Plant & Animal Genomes XVIII Conference Plant & Animal Genomes XVIII ConferenceJanuary 9-13, 2010
Town & Country Convention Center
San Diego, CA
Zhi-Qiang Du , Danielle M. Gorbach , Zhiliang Hu , Max F. Rothschild
Segmental duplications could constitute a major part of the genome, define important phenotypes, lead to genomic instability, the origination of new genes and possibly the development of disease. The latest pig genome sequences (Ensembl Build8) were downloaded, and a local database was built. Duplicated intra- and inter-chromosomal segments (>1kb, >90% identity), covering 7.5% of the whole genome, were retrieved by first using Megablast between two chromosomes and then an in-house parsing Perl scripts. Gene lists of the current pig genome (build8) were downloaded from Ensembl using Biomart, and used to find 1,269 genes having segmental duplicated regions. Gene enrichment analyses were performed using DAVID and InnateDB based on gene ontology annotation. Interestingly, 658 genes were involved in lipid, fatty acid and sterol regulation, and significantly clustered with gene expression data from adipocytes, which includes intra-chromosomal duplicated genes vital to adipogenesis, e.g. FTO, PPARG, CLOCK, IGF2BP2 and SCAP. Unlike other species, the duplication of these fatness genes appears specific to pig, potentially due to the long history of evolution and selection. Similar to humans and mice, genes involved in immunity and olfactory pathways were also enriched, as well as genes for growth and reproduction. However, the functional importance of these duplicated genes needs further investigation. Comparison using copy number variation data from the Illumina Porcine SNPchip and analysis of nucleotide substitution rates in these segmental duplication regions for sketching the evolutionary footprints of individual genes will be our next step for dissecting the role of segmental duplication in pigs.