Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1020112 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26147095.fastq.gz | Fastqsanger.gz | |||
| SRR26147095_1.fastq.gz | Fastqsanger.gz | |||
| SRR26147095_2.fastq.gz | Fastqsanger.gz | |||
| SRR26147096.fastq.gz | Fastqsanger.gz | |||
| SRR26147096_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Competition is a major determinant of plant community structure consisting of both species-specific and general interactions, either of which may influence competitive competency and plant abundance and size. In certain cases, competitive competency could arise from altered gene expression and plant function when an individual is confronted with new competitors. We explored competition at the molecular level by hybridizing transcripts from Centaurea maculosa (spotted knapweed), one of North America's most invasive exotic plant species, to an Arabidopsis microarray chip. Centaurea was grown in competition with Festuca idahoensis (Idaho fescue), a native grass species that generally has weak competitive effects against Centaurea; Gaillardia aristata (Indian blanketflower), a native herbaceous species that tends to be a much stronger competitor against Centaurea; or alone (control). The expression of some genes was found to be relatively uninfluenced by the type of plant neighbor, whereas other patterns of gene expression appeared to be more neighbor specific. To our knowledge, these results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbors and provide a new avenue of insight into the molecular aspects of plant competitive ability. Keywords: treated vs.untreated
2008-10-31 | GSE7444 | GEO
Project description:Competition is a major determinant of plant community structure consisting of both species-specific and general interactions, either of which may influence competitive competency and plant abundance and size. In certain cases, competitive competency could arise from altered gene expression and plant function when an individual is confronted with new competitors. We explored competition at the molecular level by hybridizing transcripts from Centaurea maculosa (spotted knapweed), one of North America's most invasive exotic plant species, to an Arabidopsis microarray chip. Centaurea was grown in competition with Festuca idahoensis (Idaho fescue), a native grass species that generally has weak competitive effects against Centaurea; Gaillardia aristata (Indian blanketflower), a native herbaceous species that tends to be a much stronger competitor against Centaurea; or alone (control). The expression of some genes was found to be relatively uninfluenced by the type of plant neighbor, whereas other patterns of gene expression appeared to be more neighbor specific. To our knowledge, these results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbors and provide a new avenue of insight into the molecular aspects of plant competitive ability. Keywords: treated vs.untreated
2008-10-31 | GSE7443 | GEO
Project description:Competition is a major determinant of plant community structure consisting of both species-specific and general interactions, either of which may influence competitive competency and plant abundance and size. In certain cases, competitive competency could arise from altered gene expression and plant function when an individual is confronted with new competitors. We explored competition at the molecular level by hybridizing transcripts from Centaurea maculosa (spotted knapweed), one of North America's most invasive exotic plant species, to an Arabidopsis microarray chip. Centaurea was grown in competition with Festuca idahoensis (Idaho fescue), a native grass species that generally has weak competitive effects against Centaurea; Gaillardia aristata (Indian blanketflower), a native herbaceous species that tends to be a much stronger competitor against Centaurea; or alone (control). The expression of some genes was found to be relatively uninfluenced by the type of plant neighbor, whereas other patterns of gene expression appeared to be more neighbor specific. To our knowledge, these results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbors and provide a new avenue of insight into the molecular aspects of plant competitive ability. Keywords: treated vs.untreated Files; chip 618 (12-7-05) and chip 623 (1-20-06) are replicates. One channel is root cDNA from Centaurea maculosa grown in isolation and the other channel is root cDNA from Centaurea maculosa grown with a strong competitor, Gaillardia aristata. For each chip, RNA extractions on unique biological samples were performed. Files; chip 720 (2-23-06) and chip 723 (3-17-06) are replicates. One channel is root cDNA from Centaurea maculosa grown in isolation and the other channel is root cDNA from Centaurea maculosa grown with a weak competitor, Festuca idahoensis. For each chip, RNA extractions on unique biological samples were performed.
