The Sino-Danish Pig Genome Project

Short Background

The Sino-Danish pig genome sequencing project has generated a resource of 3.8 million shotgun reads 0.66 coverage and approximately 1 million EST sequences.

Due to the funding from The National Committee of Pig Breeding, Health and Production it was possible to establish the Sino-Danish pig genome project which originally was a collaboration between the Beijing Genomics Institute, the Royal Veterinary and Agricultural University (now University of Copenhagen, faculty of Life Sciences) and the Danish Institute of Agricultural Sciences (now University of Aarhus, faculty of Agricultural Sciences). The Technical University of Denmark and University of Aarhus were concurrently involved in the project.

Resources

Here is a short list of generated resources:

• Genomic sequences.
• EST sequences.
• EST resource: Expression analysis, ncRNA, and mitochondria: pigest.ku.dk and pigest.ku.dk/more.
• EST resource: SNP analysis available at DIAS http://snp.agrsci.dk.
• Micro satelites.

Selected papers

(General screens of the data)

• EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues
  Karsten Scheibye-Alsing, Susanna Cirera, Michael J. Gilchrist, Merete Fredholm, Jan Gorodkin
  BMC Genomics, 8:367 (Oct 11), 2007.

• Detection of RNA structures in porcine EST data and related mammals
  Stefan E Seemann, Michael J Gilchrist, Ivo L Hofacker, Peter F Stadler, Jan Gorodkin
  BMC Genomics, 8:316 (Sep 10), 2007.

• SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
  Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B Madsen, Anette Høj, Rikke K Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J Nielsen, Jakob H Havgaard, Søren Brunak, Merete Fredholm, Christian Bendixen
  Bioinformatics 23(13):i387-i391, 2007.

• Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
  Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J Nielsen, Jakob H Havgaard, Carina Rosenkilde, Jun Wang, Heng Li, Ruiqiang Li, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Jun Yu, Jian Wang, Hans-Henrik Stærfeldt, Rasmus Wernersson, Lone B Madsen, Bo Thomsen, Henrik Hornshøj, Zhan Bujie, Xuegang Wang, Xuefei Wang, Lars Bolund, Søren Brunak, Huanming Yang, Christian Bendixen, Merete Fredholm
  Genome Biology, 8:R45, (Apr 2), 2007.

• Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
  Rasmus Wernersson, Mikkel H Schierup, Frank G Jorgensen, Jan Gorodkin, Frank Panitz, Hans-Henrik Staerfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshoj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane K-S Wong, Jun Yu, Jian Wang, Christian Bendixen, Merete Fredholm, Soren Brunak, Huanming Yang, Lars Bolund
  BMC Genomics, 6:70 (May 10), 2005

Funding

This resource was supported by

• The National Committee of Pig Breeding, Health and Production.
• The Ministry of Food, Agriculture and Fisheries.
• The Danish Research Councils: SJVF and STVF (now FTP).
• The Danish Center for Scientific Computing.