽  
Low Temperature Stress ◽  
Navel Orange

scholarly journals Compatative Transcriptome Analysis Reveals Sesquiterpene Biosynthesis among 1-, 2- and 3-year Old Atractylodes Chinensis

2021 ◽  
Author(s):  
Jianhua Zhao ◽  
Chengzhen Sun ◽  
Shanshan Ma ◽  
Jinshuang Zheng ◽  
Xin Du ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Bioactive Compound ◽  
Pcr Analysis ◽  
Squalene Epoxidase ◽  
Sequencing Analysis ◽  
Qrt Pcr

Abstract Background: Atractylodes chinensis (DC.) Koidz is a well-known medicinal plant containing the major bioactive compound, atrctylodin, a sesquiterpenoids. High-performance liquid chromatography (HPLC) analysis demonstrated that atrctylodin was most abundant in 3-year old A. chinensis rhizomes, compared with those from 1-year and 2-year-old plants, however, the molecular mechanisms underlying accumulation of atrctylodin in rhizomes are poorly understood. Results: In this study, we characterized the transcriptomes from 1-, 2, and 3-year old (Y1, Y2, and Y3, respectively) A. chinensis, to identify differentially expressed genes (DEGs). We identified 205 and 226 unigenes encoding the enzyme genes in the mevalonate (MVA) and methylerythritol phosphate (MEP) sesquiterpenoid biosynthesis pathways, respectively. To confirm the reliability of the RNA sequencing analysis, eleven genes key genes encoding factors involved in the sesquiterpene biosynthetic pathway, as well as in pigment, amino acid, hormone, and transcription factor functions, were selected for quantitative real time PCR (qRT-PCR) analysis. The results demonstrated similar expression patterns to those determined by RNA sequencing, with a Pearson’s correlation coefficient of 0.9 between qRT-PCR and RNA-seq data. Differential gene expression analysis of samples from different ages revealed 52 genes related to sesquiterpenoids biosynthesis. Among these, seven DEGs were identified in Y1 vs Y2, Y1 vs Y3, and Y2 vs Y3, of which five encoded four key enzymes, squalene/phytoene synthase, squalene-hopene cyclase, squalene epoxidase and dammarenediol II synthase. These four enzymes directly related to squalene biosynthesis and subsequent catalytic action. To validate the result of these seven DEGs, qRT-PCR was performed and indicated most of them displayed lower relative expression in 3-year old rhizome, similar to transcriptomic analysis. Conclusion: The enzymes SS, SHC, SE and DS down-regulated expression in 3-year old rhizome. This data corresponded to the higher content of sesquiterpenes in 3-year old rhizome, and confirmed by qRT-PCR. The results of comparative transcriptome analysis and identified key enzyme genes laid a solid foundation for investigation of production sesquiterpenoid in A. chinensis.

scholarly journals Hot Water Treatment Maintains Normal Ripening and Cell Wall Metabolism in Mango (Mangifera indica L.) Fruit

HortScience ◽  
2012 ◽  
Vol 47 (10) ◽  
pp. 1466-1471 ◽  
Author(s):  
Zhengke Zhang ◽  
Zhaoyin Gao ◽  
Min Li ◽  
Meijiao Hu ◽  
Hui Gao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Water Treatment ◽  
Low Temperature ◽  
Mangifera Indica ◽  
Water Soluble ◽  
Hot Water ◽  
Hot Water Treatment ◽  
Cell Wall Metabolism ◽  
Low Temperature Storage ◽  
Temperature Storage

‘Tainong 1’ mango fruit were treated with hot water for 10 minutes at 55 °C and then stored at 5 °C for 3 weeks. After removal from low-temperature storage, the effects of hot water treatment (HWT) on chilling injury (CI), ripening and cell wall metabolism during storage (20 °C, 5 days) were investigated. HWT reduced the CI development of the fruit as manifested by firmer texture, external browning, and fungal lesions. A more rapid ripening process, as indicated by changes in firmness, respiration rate, and ethylene production, occurred in heated fruit after exposure to low temperature as compared with non-heated fruit. At the same time, the cell wall components in heated fruit contained more water-soluble pectin and less 1,2-cyclohexylenedinitrilotetraactic acid (CDTA)-soluble pectin than those in non-heated fruit. HWT also maintained higher polygalacturonase [enzyme classification (EC) 3.2.1.15] and β-galactosidase (EC 3.2.1.23) activities as well as lower pectin methylesterase (EC 3.1.1.11) activity. In general, the changes of ripening and cell wall metabolism parameters in the heated fruit after low-temperature storage exhibited a comparable pattern to that of non-cold-stored fruit.

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