TY - CONF
T1 - Annotation of novel and conserved microRNA Genes in the Build 10 Sus scrofa Reference Genome and determination of their expression levels in ten different tissues
AU - Thomsen, B.
AU - Nielsen, M.
AU - Hornshoj, H.
AU - Nielsen, R.
AU - Groenen, M.
AU - Archibald, A.
AU - Rund, L.
AU - Schook, L.
AU - Bendixen, C.
N1 - Annotation of novel and conserved microRNA Genes in the Build 10 Sus scrofa Reference Genome and determination of their expression levels in ten different tissues
Conference paper abstract. Published NOT IN FILE Prog. 1 Proj. Author allocation: 4 ; 4 ; 4 ; 4 ; 1 ; 4 ; 4 ; 4
PY - 2011
Y1 - 2011
N2 - The DNA template used in the pig genome sequencing project was provided by a Duroc pig named TJ Tabasco. In an effort to annotate microRNA (miRNA) genes in the reference genome we have conducted deep sequencing to determine the miRNA transcriptomes in ten different tissues isolated from Pinky, a genetically identical clone of TJ Tabasco. The purpose was to generate miRNA sequences that are highly homologous to the reference genome sequence, which along with computational prediction will improve confidence in the genomic annotation of miRNA genes. Based on homology searches of the sequence data against miRBase, we identified more than 600 conserved known miRNA/miRNA*, which is a significant increase relative to the 211 porcine miRNA/miRNA* deposited in the current version of miRBase. Furthermore, the genome-wide transcript profiles provided important information on the relative abundance and tissue-specificity of miRNA expression. In addition, we are currently analyzing our data using miRDeep for de novo discovery and annotation of the pig genome with both conserved and novel miRNAs. So far this analysis revealed the identity and genomic position of 535 miRNA genes of which 97 were novel genes without similarity to entries in miRBase/rfam. These data provide the most comprehensive annotation of the pig reference genome with experimentally verified, novel and conserved porcine miRNAs to date.
AB - The DNA template used in the pig genome sequencing project was provided by a Duroc pig named TJ Tabasco. In an effort to annotate microRNA (miRNA) genes in the reference genome we have conducted deep sequencing to determine the miRNA transcriptomes in ten different tissues isolated from Pinky, a genetically identical clone of TJ Tabasco. The purpose was to generate miRNA sequences that are highly homologous to the reference genome sequence, which along with computational prediction will improve confidence in the genomic annotation of miRNA genes. Based on homology searches of the sequence data against miRBase, we identified more than 600 conserved known miRNA/miRNA*, which is a significant increase relative to the 211 porcine miRNA/miRNA* deposited in the current version of miRBase. Furthermore, the genome-wide transcript profiles provided important information on the relative abundance and tissue-specificity of miRNA expression. In addition, we are currently analyzing our data using miRDeep for de novo discovery and annotation of the pig genome with both conserved and novel miRNAs. So far this analysis revealed the identity and genomic position of 535 miRNA genes of which 97 were novel genes without similarity to entries in miRBase/rfam. These data provide the most comprehensive annotation of the pig reference genome with experimentally verified, novel and conserved porcine miRNAs to date.
M3 - Abstract
SP - abstract P605
T2 - Plant & Animal Genomes XIX Conference
Y2 - 15 January 2011 through 19 January 2011
ER -