scholarly journals Transcriptome analysis of Cinnamomum migao seed germination in medicinal plants of Southwest China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaolong Huang ◽  
Tian Tian ◽  
Jingzhong Chen ◽  
Deng Wang ◽  
Bingli Tong ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Seed Germination ◽  
Transcriptome Analysis ◽  
Energy Supply ◽  
Tricarboxylic Acid Cycle ◽  
Cell Structure ◽  
Seed Vigor ◽  
Differentially Expressed ◽  
Oil Bodies ◽  
Physiological Indexes

Abstract Background Cinnamomum migao is an endangered evergreen woody plant species endemic to China. Its fruit is used as a traditional medicine by the Miao nationality of China and has a high commercial value. However, its seed germination rate is extremely low under natural and artificial conditions. As the foundation of plant propagation, seed germination involves a series of physiological, cellular, and molecular changes; however, the molecular events and systematic changes occurring during C. migao seed germination remain unclear. Results In this study, combined with the changes in physiological indexes and transcription levels, we revealed the regulation characteristics of cell structures, storage substances, and antioxidant capacity during seed germination. Electron microscopy analysis revealed that abundant smooth and full oil bodies were present in the cotyledons of the seeds. With seed germination, oil bodies and other substances gradually degraded to supply energy; this was consistent with the content of storage substances. In parallel to electron microscopy and physiological analyses, transcriptome analysis showed that 80–90 % of differentially expressed genes (DEGs) appeared after seed imbibition, reflecting important development and physiological changes. The unigenes involved in material metabolism (glycerolipid metabolism, fatty acid degradation, and starch and sucrose metabolism) and energy supply pathways (pentose phosphate pathway, glycolysis pathway, pyruvate metabolism, tricarboxylic acid cycle, and oxidative phosphorylation) were differentially expressed in the four germination stages. Among these DEGs, a small number of genes in the energy supply pathway at the initial stage of germination maintained high level of expression to maintain seed vigor and germination ability. Genes involved in lipid metabolism were firstly activated at a large scale in the LK (seed coat fissure) stage, and then genes involved in carbohydrates (CHO) metabolism were activated, which had their own species specificity. Conclusions Our study revealed the transcriptional levels of genes and the sequence of their corresponding metabolic pathways during seed germination. The changes in cell structure and physiological indexes also confirmed these events. Our findings provide a foundation for determining the molecular mechanisms underlying seed germination.

scholarly journals Transcriptome Analysis of Cinnamomum Migao Seed Germination in Medicinal Plants of Southwest China

2020 ◽  
Author(s):  
xiaolong Huang ◽  
Tian Tian ◽  
Jingzhong Chen ◽  
Deng Wang ◽  
Bingli Tong ◽  
...  
Keyword(s):  
Seed Germination ◽  
Transcriptome Analysis ◽  
Energy Supply ◽  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Cell Structure ◽  
Seed Vigor ◽  
Differentially Expressed ◽  
Oil Bodies ◽  
Physiological Indexes

Abstract Background: Cinnamomum migao is an endangered evergreen woody plant species endemic to China. Its fruit is used as a traditional medicine by the Miao nationality of China and has a high commercial value. However, its seed germination rate is very low under natural and artificial conditions. As the foundation of plant propagation, seed germination involves a series of physiological, cellular, and molecular changes; however, the molecular events and systematic changes occurring during C. migao seed germination remain unclear.Results: In this study, combined with the changes in physiological indexes and transcription levels, we revealed the regulation characteristic of cell structures, storage substances, and antioxidant capacity during seed germination. Anatomical analysis revealed that abundant smooth and full oil bodies were present in the cotyledons of the seeds. With seed germination, the oil bodies and other substances gradually degraded to supply energy; this was consistent with the content of storage substances. In parallel to anatomical and physiological analyses, transcriptome analysis showed that 80%–90% of differentially expressed genes (DEGs) appeared after seed imbibition, reflecting important development and physiological changes. The unigenes involved in material metabolism (glycerolipid metabolism, fatty acid degradation, and starch and sucrose metabolism) and energy supply pathways (pentose phosphate pathway, glycolysis pathway, pyruvate metabolism, tricarboxylic acid cycle, and oxidative phosphorylation) were differentially expressed in the four germination stages. Among these DEGs, a small number of genes in the energy supply pathway at the initial stage of germination maintained high level of expression to maintain seed vigor and germination ability. Then, the genes involved in lipid metabolism were activated at a large scale, followed by the activation of the genes involved in CHO metabolism, which had its own species specificity. Conclusions: Our study revealed the transcriptional levels of genes during seed germination as well as determined the order of the metabolic pathways. The changes in cell structure and physiological indexes also confirmed these events. Our findings lay a foundation for determining the molecular mechanisms underlying seed germination.

