Project description:To test the conservation and evolution of long non-coding RNAs across multiple rodent species by transcriptome sequencing and histone modification mapping. Part of experiment series: E-MTAB-867 RNA-Seq, E-MTAB-959 ChIP-Seq.
Project description:To test the conservation and evolution of long non-coding RNAs across multiple rodent species by transcriptome sequencing and histone modification mapping. Part of experiment series: E-MTAB-867 RNA-Seq, E-MTAB-959 ChIP-Seq.
Project description:We have designed and experimentally validated the BactoChip, a 60-mer oligonucleotide microarray for simultaneous detection and quantification of multiple bacterial species of clinical interest. The Bactochip microarray targets a novel set of high-resolution marker genes, those genes that most unequivocally characterized each bacterial species. The accuracy of the BactoChip microarray was evaluated using the labeled total DNA of single bacterial species at different concentrations (from 65ng to more than 250ng). The specificity of the developed array was further validated using mixed cultures containing up to 15 different bacterial species in even or staggered amount. We employed the Agilent 'Custom HD-CGH 8x15k Array" (catalogue number: G4427A) and the Agilent'Genomic DNA ULS labeling Kit" (catalogue number: 5190-0419). The microarray successfully distinguished among bacterial species from 21 different genera. The BactoChip additionally proved accurate in determining species-level relative abundances over a 10-fold dynamic range in complex bacterial communities. In combination with the continually increasing number of sequenced bacterial genomes, future iterations of the technology could enable to highly accurate clinically-oriented tools for rapid assessment of bacterial community composition and relative abundances.
Project description:The Global Pandemic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of three Bd-GPL strains have enabled studies of the pathogen but the genomic features that set Bd-GPL apart from other Bd lineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used long-read DNA sequencing to assemble high-quality genomes of three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii (Ps) strain JEL0888, and compared these to genomes of previously sequenced Bd-GPL strains. The Bd-BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. Our pan-genome analysis provided insight into shared and lineage-specific gene content. The core genome of Bd consists of 6278 conserved gene families, with 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families between Bd-BRAZIL and Bd-GPL strains though none were consistently expanded in Bd-GPL or Bd-BRAZIL strains. Comparison within the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified variation in sequence and protein domain counts. We further test these new Bd-BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these genomes as reference genomes for future studies.
