Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1155196 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30568500.fastq.gz | Fastqsanger.gz | |||
| SRR30568501.fastq.gz | Fastqsanger.gz | |||
| SRR30568502.fastq.gz | Fastqsanger.gz | |||
| SRR30568503.fastq.gz | Fastqsanger.gz | |||
| SRR30568504.fastq.gz | Fastqsanger.gz |
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Project description:Brochosomes are a unique coating on the integuments of Cicadellidae produced in specialized glandular sections of Malpighian tubules. However, knowledge of the protein composition of brochosome is very limited. In this study, transcriptomic and proteomic profiling was performed to characterize the protein composition of the brochosome in rice green leafhopper Nephotettix cincticeps. Brochosomes were collected from the forewings of leafhoppers using ultrasonic treatment allowing for more effective brochosome collection and shock treatment resulting in purer brochosomes . After combined proteomic and transcriptomic analysis, 12 putative major structural proteins of the brochosome (BSM) and 10 brochosome-associated proteins (BSAP) were identified. Each BSM has specific conserved motifs containing several cysteines cross-linked by disulfide bonds. BSAP, which may be loosely linked to the outer and inner surfaces of the brochosomes, might play an important role in the proper folding of the BSM and resisting pathogens. Apart from a few BSAPs associated with cyclase, homologs of BSM and BSAP were present exclusively in the insect family Cicadellidae rather than other Hemiptera species, suggesting that these proteins might be encoded by an orphan gene family specific to the Cicadellidae. This is the first study to identify and characterize the protein composition of the brochosome of N. cincticeps, which will provide a solid foundation for further studies of brochosome synthesis, function, and evolutionary origins.
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Project description:Phylogenomics of endemic Australian Ulopinae (Hemiptera: Cicadomorpha: Cicadellidae)
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Project description:Background: Differences in levels of gene expression among individuals are an important source of phenotypic variation within populations. Recent microarray studies have revealed that expression variation is abundant in many species, including Drosophila melanogaster. However, previous expression surveys in this species generally focused on a small number of laboratory strains established from derived populations. Thus, these studies were not ideal for population genetic analyses. Results: We surveyed gene expression variation in adult males of 16 D. melanogaster strains from two natural populations, including an ancestral African population and a derived European population. Levels of expression polymorphism were nearly equal in the two populations, but a higher number of differences was detected when comparing strains between populations. Expression variation was greatest for genes associated with few molecular functions or biological processes, as well as those expressed predominantly in males. Our analysis also identified genes that differed in expression level between the European and African populations, which may be candidates for adaptive regulatory evolution. Genes involved in flight musculature and fatty acid metabolism were over-represented in the list of candidates. Conclusions: Overall, stabilizing selection appears to be the major force governing gene expression variation within populations. However, positive selection may be responsible for much of the between-population expression divergence. The nature of the genes identified to differ in expression between populations may reveal which traits were important for local adaptation to the European and African environments. Keywords: Natural variation
2008-01-21 | GSE8843 | GEO
Project description:In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations.
2009-03-23 | GSE9703 | GEO
Project description:In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations. Exon level expression on 176 HapMap cell lines.
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2014-06-03 | GSE51150 | GEO
Project description:Background: Differences in levels of gene expression among individuals are an important source of phenotypic variation within populations. Recent microarray studies have revealed that expression variation is abundant in many species, including Drosophila melanogaster. However, previous expression surveys in this species generally focused on a small number of laboratory strains established from derived populations. Thus, these studies were not ideal for population genetic analyses. Results: We surveyed gene expression variation in adult males of 16 D. melanogaster strains from two natural populations, including an ancestral African population and a derived European population. Levels of expression polymorphism were nearly equal in the two populations, but a higher number of differences was detected when comparing strains between populations. Expression variation was greatest for genes associated with few molecular functions or biological processes, as well as those expressed predominantly in males. Our analysis also identified genes that differed in expression level between the European and African populations, which may be candidates for adaptive regulatory evolution. Genes involved in flight musculature and fatty acid metabolism were over-represented in the list of candidates. Conclusions: Overall, stabilizing selection appears to be the major force governing gene expression variation within populations. However, positive selection may be responsible for much of the between-population expression divergence. The nature of the genes identified to differ in expression between populations may reveal which traits were important for local adaptation to the European and African environments. We used dual channel microarrays to compare genome-wide expression profiles in adult males from 16 inbred strains derived from two natural populations. In total 80 hybidizations were performed including dye-swaps. The hybridization scheme consisted of a balanced loop design, which allowed an unbiased comparison of relative expression levels within and between populations.
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