Natural variation in P. pacificus transcriptomes
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ABSTRACT:
PROVIDER: PRJEB27362 | ENA |
REPOSITORIES: ENA
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Project description:Pristionchus pacificus has emerged as a valuable model system for comparative and evolutionary-developmental biology (evo-devo) studies alongside the classic model nematode C. elegans. Previous studies have identified a lack of conservation of genetic networks underlying conserved traits, referred to as developmental systems drift. However, the conservation – or lack thereof – of epigenetic pathways which regulate development have not been investigated. In the manuscript associated with this study, we present an “epigenetic toolkit” for P. pacificus and C. elegans to compare and contrast epigenetic pathways. Assembly of this toolkit was done by identifying orthologous genes, including the “writers” and “erasers” of histone modifications. To complement this evolutionary approach, here we produce a data set of the suite of histone modifications present in P. pacificus.
2024-03-14 | PXD046748 | Pride
Project description:Ixodes pacificus, the vector of Borrelia burgdorferi (Bb) on the west coast, feeds on a variety of hosts including rodents, birds, and lizards. While rodents are reservoirs for Bb and can infect juvenile ticks, lizards are Bb-refractory. Despite the range of bloodmeals for I. pacificus, it is undetermined how larval host bloodmeal identity may affect future nymphal vector competence. Here, we conducted a transcriptome analysis on I. pacificus to determine whether and through what mechanisms host bloodmeal history affects vector competency of I. pacificus for the Lyme disease pathogen.
2021-04-27 | GSE173109 | GEO
Project description:Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Bacillus thuringiensis DB27, Staphylococcus aureus, and Serratia marcescens.
2012-03-21 | GSE36523 | GEO
Project description:Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Serratia marcescens for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including , Bacillus thuringiensis DB27, Serratia marcescens and Xenorhabdus nematophila.
2012-03-21 | GSE36521 | GEO
Project description:Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Staphylococcus aureus for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including , Bacillus thuringiensis DB27, Serratia marcescens and Xenorhabdus nematophila.
2012-03-21 | GSE36519 | GEO
Project description:Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Staphylococcus aureus, Serratia marcescens and Xenorhabdus nematophila.
2012-03-21 | GSE36517 | GEO
Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.
2009-12-17 | GSE19440 | GEO
Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers. Twelve C. elegans natural isolate samples were studied. There were no replicates or dye-swap hybridizations.
2010-05-17 | E-GEOD-19440 | biostudies-arrayexpress
Project description:Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Staphylococcus aureus for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including , Bacillus thuringiensis DB27, Serratia marcescens and Xenorhabdus nematophila. One-condition experiments. P. pacificus young adults: Exposed to Staphylococcus aureus versus exposed to E. coli OP50 : 4 hours. 3 biological replicates for each condition, including 2 dye-swaps.
2012-03-21 | E-GEOD-36519 | biostudies-arrayexpress
Project description:Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. Other experiments which are a part of this study include expression profiling of C. elegans and P. pacificus on other pathogens including Bacillus thuringiensis DB27, Staphylococcus aureus, and Serratia marcescens. One-condition experiments. P. pacificus young adults: Exposed to Xenorhabdus nematophila versus exposed to E. coli OP50 : 4 hours. 4 biological replicates for each condition, including 2 dye-swaps.
2012-03-21 | E-GEOD-36523 | biostudies-arrayexpress