scholarly journals Transcriptome analysis of diploid and triploid Populus tomentosa

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10204
Author(s):  
Wen Bian ◽  
Xiaozhen Liu ◽  
Zhiming Zhang ◽  
Hanyao Zhang
Keyword(s):  
Transcriptome Sequencing ◽  
Carbon Fixation ◽  
Wood Quality ◽  
Populus Tomentosa ◽  
Plant Materials ◽  
Young Tree ◽  
Mapk Signalling Pathway ◽  
Expression Of Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Triploid Populus Tomentosa

Triploid Chinese white poplar (Populus tomentosa Carr., Salicaceae) has stronger advantages in growth and better stress resistance and wood quality than diploid P. tomentosa. Using transcriptome sequencing technology to identify candidate transcriptome-based markers for growth vigor in young tree tissue is of great significance for the breeding of P. tomentosa varieties in the future. In this study, the cuttings of diploid and triploid P. tomentosa were used as plant materials, transcriptome sequencing was carried out, and their tissue culture materials were used for RT-qPCR verification of the expression of genes. The results showed that 12,240 differentially expressed genes in diploid and triploid P. tomentosa transcripts were annotated and enriched into 135 metabolic pathways. The top six pathways that enriched the most significantly different genes were plant-pathogen interaction, phenylpropanoid biosynthesis, MAPK signalling pathway-plant, ascorbate and aldarate metabolism, diterpenoid biosynthesis, and the betalain biosynthesis pathway. Ten growth-related genes were selected from pathways of plant hormone signal transduction and carbon fixation in photosynthetic organisms for RT-qPCR verification. The expression levels of MDH and CYCD3 in tissue-cultured and greenhouse planted triploid P. tomentosa were higher than those in tissue-cultured diploid P. tomentosa, which was consist ent with the TMM values calculated by transcriptome.

scholarly journals Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xue-Jiao Li ◽  
Jian-Li Yang ◽  
Bing Hao ◽  
Ying-Chun Lu ◽  
Zhi-Long Qian ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Panax Notoginseng ◽  
Chinese Medicinal Herb ◽  
Developmental Factors ◽  
Expression Of Genes ◽  
Complex Biological Process ◽  
Phenylpropanoid Biosynthesis ◽  
Coordinated Expression ◽  
Major Storage Protein

Abstract Background Taproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood. Results A total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with “plant hormone signal transduction,” “starch and sucrose metabolism,” and “phenylpropanoid biosynthesis” were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng. Conclusion The results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.

scholarly journals Cryptic oxygen cycling in anoxic marine zones

2017 ◽  
Vol 114 (31) ◽  
pp. 8319-8324 ◽  
Author(s):  
Emilio Garcia-Robledo ◽  
Cory C. Padilla ◽  
Montserrat Aldunate ◽  
Frank J. Stewart ◽  
Osvaldo Ulloa ◽  
...  
Keyword(s):  
Surface Layer ◽  
Carbon Fixation ◽  
Nitrogen Loss ◽  
Biogeochemical Cycling ◽  
Oxygenic Photosynthesis ◽  
Nitrite Oxidation ◽  
Tight Coupling ◽  
Expression Of Genes ◽  
Aerobic Processes ◽  
Oxygen Cycling

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30–50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteriaProchlorococcusspp. Free O2levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

scholarly journals Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhanru Shao ◽  
Pengyan Zhang ◽  
Chang Lu ◽  
Shaoxuan Li ◽  
Zhihang Chen ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Ribosomal Proteins ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Brown Seaweed ◽  
Saccharina Japonica ◽  
Tca Cycle ◽  
New Genes ◽  
Mannitol Metabolism

Abstract Background Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. Alginate and mannitol regulatory networks and molecular mechanisms are largely unknown. Results With WGCNA and trend analysis of 20,940 known genes and 4264 new genes produced from transcriptome sequencing of 30 kelp samples from different stages and tissues, we deduced that ribosomal proteins, light harvesting complex proteins and “imm upregulated 3” gene family are closely associated with the meristematic growth and kelp maturity. Moreover, 134 and 6 genes directly involved in the alginate and mannitol metabolism were identified, respectively. Mannose-6-phosphate isomerase (MPI2), phosphomannomutase (PMM1), GDP-mannose 6-dehydrogenase (GMD3) and mannuronate C5-epimerase (MC5E70 and MC5E122) are closely related with the high content of alginate in the distal blade. Mannitol accumulation in the basal blade might be ascribed to high expression of mannitol-1-phosphate dehydrogenase (M1PDH1) and mannitol-1-phosphatase (M1Pase) (in biosynthesis direction) and low expression of mannitol-2-dehydrogenase (M2DH) and Fructokinase (FK) (in degradation direction). Oxidative phosphorylation and photosynthesis provide ATP and NADH for mannitol metabolism whereas glycosylated cycle and tricarboxylic acid (TCA) cycle produce GTP for alginate biosynthesis. RNA/protein synthesis and transportation might affect alginate complex polymerization and secretion processes. Cryptochrome (CRY-DASH), xanthophyll cycle, photosynthesis and carbon fixation influence the production of intermediate metabolite of fructose-6-phosphate, contributing to high content of mannitol in the basal blade. Conclusions The network of co-responsive DNA synthesis, repair and proteolysis are presumed to be involved in alginate polymerization and secretion, while upstream light-responsive reactions are important for mannitol accumulation in meristem of kelp. Our transcriptome analysis provides new insights into the transcriptional regulatory networks underlying the biosynthesis of alginate and mannitol during S. japonica developments.

