A high quality reference genome for pigs
The Roslin Institute jointly led efforts to produce the first complete DNA sequence for pigs and produced the first atlas of gene expression in multiple tissues.
Pigs are an incredibly important species, providing food for millions around the globe and acting as an important model for human disease. The Roslin Institute jointly led efforts to produce the first complete DNA sequence for pigs (published in 2012). We produced the first atlas of gene expression in multiple tissues the same year, resulting in a new Affymetrix GeneChip for pigs being made available. We also created cost-effective kits for studying pig genome variation.
However, we soon discovered certain regions of the first pig genome could not be trusted and set out to create a new, higher quality reference genome. In collaboration with others we are exploiting the latest long read sequencing technology to establish an improved reference genome sequence that is more than 500x more contiguous than the published draft. This new assembly has been deposited in the public sequence databases under the pre-publication data release terms of the Toronto Statement. The annotation of the new assembly in collaboration with the Ensembl team at EMBL-EBI is supported by a joint BBSRC research grant.
Future work in this area will involve complete annotation of all full-length genes and transcripts in the reference genome and population genomics to understand genome evolution and adaptation to different environments around the globe.
- A gene expression atlas of the domestic pig. BMC Biology 10 (2012)
The First Exome Sequence Completed in Pigs (press release, 2014)
Identifying low-confidence regions in the Sscrofa10.2 reference genome. Plant and Animal Genome XXIV conference 2016.
W137: Exploiting Long Read Sequencing Technologies to Establish High Quality Highly Contiguous Pig Reference Genome Assemblies. Plant and Animal Genome XXV conference 2017
Prepublication data sharing. Nature 461:168-70 (2009)