Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1246236 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32970722_1.fastq.gz | Fastqsanger.gz | |||
| SRR32970722_2.fastq.gz | Fastqsanger.gz | |||
| SRR32970723_1.fastq.gz | Fastqsanger.gz | |||
| SRR32970723_2.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Identify differentially expressed genes between 5 pea aphid morphs Methods: Collected whole bodies of 30 adult aphids of each of the five pea morphs and three clones (total of 15 samples)
2014-06-04 | GSE56830 | GEO
Project description:Purpose: Identify differentially expressed genes between 5 pea aphid morphs Methods: Collected whole bodies of 30 adult aphids of each of the five pea morphs and three clones (total of 15 samples) 5 pea aphid morphs * 3 genotypes = 15 samples
2014-06-04 | E-GEOD-56830 | biostudies-arrayexpress
Project description:Tyrosine (Tyr, Y) and phenylalanine (Phe, F) synthesis is shared by the pea aphid and its symbiont Buchnera aphidicola.These aromatic amino acids are essential for the pea aphid growth and development. To characterize the molecular mechanisms, at gene transcriptional level, underlying this symbiotic integrated network pea aphids (Acyrthosyphon pisum, clone LL01) were reared on (i) standard artificial diet (AP3) and (ii) on the same AP3 medium depleted of Tyr (Y) and Phe (F). From each of the two groups, aphids were collected at specific time points and dissected: 12 h (D0), 1 day (D1), 2 days (D2), 3 days (D3), 4 days (D4), 5 days (D5) and 7 days (D7). Total RNA, to be used in gene expression analysis by arrays, was extracted, under the two rearing conditions, from two tissues: gut [from 20 aphids per sample at all 7 time points] and bacteriocytes [from 25 aphids per sample at 4 time points: 3 days (D3), 4 days (D4), 5 days (D5) and 7 days (D7)]. At each time point we included three biological replicates.
2017-07-18 | E-MTAB-4456 | biostudies-arrayexpress
Project description:We conducted field surveys to detect the population density of the most important invasive weed species and their associated virus vectoring aphids in crops grown under high input (HIF) vs low-input (LIF) field conditions, with and without fertilizers and pesticides. The most frequent invasive weed species were Stenactis annua, Erigeron canadensis and Solidago canadensis. These species were hosts predominantly for the aphids Brachycaudus helichrysi and Aulacorthum solani in both management systems. The 13% higher coverage of S. annua under LIF conditions resulted in a 30% higher B. helichrysi abundance and ~85% higher A. solani abundance compared with HIF conditions. To reveal virus infection in crop plants and invasive weeds high-throughput sequencing of small RNAs were carried out. Bioinformatics analysis of the results detected the presence of 16 important plant viruses, but not resulting strikingly different pattern under LIF and HIF. This could suggest that invasive weeds serves as a virus reservoir both under low and high input management systems. The lake of any management increases virus vector aphids abundances, their presence has a great impact on the viromes of the crops.
2020-06-03 | GSE132755 | GEO
Project description:A major goal of molecular evolutionary biology is to understand the fate and consequences of duplicated genes. In this context, aphids are particularly intriguing because the newly sequenced pea aphid genome is characterized by extraordinarily high levels of lineage-specific gene duplication relative to other insect genomes. While analyzing the results of a microarray comparing gene expression between male, sexual female and asexual female Myzus persicae aphids, we unexpectedly found duplicated nutrient amino acid transporters highly upregulated in males. These transporters, homologous to the Drosophila slimfast, belong to an aphid-specific gene family expansion in which other paralogs are thought to have functionally diverged to fill a role in mediating interactions between aphids and their nutrititonally required bacterial symbiont. The lack of a known male role for slimfast in other insects suggests that aphid slimfast paralogs have been retained as a result of functional divergence to fill multiple novel functional roles in symbiosis and in males.
2011-09-14 | GSE31024 | GEO
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
2008-02-08 | GSE10119 | GEO
Project description:Background: The best studied insect-symbiont system is that of aphids and their primary bacterial endosymbiont Buchnera aphidicola. Buchnera inhabits specialized host cells called bacteriocytes, provides nutrients to the aphid and has co-speciated with its aphid hosts for the past 150 million years. We have used a single microarray to examine gene expression in the pea aphid, Acyrthosiphon pisum, and its resident Buchnera. Very little is known of gene expression in aphids, few studies have examined gene expression in Buchnera, and no study has examined simultaneously the expression profiles of a host and its symbiont. Expression profiling of aphids, in studies such as this, will be critical for assigning newly discovered A. pisum genes to functional roles. In particular, because aphids possess many genes that are absent from Drosophila and other holometabolous insect taxa, aphid genome annotation efforts cannot rely entirely on homology to the best-studied insect systems. Development of this dual-genome array represents a first attempt to characterize gene expression in this emerging model system. Results: We chose to examine heat shock response because it has been well characterized both in Buchnera and in other insect species. Our results from the Buchnera of A. pisum show responses for the same gene set as an earlier study of heat shock response in Buchnera for the host aphid Schizaphis graminum. Additionally, analyses of aphid transcripts showed the expected response for homologs of known heat shock genes as well as responses for several genes with unknown functional roles. Conclusions: We examined gene expression under heat shock of an insect and its bacterial symbiont in a single assay using a dual-genome microarray. Further, our results indicate that microarrays are a useful tool for inferring functional roles of genes in A. pisum and other insects and suggest that the pea aphid genome may contain many gene paralogs that are differentially regulated. Keywords: Stress response
2005-12-31 | GSE3742 | GEO
Project description:Transcriptional analysis of wing induction in pea aphids
| PRJNA79843 | ENA
Project description:Ascochyta blight (AB) is a devastating and aggressive disease of field peas caused by multiple pathogens and the occurrence of the combinations of these pathogens forms a disease complex of which Peyronellaea pinodes, is the most aggressive. AB symptoms include necrotic lesions on all above ground parts of the plant, which can reduce crop yield by up to 70% and result in major economic losses globally. Crop resistance to the disease is reported to be quantitative and, although several genes have been reported to be AB response genes in Spanish pea genotypes, the lines or genotypes of the Australian field pea breeding program have not been investigated. Plants have specialized defence mechanisms that enable them respond to pathogen invasion, and this involves a cascade of genes which are differentially regulated upon infection. In this study, the time-course gene expression profiles of four Australian field pea genotypes including commercial varieties, known to have varying levels of AB resistance were investigated in response to P. pinodes infection. Infected and control plants at 0, 6, 24, 48, 72 and 96HPI were sampled for RNA seq. Mapping of transcriptome sequencing data against the field pea genome resulted in about the identification of c. 6,700 differentially expressed genes. Of the 21 AB resistance genes reported in previously published studies, only seven were present on the list of DEGs generated in this study. No significant pattern was identified in gene expression for the seven genes to differentiate resistant from susceptible genotypes. However, four key genes i.e., disease response protein, malate dehydrogenase, isoflavone 2 hydrogenase and Isoflavone reductase were shown to be associated with suppression of AB disease phenotype after 96HPI. Furthermore, GO functional annotation revealed several genes associated with defence including genes associated with the Salicylic acid pathway, reactive oxygen species, programmed cell death and hypersensitive response. Although the overall result showed a lack of strong resistance in the Australian pea genotypes as well as the fact that disease suppression does not directly equal resistance, we however were able to identify potential candidates that could be pyramided from exotic material into the breeding program to assess for improved resistance.
2023-11-23 | GSE222997 | GEO