Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization

2008-10-09 | GSE13128 | GEO

New Records of Xylaria Species in Korea: X. ripicola sp. nov. and X. tentaculata.

Project description:During a Korean mushroom diversity survey from 2011 to 2014, we found one new Xylaria species (X. ripicola sp. nov.) and one Xylaria species that had not been previously observed in Korea (X. tentaculata). To confirm the phylogenetic placement of the new species, we conducted a phylogenetic investigation based on internal transcribed spacer regions of ribosomal DNA sequences. Additionally, the new species, X. ripicola, was subsequently analyzed for RNA polymerase II subunit sequences. We also evaluated the macroscopic and microscopic features of this species. Herein, X. ripicola is described as a new species that was collected from a natural beach habitat and X. tentaculata is formally reported as newly found in Korea.

| S-EPMC4838588 | biostudies-literature

SNP genotyping analyses for the Chinese indigenous pig breeds and commercial pig breeds

2013-05-09 | GSE46733 | GEO

SNP genotyping analyses for the Chinese indigenous pig breeds and commercial pig breeds

Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification. 9 Chinese indigenous pig, 4 commercial pigs and 1 wild pig were genotyped by PorcineSNP60 array (Illumina) for exploring the phylogeny relationships among them.

2013-05-09 | E-GEOD-46733 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data