scholarly journals Transcriptome Dynamics of Floral Organs Approaching Blooming in the Flowering Cherry (Cerasus × yedoensis) Cultivar 'Somei-Yoshino'

2021 ◽  
Author(s):  
Kenta Shirasawa ◽  
Tomoya Esumi ◽  
Akihiro Itai ◽  
Sachiko Isobe
Keyword(s):  
Time Course ◽  
Gene Transcript ◽  
Rna Seq ◽  
Flower Opening ◽  
Open Flower ◽  
Time Points ◽  
Floral Buds ◽  
Genes Encoding ◽  
Genetic Mechanisms ◽  
Flowering Cherry

To gain insights into the genetic mechanisms underlying blooming and petal movement in flowering cherry (Cerasus × yedoensis), we performed time-course RNA-seq analysis of the floral buds and open-flowers of the most popular flowering cherry cultivar, 'Somei-Yoshino'. Independent biological duplicate samples of floral buds and open-flowers were collected from 'Somei-Yoshino' trees grown at three different locations in Japan. RNA-seq reads obtained from floral bud and open-flower samples collected in the current study (in 2019) and in a previous study (in 2017) were aligned against the genome sequence of 'Somei-Yoshino' to quantify gene transcript levels. Clustering analysis of RNA-seq reads revealed dynamic changes in the transcriptome, with genes in seven modules predominantly expressed at specific time points, ranging from 5 weeks before flowering to 2 weeks after flowering. Based on the identified gene modules and Gene Ontology (GO) terms enriched at different floral stages, we speculate that the genetic mechanisms underlying petal movement and flower opening in cherry involve the processes of development, cell wall organization, reproduction, and metabolism, which are executed by genes encoding transcription factors, phytohormones, transporters, and polysaccharide metabolic enzymes. Furthermore, we propose a method for cherry bloom forecasting, based on gene expression levels at different time points before flowering as RNA markers.

scholarly journals A high-resolution mRNA expression time course of embryonic development in zebrafish

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Richard J White ◽  
John E Collins ◽  
Ian M Sealy ◽  
Neha Wali ◽  
Christopher M Dooley ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Developmental Time ◽  
Rna Seq ◽  
Time Points ◽  
New Genes ◽  
Expression Atlas ◽  
Genome Activation ◽  
Expression Time

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.

scholarly journals A high-resolution mRNA expression time course of embryonic development in zebrafish

2017 ◽  
Author(s):  
Richard J. White ◽  
John E. Collins ◽  
Ian M. Sealy ◽  
Neha Wali ◽  
Christopher M. Dooley ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Developmental Time ◽  
Rna Seq ◽  
Temporal Expression ◽  
Time Points ◽  
Expression Atlas ◽  
Genome Activation ◽  
Expression Time

AbstractWe have produced an mRNA expression time course of zebrafish development across 18 time points from 1-cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise the temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5,024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. The data reveal complex and widespread differential use of exons and previously unidentified 3′ ends across development, new primary microRNA transcripts and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data are accessible to browse and download at Expression Atlas and Ensembl.

High floral bud abscission and lack of open flower abscission in Dendrobium cv. Miss Teen: rapid reduction of ethylene sensitivity in the abscission zone

2006 ◽  
Vol 33 (6) ◽  
pp. 539 ◽  
Author(s):  
Kanokpon Bunya-atichart ◽  
Saichol Ketsa ◽  
Wouter G. van Doorn
Keyword(s):  
Abscission Zone ◽  
Flower Opening ◽  
Open Flower ◽  
Rapid Reduction ◽  
Ethylene Sensitivity ◽  
Floral Buds ◽  
Endogenous Ethylene ◽  
Ethylene Insensitivity ◽  
Floral Bud ◽  
Flower Abscission

We studied the abscission of floral buds and open flowers in cut Dendrobium inflorescences. Abscission of floral buds was high and sensitive to ethylene in all cultivars studied. Many open flowers abscised in most cultivars, but cv. Willie exhibited only small amount of floral fall and cv. Miss Teen none. Applied ethylene (0.4 μL L–1 for 24 h at 27°C) greatly hastened abscission of open flowers in most cultivars, but had only a small effect in cv. Willie and no effect in cv. Miss Teen. Flower fall, if it occurred, was completely inhibited by 1-methylcyclopropene (1-MCP), showing that it was regulated by endogenous ethylene. Ethylene production from the abscission zones was low in all cultivars studied. In cv. Miss Teen the abscission zone changed from highly ethylene sensitive to completely insensitive in ~30 h, coinciding with floral opening. Removal of the floral buds somewhat reduced abscission in open flowers, but the lack of open flower abscission in cv. Miss Teen could not be explained by higher bud fall. The ovary did not grow in the (unpollinated) flowers, showing that lack of abscission in cvv. Willie and Miss Teen was not due to parthenocarpy. Flower removal in cv. Miss Teen had no effect on ethylene sensitivity of the abscission of the remaining pedicel. However, removal of the distal 2 cm of the 3-cm-long pedicels dramatically increased ethylene sensitivity. This suggests that the pedicel is important for the low ethylene insensitivity of abscission, in this cultivar. It is concluded that the abscission zones in the cvv. Willie and Miss Teen, in contrast with the other cultivars investigated, became rapidly insensitive to ethylene at the time of flower opening. At least part of the ethylene sensitivity in Miss Teen seems to be due to a factor in the pedicel.

