Ontology highlight
ABSTRACT:
PROVIDER: PRJNA541034 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9008940_1.fastq.gz | Fastqsanger.gz | |||
| SRR9008940_2.fastq.gz | Fastqsanger.gz | |||
| SRR9008941_1.fastq.gz | Fastqsanger.gz | |||
| SRR9008941_2.fastq.gz | Fastqsanger.gz | |||
| SRR9008942_1.fastq.gz | Fastqsanger.gz |
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Project description:Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximise fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4 °C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4 °C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developingin specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.
2024-04-01 | GSE176054 | GEO
Project description:Our previous studies have shown that exogenous ethylene (ETH) may induce plant adventitious root development in cucumber. In this study, transcriptome technique was used to explore the key genes in ETH-induced rooting. The results revealed that ETH regulated 1415 diferentially expressed genes (DEGs) during rooting, among which 687 DEGs were up-regulated and 728 DEGs were down-regulated. According to Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, the critical pathways involved in ETH-induced adventitious root development were selected for further study, including carbon metabolism [starch and sucrose metabolism, glycolysis / gluconeogenesis, citrate cycle (TCA cycle), oxidative phosphorylation, fatty acid biosynthesis and fatty acid degradation], secondary metabolite biosynthesis (phenylalanine metabolism and flavonoid biosynthesis) and plant hormone signal transduction. In carbon metabolism, ETH reduced t the expression of CsHK2, CsPK2 and CsCYP86A1, whereas enhanced the expression of CsBAM1 and CsBAM3. Moreover, ETH negatively regulated the transcript level of CsPAL and CsF3’M and positively mediated that of CsPAO in secondary metabolite biosynthesis pathway. Additionally, ETH could induce adventitious rooting by negatively regulating auxin and ETH signal transduction-related genes (CsLAX5, CsGH3.17, CsSUAR50 and CsERS) and positively regulating ABA and BR signaling transduction-related genes (CsPYL1, CsPYL5, CsPYL8, CsBAK1 and CsXTH3) . Furthermore, the results of real-time PCR about the mRNA levels of these genes were consistent with transcriptome results. Therefore, ETH may induce adventitious root development by regulating carbon metabolism-related genes, secondary metabolite biosynthesis-related genes and plant hormone signal transduction-related genes.
2021-11-30 | GSE189315 | GEO
Project description:Background: The change from juvenile to mature phase in woody plants is often accompanied by a gradual loss of rooting ability, as well as by reduced microRNA (miR) 156 and increased miR172 expression. Results: We characterized the population of miRNAs of Eucalyptus grandis and compared by Northern blot the gradual reduction in miR156 and increase in miR172 expression during development to the loss of rooting ability. Forty known and eight novel miRNAs were discovered and their predicted targets are listed. The expression pattern of nine miRNAs was determined during adventitious root formation in juvenile and mature cuttings. While the expression levels of miR156 and miR172 were inverse in juvenile and mature tissues, no mutual relationship was found between high miR156 expression and rooting ability, or high miR172 expression and loss of rooting ability. This is shown both in E. grandis and also in E. brachyphylla, in which explants that underwent rejuvenation in tissue culture conditions were also examined. Conclusions: It is suggested that in these Eucalyptus species, there is no correlation between the switch of miR156 with miR172 expression in the stems and the loss of rooting ability.