2010-05-17 | E-GEOD-7444 | biostudies-arrayexpress
Project description:Competition is a major determinant of plant community structure consisting of both species-specific and general interactions, either of which may influence competitive competency and plant abundance and size. In certain cases, competitive competency could arise from altered gene expression and plant function when an individual is confronted with new competitors. We explored competition at the molecular level by hybridizing transcripts from Centaurea maculosa (spotted knapweed), one of North America's most invasive exotic plant species, to an Arabidopsis microarray chip. Centaurea was grown in competition with Festuca idahoensis (Idaho fescue), a native grass species that generally has weak competitive effects against Centaurea; Gaillardia aristata (Indian blanketflower), a native herbaceous species that tends to be a much stronger competitor against Centaurea; or alone (control). The expression of some genes was found to be relatively uninfluenced by the type of plant neighbor, whereas other patterns of gene expression appeared to be more neighbor specific. To our knowledge, these results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbors and provide a new avenue of insight into the molecular aspects of plant competitive ability. Keywords: treated vs.untreated First file, Chip 508 (9-9-05) is preliminary hyb data to see if this cross species hybridization is possible using the OAR27K chip Experiment 1 (chip 508): The Arabidopsis OAR27K gene chip was hybridized with labeled cDNA probes produced from samples of Centaurea RNA at the W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University. The OAR27K gene chip consists of 70-mer oligos representing approximately 27,000 genes from Arabidopsis. Leaf and root samples were reverse-transcribed into cDNA and labeled with different fluorescent dyes (Cy3 and Cy5) using the Genisphere Array 900 kit (Cat No.W500180) (Genisphere, Hatfield PA). Labeled cDNAs were hybridized to the OAR27Kchip using the Advalytix ArrayBooster DNA Microarray Incubator (Advalytix, Boston MA). Approximately 10ug of each sample was used for hybridization.Experiment 2: Hybridization and labeling followed the procedure above, except the experimental control was Centaurea plants grown alone, and the test situations were Centaurea grown with Gaillardia or Festuca neighbors. In each experiment, RNA from Centaurea grown alone was used as the control (labeled with Cy3) and RNA from Centaurea grown with a neighbor was used as the test (labeled with Cy5). Two replicates were performed for each test situation.
2010-05-17 | E-GEOD-7443 | biostudies-arrayexpress
Project description:Invasive plant species native to Europe.
| PRJNA39131 | ENA
Project description:Understanding the mechanisms underlying the establishment of invasive plants is critical in community ecology. According to a widely accepted theory, plant-soil-microbe interactions mediate the effects of invasive plants on native species, thereby affecting invasion success. However, the roles and molecular mechanisms associated with such microbes remain elusive. Using high throughput sequencing and a functional gene microarray, we found that soil taxonomic and functional microbial communities in plots dominated by Ageratina adenophora developed to benefit the invasive plant. There were increases in nitrogen-fixing bacteria and labile carbon degraders, as well as soil-borne pathogens in bulk soil, which potentially suppressed native plant growth. Meanwhile, there was an increase of microbial antagonism in the A. adenophora rhizosphere, which could inhibit pathogenicity against plant invader. These results suggest that the invasive plant A. adenophora establishes a self-reinforcing soil environment by changing the soil microbial community. It could be defined as a ‘bodyguard/mercenary army’ strategy for invasive plants, which has important insights for the mitigation of plant invasion.
2019-05-01 | GSE114498 | GEO
Project description:[original Title] Transcriptomic responses to heat-stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success. Invasive species are increasingly prevalent in marine ecosystems worldwide. Although many studies have examined the ecological effects of invasives, little is known about physiological mechanisms that might contribute to invasive success. The mussel Mytilus galloprovincialis, a native of the Mediterranean Sea, is a successful invader on the central and southern coasts of California, where it has largely displaced the native congener, Mytilus trossulus. It has been previously shown that thermal responses of several physiological traits may underlie the capacity of M. galloprovincialis to out-compete M. trossulus in warm habitats. To elucidate possible differences in stress-induced gene expression between these congeners, we developed an oligonucleotide microarray with 8,874 probes representing 4,488 different genes that recognized mRNAs of both species. In acute heat-stress experiments, 1,531 of these genes showed temperature-dependent changes in gene expression that were highly similar in the two congeners. In contrast, 96 genes showed species-specific responses to heat-stress, functionally characterized by their involvement in oxidative stress, proteolysis, energy metabolism, ion transport, cell signaling, and cytoskeletal reorganization. The gene that showed the biggest difference between the species was the gene for the molecular chaperone small heat shock protein 24, which was highly induced in M. galloprovincialis and showed only a small change in M. trossulus. These different responses to acute heat-stress may help to explain—and predict—the invasive success of M. galloprovincialis in a warming world.
2010-10-11 | GSE19031 | GEO
Project description:Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably in Northern Europe. To explore adaptation on reproductive traits of population considered as invasive, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark. A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several genes differentially expressed between the Danish and French progenies, and with an intermediate expression level in hybrids (additive behavior). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism known to be implicated in coordinated control of reproduction. Our results suggest adaptation of invasive populations during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, fertility and gamete quality. A common garden experiment was performed in order to compare progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Progenies were reared under standard hatchery and nursery conditions until gonadal maturation. The employed arrays were Agilent 60-mer 4x44K custom microarrays, containing 31,918 C. gigas ESTs, designed by Dheilly et al. (2011).
2015-02-20 | E-GEOD-66103 | biostudies-arrayexpress