scholarly journals MeDAS: a Metazoan Developmental Alternative Splicing database

2020 ◽  
Vol 49 (D1) ◽  
pp. D144-D150
Author(s):  
Zhidan Li ◽  
Yiming Zhang ◽  
Stephen J Bush ◽  
Chao Tang ◽  
Li Chen ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Time Course ◽  
Added Value ◽  
Genomic Feature ◽  
Gene Transcript ◽  
Rna Seq ◽  
Developmental Context ◽  
Alternative Splicing Events ◽  
Time Courses ◽  
Data Tables

Abstract Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcriptomic diversity. Many alternative isoforms have functional roles in developmental processes and are precisely temporally regulated. To facilitate the study of alternative splicing in a developmental context, we created MeDAS, a Metazoan Developmental Alternative Splicing database. MeDAS is an added-value resource that re-analyses publicly archived RNA-seq libraries to provide quantitative data on alternative splicing events as they vary across the time course of development. It has broad temporal and taxonomic scope and is intended to assist the user in identifying trends in alternative splicing throughout development. To create MeDAS, we re-analysed a curated set of 2232 Illumina polyA+ RNA-seq libraries that chart detailed time courses of embryonic and post-natal development across 18 species with a taxonomic range spanning the major metazoan lineages from Caenorhabditis elegans to human. MeDAS is freely available at https://das.chenlulab.com both as raw data tables and as an interactive browser allowing searches by species, tissue, or genomic feature (gene, transcript or exon ID and sequence). Results will provide details on alternative splicing events identified for the queried feature and can be visualised at the gene-, transcript- and exon-level as time courses of expression and inclusion levels, respectively.

scholarly journals Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1391
Author(s):  
Jian Zhang ◽  
Ziai Peng ◽  
Qiling Liu ◽  
Guili Yang ◽  
Libin Zhou ◽  
...  
Keyword(s):  
Time Course ◽  
Expression Profiles ◽  
Ion Beam ◽  
Heavy Ion ◽  
Rna Seq ◽  
Carbon Ion ◽  
Time Points ◽  
Post Irradiation ◽  
Initial Stage ◽  
Carbon Ion Beam

Heavy-ion irradiation is a powerful mutagen and is widely used for mutation breeding. In this study, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques, we comprehensively characterized these dynamic changes caused by mutations at three time points (48, 96, and 144 h after irradiation) and the expression profiles of rice seeds irradiated with C ions at two doses. Subsequent WGS analysis revealed that more mutations were detected in response to 40 Gy carbon ion beam (CIB) irradiation than 80 Gy of CIB irradiation at the initial stage (48 h post-irradiation). In the mutants generated from both irradiation doses, single-base substitutions (SBSs) were the most frequent type of mutation induced by CIB irradiation. Among the mutations, the predominant ones were C:T and A:G transitions. CIB irradiation also induced many short InDel mutations. RNA-seq analysis at the three time points showed that the number of differentially expressed genes (DEGs) was highest at 48 h post-irradiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs showed that the “replication and repair” pathway was enriched specifically 48 h post-irradiation. These results indicate that the DNA damage response (DDR) and the mechanism of DNA repair tend to quickly start within the initial stage (48 h) after irradiation.

scholarly journals Transcriptional Response of Enterococcus faecalis V583 to Erythromycin

2005 ◽  
Vol 49 (6) ◽  
pp. 2246-2259 ◽  
Author(s):  
Ågot Aakra ◽  
Heidi Vebø ◽  
Lars Snipen ◽  
Helmut Hirt ◽  
Are Aastveit ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Time Course ◽  
Transcriptional Response ◽  
Transcriptional Profile ◽  
Specific Response ◽  
Natural Environments ◽  
Time Points ◽  
A Genome ◽  
Study Gene Expression ◽  
Genes Encoding