2014-10-01 | GSE58367 | GEO
Project description:Background: The change from juvenile to mature phase in woody plants is often accompanied by a gradual loss of rooting ability, as well as by reduced microRNA (miR) 156 and increased miR172 expression. Results: We characterized the population of miRNAs of Eucalyptus grandis and compared by Northern blot the gradual reduction in miR156 and increase in miR172 expression during development to the loss of rooting ability. Forty known and eight novel miRNAs were discovered and their predicted targets are listed. The expression pattern of nine miRNAs was determined during adventitious root formation in juvenile and mature cuttings. While the expression levels of miR156 and miR172 were inverse in juvenile and mature tissues, no mutual relationship was found between high miR156 expression and rooting ability, or high miR172 expression and loss of rooting ability. This is shown both in E. grandis and also in E. brachyphylla, in which explants that underwent rejuvenation in tissue culture conditions were also examined. Conclusions: It is suggested that in these Eucalyptus species, there is no correlation between the switch of miR156 with miR172 expression in the stems and the loss of rooting ability. Examination of microRNA in seedlings of Eucalyptus grandis
2014-10-01 | E-GEOD-58367 | biostudies-arrayexpress
Project description:RNA-seq during adventitious rooting in tomato mars1 mutants
| PRJNA1289037 | ENA
Project description:In order to identify genes specifically induced during various developmental stages of Adventitious Root (AR) formation (described in Ahkami et al. 2009) in leafy cuttings of Petunia hybrida (line W115) and to describe the series of physiological processes during adventitious rooting, a microarray-based transcriptome analysis in the stem base of the cuttings was conducted. The microarray was described by Breuillin et al. (2010) and included a normalized cDNA library from different time points after taking the cuttings from mother plant. Because physiological processes and molecular changes specifically involved in AR formation were considered as of major interest, rather than those associated with wound responses, a filtration approach was chosen to eliminate primarily wound-responsive genes. This study is mainly focused on changes in transcript abundances of genes related to specific metabolic pathways or cellular events including primary metabolism, membrane transport, cell division or signalling during various phases of AR formation.
2014-05-17 | GSE57752 | GEO
Project description:Ethylene, as a signaling hormone molecule, is proved to have essential role in the process of root development. In the present study, cucumber (Cucumis sativus L.) seedlings were employed to estimate differentially expressed proteins (DEPs) during the adventitious rooting using iTRAQ technique and proteomics analysis. Out of the 5014 DEPs, 115 DEPs were considered as identified proteins, and among them, 24 DEPs are interesting proteins abundance.
2020-01-15 | PXD016444 | Pride
Project description:Oligoarray analysis was used to identify genes differentially expressed in 2 mm sections of the basal stem region of wild type T89, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides 24h and 72h after adventitious rooting induction.
2012-11-01 | GSE34162 | GEO
Project description:Oligoarray analysis was used to identify genes differentially expressed in 2 mm sections of the basal stem region of wild type T89, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides 24h and 72h after adventitious rooting induction. The Populus trichocarpa custom-exon expression array (12x135K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 43,929 annotated gene models (Populus trichocarpa genome v2 ; Phytozome 5.0), 5,859 random 60-mer control probes and labelling controls. We performed 27 hybridizations from wildtype, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides at time 0, 24h and 72h after adventitious rooting induction. For each timepoint we performed three biological replicates.
2012-11-01 | E-GEOD-34162 | biostudies-arrayexpress
Project description:Purpose: The goals of this study was to obtain transcriptome data from five developmental stages of adventitious roots of Pyrus ussuriensis Maxim using transcriptome analysis (RNA-Seq) and qRT-PCR analysis. Mathods: The mRNA profiles of the adventitious root development of Pyrus ussuriensis on day 0, day 3, day 6, day 9, and day 12 were examined by deep sequencing, in triplicate, using Illumina HiSeq 2000. Ultra™ RNA LibraryPrep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and indexcodes were added to attribute sequences to each sample. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: The transcriptome regulation analysis of the Pyrus ussuriensis adventitious root formation was performed on this study. And a total of 19,470 DEGs (Differentially Expressed Gene), which were mainly enriched in hormone synthesis and signaling pathways, energy metabolism, synthesis and metabolism of secondary products, were detected. the key regulatory genes of adventitious root formation were screened, mainly including the gene family WOX, LBD and SRS. Auxin, plays a key role in the induction and development of root primordium, its signal transduction pathway-related genes were up-regulated during the induction period of root primordium, and down-regulated during the development of root primordia. Carotenoids is the precursor substance of abscisic acid synthetize. And for the reasons that the genes of carotenoid synthesis and signal transduction pathway of abscisic acid were down-regulated during the period of stable development and the root primordium induction, and up-regulated during the period of root primordium development of adventitious root, it was supposed that abscisic acid was a control substance, that regulated the metabolic network of development of adventitious roots. Conclusions: Our results provide a comprehensive high-resolution characterization of gene expression profiles during the pear root transition process.A number of DEGs were detected from the root primordium to adventitious root growth stages, and these belonged to hormone metabolism pathways.These results provide a valuable resource for studies in other closely related species with similar agricultural and productive value. The differentially expressed genes dataset will also provide useful candidate genes for functional analysis of pear rooting.
2021-08-13 | GSE118485 | GEO