High-pressure freezing of cells in suspension for low-voltage scanning electron microscopy (LVSEM)

1991 ◽  
Vol 49 ◽  
pp. 64-65
Author(s):  
Marek Malecki ◽  
James Pawley ◽  
Hans Ris
Keyword(s):  
Electron Microscopy ◽  
High Pressure ◽  
Low Voltage ◽  
Culture Media ◽  
Cell Structure ◽  
Freeze Substitution ◽  
Ice Crystal ◽  
High Pressure Freezing ◽  
Cell Culture Media ◽  
Voltage Scanning

The ultrastructure of cells suspended in physiological fluids or cell culture media can only be studied if the living processes are stopped while the cells remain in suspension. Attachment of living cells to carrier surfaces to facilitate further processing for electron microscopy produces a rapid reorganization of cell structure eradicating most traces of the structures present when the cells were in suspension. The structure of cells in suspension can be immobilized by either chemical fixation or, much faster, by rapid freezing (cryo-immobilization). The fixation speed is particularly important in studies of cell surface reorganization over time. High pressure freezing provides conditions where specimens up to 500μm thick can be frozen in milliseconds without ice crystal damage. This volume is sufficient for cells to remain in suspension until frozen. However, special procedures are needed to assure that the unattached cells are not lost during subsequent processing for LVSEM or HVEM using freeze-substitution or freeze drying. We recently developed such a procedure.

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

scholarly journals Understanding Rice-Magnaporthe Oryzae Interaction in Resistant and Susceptible Cultivars of Rice under Panicle Blast Infection Using a Time-Course Transcriptome Analysis

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 301
Author(s):  
Vishesh Kumar ◽  
Priyanka Jain ◽  
Sureshkumar Venkadesan ◽  
Suhas Gorakh Karkute ◽  
Jyotika Bhati ◽  
...  
Keyword(s):  
Cell Wall ◽  
Secondary Metabolites ◽  
Magnaporthe Oryzae ◽  
Transcriptome Analysis ◽  
Hormonal Regulation ◽  
Rice Blast ◽  
Blast Resistance ◽  
Differentially Expressed ◽  
Specific Response ◽  
Panicle Blast

Rice blast is a global threat to food security with up to 50% yield losses. Panicle blast is a more severe form of rice blast and the response of rice plant to leaf and panicle blast is distinct in different genotypes. To understand the specific response of rice in panicle blast, transcriptome analysis of blast resistant cultivar Tetep, and susceptible cultivar HP2216 was carried out using RNA-Seq approach after 48, 72 and 96 h of infection with Magnaporthe oryzae along with mock inoculation. Transcriptome data analysis of infected panicle tissues revealed that 3553 genes differentially expressed in HP2216 and 2491 genes in Tetep, which must be the responsible factor behind the differential disease response. The defense responsive genes are involved mainly in defense pathways namely, hormonal regulation, synthesis of reactive oxygen species, secondary metabolites and cell wall modification. The common differentially expressed genes in both the cultivars were defense responsive transcription factors, NBS-LRR genes, kinases, pathogenesis related genes and peroxidases. In Tetep, cell wall strengthening pathway represented by PMR5, dirigent, tubulin, cell wall proteins, chitinases, and proteases was found to be specifically enriched. Additionally, many novel genes having DOMON, VWF, and PCaP1 domains which are specific to cell membrane were highly expressed only in Tetep post infection, suggesting their role in panicle blast resistance. Thus, our study shows that panicle blast resistance is a complex phenomenon contributed by early defense response through ROS production and detoxification, MAPK and LRR signaling, accumulation of antimicrobial compounds and secondary metabolites, and cell wall strengthening to prevent the entry and spread of the fungi. The present investigation provided valuable candidate genes that can unravel the mechanisms of panicle blast resistance and help in the rice blast breeding program.

