Transcriptome Comparative Analysis of Salt Stress Responsiveness in Chrysanthemum (Dendranthema grandiflorum) Roots by Illumina- and Single-Molecule Real-Time-Based RNA Sequencing

2018 ◽  
Vol 37 (12) ◽  
pp. 1016-1030 ◽  
Author(s):  
Qian Zhao ◽  
Ling He ◽  
Bei Wang ◽  
Qing-Lin Liu ◽  
Yuan-Zhi Pan ◽  
...  
Keyword(s):  
Salt Stress ◽  
Comparative Analysis ◽  
Real Time ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Dendranthema Grandiflorum ◽  
Stress Responsiveness

scholarly journals Single molecule real time (SMRT) full length RNA-sequencing reveals novel and distinct mRNA isoforms in human bone marrow cell subpopulations

2019 ◽  
Author(s):  
Anne Deslattes Mays ◽  
Marcel O. Schmidt ◽  
Garrett T. Graham ◽  
Elizabeth Tseng ◽  
Primo Baybayan ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Real Time ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Marrow Cell ◽  
Full Length ◽  
Protein Isoforms ◽  
Mrna Isoforms ◽  
Transcript Isoforms ◽  
Cell Subpopulations

AbstractHematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by single molecule, real time (SMRT) full length RNA sequencing. This analysis revealed a ∼5-fold higher number of transcript isoforms than previously detected and showed a distinct composition of individual transcript isoforms characteristic for bone marrow subpopulations. A detailed analysis of mRNA isoforms transcribed from the ANXA1 and EEF1A1 loci confirmed their distinct composition. The expression of proteins predicted from the transcriptome analysis was validated by mass spectrometry and validated previously unknown protein isoforms predicted e.g. for EEF1A1. These protein isoforms distinguished the lineage negative cell population from the lineage positive cell population. Finally, transcript isoforms expressed from paralogous gene loci (e.g. CFD, GATA2, HLA-A, B & C) also distinguished cell subpopulations but were only detectable by full length RNA sequencing. Thus, qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cell subpopulations indicating complex transcriptional regulation and protein isoform generation during hematopoiesis.

scholarly journals A Comparative Transcriptional Landscape of Two Castor Cultivars Obtained by Single-Molecule Sequencing Comparative Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yaxing Zhou ◽  
Guoli Zhu ◽  
Yun Wang ◽  
Zhibiao He ◽  
Wei Zhou
Keyword(s):  
Transcription Factors ◽  
Comparative Analysis ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Ricinus Communis ◽  
Full Length ◽  
Transcriptional Analysis ◽  
Oilseed Crop ◽  
Sequencing Analysis ◽  
Short Read

Background and Objectives: Castor (Ricinus communis L.) is an important non-edible oilseed crop. Lm-type female strains and normal amphiprotic strains are important castor cultivars, and are mainly different in their inflorescence structures and leaf shapes. To better understand the mechanisms underlying these differences at the molecular level, we performed a comparative transcriptional analysis.Materials and Methods: Full-length transcriptome sequencing and short-read RNA sequencing were employed.Results: A total of 76,068 and 44,223 non-redundant transcripts were obtained from high-quality transcripts of Lm-type female strains and normal amphiprotic strains, respectively. In Lm-type female strains and normal amphiprotic strains, 51,613 and 20,152 alternative splicing events were found, respectively. There were 13,239 transcription factors identified from the full-length transcriptomes. Comparative analysis showed a great variety of gene expression of common and unique transcription factors between the two cultivars. Meanwhile, a functional analysis of the isoforms was conducted. The full-length sequences were used as a reference genome, and a short-read RNA sequencing analysis was performed to conduct differential gene analysis. Furthermore, the function of DEGs were performed to annotation analysis.Conclusion: The results revealed considerable differences and expression diversity between the two cultivars, well beyond what was reported in previous studies and likely reflecting the differences in architecture between these two cultivars.

scholarly journals Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 253 ◽  
Author(s):  
Anne Deslattes Mays ◽  
Marcel Schmidt ◽  
Garrett Graham ◽  
Elizabeth Tseng ◽  
Primo Baybayan ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Real Time ◽  
Rna Sequencing ◽  
Cell Population ◽  
Single Molecule ◽  
Full Length ◽  
Protein Isoforms ◽  
Mrna Isoforms ◽  
Transcript Isoforms ◽  
Cell Subpopulations

Hematopoietic cells are continuously replenished from progenitor cells that reside in thebone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomesof freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineagepositive)cells by single-molecule real-time (SMRT) full-length RNA-sequencing. This analysisrevealed a ~5-fold higher number of transcript isoforms than previously detected and showed adistinct composition of individual transcript isoforms characteristic for bone marrowsubpopulations. A detailed analysis of messenger RNA (mRNA) isoforms transcribed from theANXA1 and EEF1A1 loci confirmed their distinct composition. The expression of proteins predictedfrom the transcriptome analysis was evaluated by mass spectrometry and validated previouslyunknown protein isoforms predicted e.g., for EEF1A1. These protein isoforms distinguished thelineage negative cell population from the lineage positive cell population. Finally, transcriptisoforms expressed from paralogous gene loci (e.g., CFD, GATA2, HLA-A, B, and C) alsodistinguished cell subpopulations but were only detectable by full-length RNA sequencing. Thus,qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cellsubpopulations indicating complex transcriptional regulation and protein isoform generationduring hematopoiesis.