Influences of Laccase Mediator System on Bleachability and Fiber Properties of APMP Pulp

2014 ◽  
Vol 1081 ◽  
pp. 299-303
Author(s):  
Hui Mei Wang ◽  
Yu Liu ◽  
Jia Chuan Chen ◽  
Zhen Wang
Keyword(s):  
Hydrogen Peroxide ◽  
Populus Tomentosa ◽  
Fiber Morphology ◽  
Alkaline Hydrogen Peroxide ◽  
Obvious Effect ◽  
Peroxide Bleaching ◽  
Fiber Properties ◽  
Mediator System ◽  
Laccase Mediator System ◽  
Triploid Populus Tomentosa

In this research, the laccase mediator system (LMS) was used to modify the unbleached triploid populus tomentosa alkaline hydrogen peroxide pulp (APMP). The changes of pulp brightness were measured and the effects of LMS on the subsequent hydrogen peroxide bleaching were also determined. Besides, the fiber morphology was analyzed by ESEM, and then the obvious changes of pulp have been recovered. In a word, the LMS has obvious effect on cellulose.

scholarly journals Expression of Genes Related to Phenylpropanoid Biosynthesis in Different Organs of Ixeris dentata var. albiflora

Molecules ◽  
2017 ◽  
Vol 22 (6) ◽  
pp. 901 ◽  
Author(s):  
Sang-Hoon Lee ◽  
Yun-Ji Park ◽  
Sang Un Park ◽  
Sang-Won Lee ◽  
Seong-Cheol Kim ◽  
...  
Keyword(s):  
Expression Of Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Ixeris Dentata

scholarly journals Antioxidative low molecular weight extractives from triploid Populus tomentosa xylem

BioResources ◽  
2010 ◽  
Vol 6 (1) ◽  
pp. 232-242
Author(s):  
Chuan-Ling Si ◽  
Yi-Yuan Lu ◽  
Yu Zhang ◽  
Jie Xu ◽  
Pan-Pan Qin ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Paper Industry ◽  
Radical Scavenging ◽  
Good Alternative ◽  
Populus Tomentosa ◽  
Low Molecular Weight ◽  
Phytochemical Investigation ◽  
Populus Tomentosa Carr ◽  
Triploid Populus Tomentosa ◽  
Bioactive Potential

Triploid Populus tomentosa Carr. (Salicaceae) is a good alternative to meet the increasing need of the global pulp and paper industry. Meanwhile, the xylem of this species could be a useful bioresource to develop low molecular extractives with significant bioactive potential. In the present work, a phytochemical investigation on aqueous EtOH extractives of Triploid P. tomentosa xylem, by systematical performance of Sephadex LH-20 open column chromatography and Thin Layer Chromatography (TLC), resulted in the isolation of two phenolic acids (ρ-coumaric acid (I) and caffeic acid (II)), two flavonoids (apigenin (III) and luteolin (IV)), and three phenolic glucosides (salicortin (V), salireposide (VI) and populoside (VII)). The structure elucidation and determination of the isolated extractives were based on their spectroscopical data and physiochemical evidences. This was the first time to report the low molecular weight extractives of Triploid P. tomentosa. Various low molecular weight extractives fromTriploid P. tomentosa xylem exhibited significant antioxidative activities by DPPH and hydroxyl radical scavenging assays.

scholarly journals iTRAQ-based comparative proteomic analysis of differences in the protein profiles of stems and leaves from two alfalfa genotypes

2020 ◽  
Author(s):  
Hao Sun ◽  
Jie Yu ◽  
Fan Zhang ◽  
Junmei Kang ◽  
Mingna Li ◽  
...  
Keyword(s):  
Leaf Development ◽  
Proteomic Analysis ◽  
Regulatory Networks ◽  
Carbon Fixation ◽  
Chlorophyll Biosynthesis ◽  
Chlorophyll Synthesis ◽  
Phenylpropanoid Pathway ◽  
Chlorophyll Metabolism ◽  
Phenylpropanoid Biosynthesis ◽  
Proteomic Study