scholarly journals Transcriptome Analysis of Pre-Storage 1-MCP and High CO2-Treated ‘Madoka’ Peach Fruit Explains the Reduction in Chilling Injury and Improvement of Storage Period by Delaying Ripening

2021 ◽  
Vol 22 (9) ◽  
pp. 4437
Author(s):  
Han Ryul Choi ◽  
Min Jae Jeong ◽  
Min Woo Baek ◽  
Jong Hang Choi ◽  
Hee Cheol Lee ◽  
...  
Keyword(s):  
Cold Storage ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Chilling Injury ◽  
Chemical Properties ◽  
Storage Period ◽  
Differentially Expressed ◽  
Peach Fruit ◽  
High Co2 ◽  
Physico Chemical

Cold storage of peach fruit at low temperatures may induce chilling injury (CI). Pre-storage 1-MCP and high CO2 treatments were reported among the methods to ameliorate CI and reduce softening of peach fruit. However, molecular data indicating the changes associated with pre-storage 1-MCP and high CO2 treatments during cold storage of peach fruit are insufficient. In this study, a comparative analysis of the difference in gene expression and physico-chemical properties of fruit at commercial harvest vs. stored fruit for 12 days at 0 °C (cold-stored (CS), pre-storage 1-MCP+CS, and pre-storage high CO2+CS) were used to evaluate the variation among treatments. Several genes were differentially expressed in 1-MCP+CS- and CO2+CS-treated fruits as compared to CS. Moreover, the physico-chemical and sensory data indicated that 1-MCP+CS and CO2+CS suppressed CI and delayed ripening than the CS, which could lead to a longer storage period. We also identified the list of genes that were expressed commonly and exclusively in the fruit treated by 1-MCP+CS and CO2+CS and compared them to the fruit quality parameters. An attempt was also made to identify and categorize genes related to softening, physiological changes, and other ripening-related changes. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR). These results add information on the molecular mechanisms of the pre-storage treatments during cold storage of peach fruit. Understanding the genetic response of susceptible cultivars such as ‘Madoka’ to CI-reducing pre-storage treatments would help breeders release CI-resistant cultivars and could help postharvest technologists to develop more CI-reducing technologies.

scholarly journals Odontoblast processes in dentin revealed by fluorescent Di-I.

1995 ◽  
Vol 43 (2) ◽  
pp. 159-168 ◽  
Author(s):  
M R Byers ◽  
A Sugaya
Keyword(s):  
Electron Microscopy ◽  
Confocal Microscopy ◽  
Cell Structure ◽  
Carbocyanine Dyes ◽  
Carbocyanine Dye ◽  
Reparative Dentin ◽  
Hard Tissues ◽  
Odontoblast Process ◽  
Odontoblast Processes ◽  
Rat Molars

There has been controversy about the length and structure of the odontoblast process within dentin since the earliest histologic studies of teeth. Our objective was to use the fluorescent carbocyanine dye Di-I combined with a new gelatin embedment procedure and confocal microscopy to determine the structure and extent of odontoblast processes in developing and mature rat teeth, injured rat molars, reparative dentin, and adult monkey teeth. We found that odontoblast processes do not extend into outer dentin or to the dentin-enamel junction except during early stages of development. Those in innervated regions of crown are long and straight, whereas those in roots are extensively branched and shorter. Cavity injury to crown dentin caused odontoblast fragments to be aspirated into outer dentin. In reparative dentin the odontoblast processes were branched and similar to those in roots. We used photoconversion and electron microscopy to show that Di-I fills the entire odontoblast after gelatin embedment, including the cytoplasm. This is a different type of carbocyanine staining from any previously reported, and it also stains other cells in adjacent hard tissues such as bone and cementum. The Di-I-gelatin method is a new way to use carbocyanine dyes. It has enabled us to solve a long-standing controversy about the histology of teeth, and it should be useful for many other studies of cell structure.

Transcriptome analysis reveals differentially expressed genes associated with the mantled homeotic flowering abnormality in oil palm (Elaeis guineensis)

2010 ◽  
Vol 7 (1) ◽  
pp. 169-182 ◽  
Author(s):  
Thierry Beulé ◽  
Céline Camps ◽  
Ségolène Debiesse ◽  
Christine Tranchant ◽  
Stéphane Dussert ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Differentially Expressed

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

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