scholarly journals Comparative Transcriptome Analyses of Gene Response to Different Light Conditions of Camellia oleifera Leaf Using Illumina and Single-Molecule Real-Time-Based RNA-Sequencing

Forests ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 91
Author(s):  
Qianqian Song ◽  
Shipin Chen ◽  
Yuefeng Wu ◽  
Yifan He ◽  
Jinling Feng ◽  
...  
Keyword(s):  
Real Time ◽  
Rna Sequencing ◽  
Blue Light ◽  
Differentially Expressed Genes ◽  
Single Molecule ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Phenotypic Traits ◽  
Camellia Oleifera ◽  
Light Conditions

Camellia oleifera Abel. is a critical oil tree species. Camellia oil, which is extracted from the seeds, is widely regarded as a premium cooking oil, with the content of oleic acid being over 80%. Light is thought to be one of the largest essential natural components in the regulation of plant developmental processes, and different light qualities can considerably influence plant physiological and phenotypic traits. In this research, we examined the growth and physiological responses of C. oleifera “MIN 43” cultivar plantlets to three different wavelengths of light, containing white, red, and blue light, and we utilized the combination of the PacBio single-molecule real-time (SMRT) and Illumina HiSeq RNA sequencing to obtain the mRNA expression profiles. The results showed that plantlets growing under blue light conditions displayed superior growth performance, including stimulated enhancement of the leaf area, increased leaf number, increased chlorophyll synthesis, and improved photosynthesis. Furthermore, SMAT sequencing created 429,955 reads of inserts, where 406,722 of them were full-length non-chimeric reads, and 131,357 non-redundant isoforms were produced. Abundant differentially expressed genes were found in leaves under different light qualities by RNA-sequencing. Gene expression profiles of actin, dynein, tubulin, defectively organized tributaries 3 (DOT3), and ADP ribosylation factor 5 (ARF5) were associated with the greatest leaf performance occurring under blue light conditions. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified hundreds of pathways involved in different light conditions. The pathways of the plant circadian rhythm and hormone signal transduction were associated with different light quality responses in C. oleifera. Phytochrome B (PHYB), constitutively photomorphogenic 1 (COP1), long hypocotyl 5 (HY5), auxin/indole-3-acetic acid (AUX/IAA), Gretchen Hagen 3 (GH3), and small auxin-up RNA (SAUR), which were differentially expressed genes involved in these two pathways, play a vital role in responses to different wavelengths of light in C. oleifera. In addition, blue light significantly promotes flavonoid biosynthesis via changing expression of related genes.

REAL CONDITION AND PROSPECTS OF DEVELOPMENT OF THE RADAR STATIONS OF THE COUNTER BATTERY FIGHTINGV

2019 ◽  
Vol 1 (12) ◽  
pp. 30-40
Author(s):  
V. Нolovan ◽  
V. Gerasimov ◽  
А. Нolovan ◽  
N. Maslich
Keyword(s):  
Comparative Analysis ◽  
Real Time ◽  
Weather Conditions ◽  
Time Of Day ◽  
Current Position ◽  
Real Condition ◽  
Leading Role ◽  
Artillery Shell

Fighting in the Donbas, which has been going on for more than five years, shows that a skillful counter-battery fight is an important factor in achieving success in wars of this kind. Especially in conditions where for the known reasons the use of combat aviation is minimized. With the development of technical warfare, the task of servicing the counter-battery fight began to rely on radar stations (radar) to reconnaissance the positions of artillery, which in modern terms are called counter-battery radar. The principle of counter-battery radar is based on the detection of a target (artillery shell, mortar mine or rocket) in flight at an earlier stage and making several measurements of the coordinates of the current position of the ammunition. According to these data, the trajectory of the projectile's flight is calculated and, on the basis of its prolongation and extrapolation of measurements, the probable coordinates of the artillery, as well as the places of ammunition falling, are determined. In addition, the technical capabilities of radars of this class allow you to recognize the types and caliber of artillery systems, as well as to adjust the fire of your artillery. The main advantages of these radars are:  mobility (transportability);  inspection of large tracts of terrain over long distances;  the ability to obtain target's data in near real-time;  independence from time of day and weather conditions;  relatively high fighting efficiency. The purpose of the article is to determine the leading role and place of the counter-battery radar among other artillery instrumental reconnaissance tools, to compare the combat capabilities of modern counter-battery radars, armed with Ukrainian troops and some leading countries (USA, China, Russia), and are being developed and tested in Ukraine. The method of achieving this goal is a comparative analysis of the features of construction and combat capabilities of modern models of counter-battery radar in Ukraine and in other countries. As a result of the conducted analysis, the directions of further improvement of the radar armament, increasing the capabilities of existing and promising counter-battery radar samples were determined.

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