Project description:The evolutionary and functional analysis of Korean native pig was performed using single nucleotide polymorphism data by comparative and population genomic approaches with six different mammalian species and five pig breeds.
2019-09-16 | PRJEB34412 | EVA
Project description:Population and evolutionary analysis of Korean native duck using whole-genome sequencing data
Project description:The population and evolutionary analysis of Korean native duck was performed using single nucleotide polymorphism data by comparative and population genomic approaches with fourteen different duck breeds.
Project description:Anim Genet. 2009 Feb;40(1):115-8. Epub 2008 Oct 17. Differentially expressed transcripts in adipose tissue between Korean native pig and Yorkshire breeds. Moon JK, Kim KS, Kim JJ, Choi BH, Cho BW, Kim TH, Lee CK. Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, South Korea. We measured and compared the transcripts of adipose tissue from Korean native pig (KNP) and Yorkshire (YS) breeds to investigate breed-specific transcription changes. We employed both the Affymetrix porcine genome array and quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We found eight genes showing significant changes between the two breeds. Based on a literature review, these genes were indicative of differences in extracellular structure density and differences in the potential to metabolize xenobiotic chemicals and lipids. The differentially expressed genes indicated that KNP has a lower extracellular structure density and a lower potential to metabolize xenobiotic chemicals than YS. PMID: 18945290
Project description:Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in gut microbial metagenome and host genome but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from non-synonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remain quite unexplored for human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes.
Project description:Although mitochondrial DNA single nucleotide polymorphisms have been associated with Parkinsons disease their functional effects are unclear. Here, we functionalized a PD-associative mtSNP and found that it affects a mitochondrial-derived peptide MDP.