ABSTRACT A transcriptional profile of Enterococcus faecalis V583 (V583) treated with erythromycin is presented. This is the first study describing a complete transcriptional profile of Enterococcus. E. faecalis is a common and nonvirulent bacterium in many natural environments, but also an important cause of nosocomial infections. We have used a genome-wide microarray based on the genome sequence of V583 to study gene expression in cells exposed to erythromycin. V583 is resistant to relatively high concentrations of erythromycin, but growth is retarded by the treatment. The effect of erythromycin treatment on V583 was studied by a time course experiment; samples were extracted at five time points over a period of 90 min. A drastic change in gene transcription was seen with the erythromycin-treated cells compared to the untreated cells. Altogether, 260 genes were down-regulated at one or more time points, while 340 genes were up-regulated. Genes encoding hypothetical proteins and genes encoding transport and binding proteins were the two most dominating groups of differentially expressed genes. The gene encoding ermB (EFA0007) was expressed, but not differentially, which indicated that other genes are important for the survival and growth maintenance of V583 treated with erythromycin. One of these genes is a putative MsrC-like protein, which was up-regulated at all time points studied. Other specific genes that were found to be up-regulated were genes encoding ABC transporters and two-component regulatory systems, and these may be genes that are important for the specific response of V583 to erythromycin.

Time Course of Simulator Sickness in Asian Military Pilots

2020 ◽  
Vol 91 (11) ◽  
pp. 892-896
Author(s):  
Janine En Qi Loi ◽  
Magdalene Li Ling Lee ◽  
Benjamin Boon Chuan Tan ◽  
Brian See
Keyword(s):  
Air Force ◽  
Time Course ◽  
Simulator Training ◽  
Simulator Sickness ◽  
Time Points ◽  
True Prevalence ◽  
Subjective Scale ◽  
Significant Difference ◽  
Simulator Sickness Questionnaire ◽  
Military Pilots

INTRODUCTION: This study sought to determine the incidence, severity, and time-course of simulator sickness (SS) among Asian military pilots following flight simulator training.METHODS: A survey was conducted on Republic of Singapore Air Force pilots undergoing simulator training. Each subject completed a questionnaire immediately after (0H), and at the 3-h (3H) and 6-h (6H) marks. The questionnaire included the simulator sickness questionnaire (SSQ) and a subjective scale to rate their confidence to fly.RESULTS: In this study, 258 pilots with a median age of 31.50 yr (range, 2155 yr) and mean age of 32.61 6.56 yr participated. The prevalence of SS was 48.1% at 0H, 30.8% at 3H, and 16.4% at 6H. Based on a threshold of an SSQ score >10, the prevalence of operationally significant SS was 33.3% at 0H, 13.2% at 3H, and 8.1% at 6H. The most frequent symptoms were fatigue (38.1%), eye strain (29.0%), and fullness of head (19.9%). There was no significant difference in mean scores between rotary and fixed wing pilots. Older, more experienced pilots had greater scores at 0H, but this association did not persist. A correlation was found between SSQ score and self-reported confidence.DISCUSSION: To our knowledge, this study is the first to report the prevalence of operationally significant SS in Asian military pilots over serial time points. Most pilots with SS are able to subjectively judge their fitness to fly. Sensitivity analysis suggests the true prevalence of SS symptoms at 3H and 6H to be closer to 23.8% and 12.0%, respectively.Loi JEQ, Lee MLL, Tan BBC, See B. Time course of simulator sickness in Asian military pilots. Aerosp Med Hum Perform. 2020; 91(11):892896.

scholarly journals Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1153
Author(s):  
Jutta Ludwig-Müller ◽  
Roman Rattunde ◽  
Sabine Rößler ◽  
Katja Liedel ◽  
Freia Benade ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Growth Stages ◽  
Auxin Response ◽  
Time Points ◽  
Genes Encoding ◽  
Different Temperatures ◽  
Indigenous Plant ◽  
Over Time

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

scholarly journals The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
James G Baldwin-Brown ◽  
Scott M Villa ◽  
Anna I Vickrey ◽  
Kevin P Johnson ◽  
Sarah E Bush ◽  
...  
Keyword(s):  
Low Cost ◽  
Single Copy ◽  
Odorant Receptors ◽  
Rna Seq ◽  
Pediculus Humanus ◽  
Final Assembly ◽  
Oxford Nanopore ◽  
Genes Encoding ◽  
Host Parasite ◽  
G Protein Coupled

Abstract The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.

scholarly journals Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanlei Yue ◽  
Ze Jiang ◽  
Enoch Sapey ◽  
Tingting Wu ◽  
Shi Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Chromosome Structure ◽  
Clock Genes ◽  
Expression Profiles ◽  
Circadian Rhythmicity ◽  
Rna Seq ◽  
Night Time ◽  
Time Points ◽  
Circadian Clock Genes

Abstract Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

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