Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microsatellite markers from RNA-seq of 24 useful tropical trees

ABSTRACT: Microsatellite markers from RNA-seq of 24 useful tropical trees

OTHER RELATED OMICS DATASETS IN: E-MTAB-2809E-MTAB-2764

PROVIDER: PRJEB5301 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR420511_1.fastq.gz	Fastqsanger.gz
	ERR420511_2.fastq.gz	Fastqsanger.gz
	ERR420512_1.fastq.gz	Fastqsanger.gz
	ERR420512_2.fastq.gz	Fastqsanger.gz
	ERR420513_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Polymorphic microsatellite markers for Microbotryum saponariae

Project description:Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing.

| PRJEB11435 | ENA

Crambe sventenii SSR markers

Project description:Characterization of 21 microsatellite markers for Crmabe sventenii

| PRJEB27156 | ENA

Moricandia Microsatellite

Project description:Development and characterization of microsatellite markers for Moricandia moricandioides (Brassicaceae) and cross-amplification in related species

| PRJEB27279 | ENA

Drought tolerance and tree microbiota in tropical trees

Project description:Leaf microbiota contributes to drought tolerance in Amazonian tropical trees

| PRJEB42566 | ENA

Structural, biochemical, and molecular analyses of cambial stem cells reveal longevity mechanisms in old Ginkgo biloba trees

Project description:High-throughput RNA, sRNA and degradome sequencing were performed to identify a large number of mRNA, miRNAs and their targets in G. biloba cambium at different ages to provide useful information for uncovering the regulatory networks of ageing in long-lived old trees.

2018-09-08 | GSE119213 | GEO

Transcriptional response of Scots pine trees to Heterobasidion annosum infection: analyses of antimicrobial protein Sp-AMP2

Project description:Understanding of mechanisms of resistance of forest trees against microbial pathogens is an essential prerequisite for the development of sustainable forestry practices and for the improvement of commercially-grown trees via either conventional breeding or rational genetic engineering. We have studied the transcriptional response of Scots pine trees to Heterobasidion annosum infection under field conditions. By comparing responses of trees to wounding and to fungal inoculation we could identify a set of genes that were specifically responding to fungal infection. We have also investigated a contribution of Scots pine antimicrobial protein Sp-AMP2 to the host antimicrobial defense to evaluate the potential of Sp-AMP genes as molecular markers for resistance breeding.

2017-12-31 | GSE87881 | GEO

Microsatellite markers: what they mean and why they are so useful.

Project description:Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. Motivated by the importance of these sequences over the last decades this review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function. The methodologies for the development of SSR loci, genotyping and their applications as molecular markers are also reviewed. Finally, two data surveys are presented. The first was conducted using the main database of Web of Science, prospecting for articles published over the period from 2010 to 2015, resulting in approximately 930 records. The second survey was focused on papers that aimed at SSR marker development, published in the American Journal of Botany's Primer Notes and Protocols in Plant Sciences (over 2013 up to 2015), resulting in a total of 87 publications. This scenario confirms the current relevance of SSRs and indicates their continuous utilization in plant science.

| S-EPMC5004837 | biostudies-literature

Transcriptome analysis in buds of citrus trees of different Huanglongbing severity levels

Project description:Devastating citrus disease Huanglongbing (HLB) is without existing cures. Herein, we present results demonstrating the possible mechanisms (hypoxia stress) behind HLB-triggered shoot dieback by comparing the transcriptomes, hormone profiles, and key enzyme activities in buds of severely and mildly symptomatic ‘Hamlin’ sweet orange (Citrus sinensis). Within six months (October – May) in field conditions, severe trees had 23% bud dieback, greater than mild trees (11%), with a concomitant reduction in canopy density. In February, differentially expressed genes (DEGs) associated with responses to osmotic stress, low oxygen levels, and cell death were upregulated, with those for photosynthesis and cell cycle downregulated in severe versus mild trees. For severe trees, not only were the key markers for hypoxia, including anaerobic fermentation, reactive oxygen species (ROS) production, and lipid oxidation, transcriptionally upregulated, but also alcohol dehydrogenase activity was significantly greater compared to mild trees, indicating a link between bud dieback and hypoxia. Tricarboxylic acid cycle revival, given the upregulation of glutamate dehydrogenase and alanine aminotransferase DEGs, suggests that ROS may also be generated during hypoxiareoxygenation. Greater (hormonal) ratios of abscisic acid to cytokinins and jasmonates and upregulated DEGs encoding NADPH oxidases in severe versus mild trees indicate additional ROS production under limited oxygen availability due to stomata closure. Altogether, our results provided evidence that as HLB progresses, excessive ROS produced in response to hypoxia and during hypoxia-reoxygenation likely intensify the oxidative stress in buds leading to cell death, contributing to marked bud and shoot dieback and decline of the severely symptomatic sweet orange trees.

2023-04-03 | GSE228890 | GEO

Recent demographic histories of temperate deciduous trees inferred from microsatellite markers.

Project description:BackgroundAccurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM.ResultsThis study aims to reconstruct the recent demographic histories of five cool-temperate tree species in Eastern Asia, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, by using 19 microsatellite markers with two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both programs revealed that all the five species experienced expansions after the Last Glacial Maximum (LGM). Within butternuts, J. cathayensis experienced a more serious bottleneck than the other species, and within oaks, Q. mongolica showed a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the GSM model (pGSM) for all five species were between 0.50 and 0.65, indicating that when inferring population demographic history of the cool-temperate forest species using microsatellite markers, it is better to assume a GSM rather than a SMM.ConclusionsThis study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM with microsatellite data. Considering the mutation model of microsatellite has a vital influence on demographic inference, combining multiple programs such as MIGRAINE and VarEff can effectively reduce errors caused by inappropriate model selection and prior setting.

| S-EPMC8130339 | biostudies-literature

SSR markers Spartocytisus supranubius

Project description:Characterization of 20 microsatellite markers for Spartocytisus supranubius, endemic to the Canary Islands

| PRJEB28625 | ENA