Papaipema
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA380623 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Background: Aphids are economically important pests and that display exceptional variation in host range. The underlying mechanism of diverse aphid host ranges are not well understood, but it is likely that molecular interactions are involved. With significant progress being made towards understanding host responses upon aphid attack, the mechanisms underlying nonhost resistance remain to be elucidated. Here, we investigated and compared Arabidopsis host and nonhost responses to aphids at the transcriptome level using three different aphid species. Results: Gene expression analyses revealed a surprising level of overlap in the overall gene expression changes during host and nonhost interactions with regards to the sets of genes differentially expressed and the direction of expression changes. Despite the overlap in transcriptional responses across interactions, there was a stronger repression of genes involved in metabolism and oxidative responses specifically during the host interaction. In addition we indentified a set of genes with opposite gene expression patterns during host versus nonhost interactions. Aphid performance assays on Arabidopsis mutants selected based on our transcriptome analyses identified genes involved in host and nonhost interactions. Conclusions: Understanding how plants respond to aphid species that differ in their ability to infest plant species, and identifying the genes and signaling pathways involved, is essential for the development of novel and durable aphid control in crop plants. Our work is an important step forward to provide such essential insights in that we identified novel genes contributing to host susceptibility, host defences as well nonhost resistance to aphids.
2015-05-01 | E-MTAB-3223 | biostudies-arrayexpress
Project description:DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing reduced CHG methylation levels and also reduced or loss of CG gene-body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species. Bisulfite-seq of leaf tissue from plants representing diverse angiosperms. RNA-seq and small RNA-seq was performed on leaf tissue of a subset of the species.
2016-09-02 | E-GEOD-79526 | biostudies-arrayexpress
Project description:DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing reduced CHG methylation levels and also reduced or loss of CG gene-body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species.
2016-09-02 | GSE79526 | GEO
Project description:A genetically diverse strain (labelled as London) of the phytophagous mite Tetranychus urticae was transferred from its common host (bean) to other host plants (cotton, maize or soy). Three different host plant species were included in the experimental set-up: cotton (Gossypium spp.), maize (Zea mays cv. Ronaldinio) and soy (Glycine max cv. Merlin). Five generations after host-transfer, total RNA of all mite populations (London, London-SOY, London-MAIZE and London-COTTON) was collected and used in a genome-wide gene expression microarray (Sureprint G3 microarray, Agilent) Microarray analysis revealed large-scale differential expression of genes coding for enzymes of detoxification families, secreted proteins with unknown functions and regulatory enzymes.
2016-10-10 | GSE80337 | GEO
Project description:The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum parasitizes more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program driven by core and host-response co-expression (SPREx) gene clusters. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Inter-specific transcriptome analyses revealed a lack of transcriptional response to camalexin in S. trifoliorum and provide evidence that cis-regulatory variation associates with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work demonstrates adaptive plasticity of a broad host range pathogen with specific responses to different host plants and demonstrates the co-existence of signatures for generalist and polyspecialist life styles in the genome of a plant pathogen. We reason that this mechanism enables the emergence of new disease with no or limited gene flow between strains and species, and could underlie the emergence of new epidemics originating from wild plants in agricultural settings.
2021-07-20 | GSE159792 | GEO
Project description:Host-pathogen co-evolutionary dynamics force microbial plant pathogens to constantly develop and adjust specific adaptations to thrive in their plant host, and therefore also act as strong drivers of divergence and speciation in pathogens. Factors that confer host specialization and determine host specificity are very diverse and range from molecular and morphological strategies to metabolic and reproductive adaptations. Identification of these key factors is a major goal in the study of pathogen evolution and may aid the development of sustainable crops and crop protection strategies. We here took a novel experimental approach and conducted comparative microscopy and transcriptome analyses of the closely related, recently diverged fungal pathogens Zymoseptoria tritici, Z. pseudotritici, and Z. ardabiliae that establish compatible and incompatible interactions with wheat. Although infections of the incompatible species induce plant defense response during invasion of stomatal openings, we found a highly conserved early-infection program among the three species. The transcriptional programs of the three pathogens are conserved to a large extent, as only 9.2% of the 8,885 orthologous genes are significantly differentially expressed during initial infection of wheat. The genes up-regulated in the compatible pathogen reflect adaptation to growth in wheat tissue e.g., by re-programming of fungal metabolism. In contrast, genes primarily involved in counteracting cell stress and damage are strongly induced in the incompatible species. Based on the species-specific gene expression profiles, we further identified nine candidate genes encoding putative effectors and host-specificity determinants in Z. tritici. These effectors are strongly induced in the compatible species and may interfere with host immune suppression. We also identify putative necrotrophic effectors which are induced at the onset of necrotrophic growth. Together, the results presented here indicate that host specialization has involved transcriptional adaptation of a relatively small number of genes. Our findings demonstrate the potential comparative analyses of compatible and incompatible infections present for identifying traits involved in pathogen evolution and host specialization.
2023-07-25 | GSE237842 | GEO
Project description:A hallmark of the interactions between endoparasites (parasites that live within plant tissue) and their hosts, is the parasites' ability to hijack host gene expression to support their own existence. While a number of studies have been performed to identify plant genes that are recruited in this manner, there is much that remains unknown. One mechanism by which this behavior can be explored is by using a traditional genetics approach: identifying connections between genetic variation and phenotype variation. To that end, we leverage experiments examining tissue from three host plant species, each infected with one of two genetically distinct strains of the endoparasite Meloidogyne hapla. Using RNA-Seq data, we identify plant gene expression patterns that differ according to the genetic background of the parasite they are infected with. We also show that parasite genotype-host expression phenotype associations are consistent across plant species. These results indicate that the plant genes recruited by the parasite are influenced by the parasite's genetic background, and that these differential choices are conserved across evolutionarily distant hosts. We also leverage public data to identify conserved host expression differences when comparing M. hapla-infected plants to uninfected plants. Finally, we demonstrate that parasite gene expression varies according to the parasites' genetic background, and show that these signals are also conserved under different host species.
2026-03-24 | GSE325830 | GEO
Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization.
2011-05-01 | GSE25575 | GEO
Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization.
2011-05-01 | GSE25572 | GEO
Project description:Phytophthora cinnamomi is a devastating soil-borne oomycete with a very broad host range however there remains a major gap in the understanding of plant resistance responses to the pathogen, furthermore, necrotrophic plant-pathogen interactions, particularly those of root pathogens, remain poorly understood. Zea mays exhibits non-host resistance to the pathogen and has been well characterised as a model species. Using the maize Affymetrix GeneChip array we conducted genome-wide gene expression profiling to elucidate the defence genes and pathways which are induced in the root tissue of a resistant plant species to the pathogen.
2011-03-02 | GSE27626 | GEO