Symbiont metagenome
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ABSTRACT:
PROVIDER: PRJNA182333 | ENA |
REPOSITORIES: ENA
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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: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: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: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: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. Two biological replicates, four treatments (males, asexual females at long day, asexual females at short day, sexual females), dye flip
2011-09-13 | E-GEOD-31024 | biostudies-arrayexpress
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:Intra-host symbiont diversity and extended symbiont maintenance in photosymbiotic Acantharea (clade F)
| PRJEB24538 | ENA
Project description:To study the population genetics context of the Saqqaq individual we carried out Illumina Bead-Array-based genotyping on four native North American and twelve north Asian populations.
2010-11-30 | GSE22494 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE11944: Mucosal Glycan Foraging Enhances the Fitness and Transmission of a Saccharolytic Human Distal Gut Symbiont GSE11953: Mucosal Glycan Foraging Enhances the Fitness and Transmission of a Saccharolytic Human Distal Gut Symbiont: ECF mutant GSE11962: Growth of B. thetaiotaomicron on purified host mucosal glycans and glycan fragments Refer to individual Series
2008-11-20 | E-GEOD-11980 | biostudies-arrayexpress