Abstract Background: To explore the molecular regulatory mechanisms of early stem and leaf development, proteomic analysis was performed on leaves and stems of F genotype alfalfa, with thin stems and small leaves, and M genotype alfalfa, with thick stems and large leaves.Results: Based on fold-change thresholds of >1.20 or <0.83 (p<0.05), a large number of proteins were identified as being differentially enriched between the M and F genotypes: 249 downregulated and 139 upregulated in stems and 164 downregulated and 134 upregulated in leaves. The differentially enriched proteins in stems were mainly involved in amino acid biosynthesis, phenylpropanoid biosynthesis, carbon fixation, and phenylalanine metabolism. The differentially enriched proteins in leaves were mainly involved in porphyrin and chlorophyll metabolism, phenylpropanoid biosynthesis, starch and sucrose metabolism, and carbon fixation in photosynthetic organisms. Six differentially enriched proteins were mapped onto the porphyrin and chlorophyll metabolism pathway in leaves of the M genotype, including five upregulated proteins involved in chlorophyll biosynthesis and one downregulated protein involved in chlorophyll degradation. Eleven differentially enriched proteins were mapped onto the phenylpropanoid pathway in stems of the M genotype, including two upregulated proteins and nine downregulated proteins. Conclusion: Enhanced chlorophyll synthesis and decreased lignin synthesis provided a reasonable explanation for the larger leaves and lower levels of stem lignification in M genotype alfalfa. This proteomic study aimed to classify the functions of differentially enriched proteins and to provide information on the molecular regulatory networks involved in stem and leaf development.

scholarly journals Transcriptome Analysis of Differentially Expressed Genes in Wild Jujube Seedlings under Salt Stress

2020 ◽  
Vol 145 (3) ◽  
pp. 174-185 ◽  
Author(s):  
Xinyi Chang ◽  
Junli Sun ◽  
Lianling Liu ◽  
Wang He ◽  
Baolong Zhao
Keyword(s):  
Salt Stress ◽  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Carbon Fixation ◽  
Acid Metabolism ◽  
Chlorophyll Synthesis ◽  
Differentially Expressed ◽  
Gene Encoding ◽  
Chlorophyll Metabolism ◽  
Photosynthetic Antenna

Wild jujube (Ziziphus acidojujuba) and cultivated jujube (Ziziphus jujuba) belong to the family Rhamnaceae. Jujubes have marked drought- and salt-tolerant properties. After salt stress, wild jujube seedling growth was inhibited and photosynthetic efficiency was reduced. A bioinformatics approach was used to analyze the transcriptomics data from wild jujube seedlings grown under salt stress, and the genes differentially expressed under the salt stress were identified to provide a theoretical basis for the development and use of wild jujube plantations in salinized soil. The transcriptome sequencing from leaves of wild jujube seedlings was carried out using second-generation sequencing technology. The effects of salt stress on the differential expression of photosynthesis-related genes in wild jujube seedlings were analyzed. Transcriptome sequencing revealed a total of 5269 differentially expressed genes (DEGs), of which 2729 were up-regulated and 2540 were down-regulated. DEGs were mainly enriched with respect to photosynthesis, photosynthetic antenna proteins, glyoxylic acid and dicarboxylic acid metabolism, linolenic acid metabolism, cysteine and methionine metabolism, and porphyrin and chlorophyll metabolism. Among them, the photosynthesis pathway-related DEGs were most highly enriched. Further analysis of porphyrin and chlorophyll synthesis and photosynthesis-related pathways revealed that they were significantly enriched by 97 photosynthesis-related DEGs. The DEGs in the photosynthesis and photosynthetic antenna protein pathways were down-regulated, whereas the DEGs glutamyl-tRNA reductase (HEMA), ferrochelatase (HEMH), and pheophorbide a oxygenase (PAO) in the porphyrin and chlorophyll synthesis pathways were up-regulated, with the remainder being down-regulated. The nuclear gene encoding Rubisco, the key enzyme in the photosynthetic carbon fixation pathway, was also down-regulated. The results showed that the photosynthetic rate of wild jujube seedlings decreased following exposure to salinity stress, an effect that was related to the increased synthesis of 5-aminolevulinic acid and heme, and the up-regulation of expression of a gene encoding a chlorophyll-degrading enzyme, and was related to the down-regulation of gene expression in photosynthesis-related pathways such as light energy capture and carbon fixation. Selection of nine DEGs related to photosynthesis and chlorophyll biosynthesis by quantitative real-time-PCR confirmed that expression changes of these nine DEGs were consistent with the transcriptome sequencing results.

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