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Open Access Research

Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17

Elizabeth A Hart1*, Mario Caccamo1, Jennifer L Harrow1, Sean J Humphray1, James GR Gilbert1, Steve Trevanion1, Tim Hubbard1, Jane Rogers1 and Max F Rothschild2

Author Affiliations

1 Wellcome Trust Sanger Institute, Wellcome Tust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

2 Centre for Integrated Animal Genomics, Kildee Hall, Iowa State University, Ames, IA 50011, USA

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Genome Biology 2007, 8:R168  doi:10.1186/gb-2007-8-8-r168

Published: 17 August 2007

Abstract

Background

We describe here the sequencing, annotation and comparative analysis of an 8 Mb region of pig chromosome 17, which provides a useful test region to assess coverage and quality for the pig genome sequencing project. We report our findings comparing the annotation of draft sequence assembled at different depths of coverage.

Results

Within this region we annotated 71 loci, of which 53 are orthologous to human known coding genes. When compared to the syntenic regions in human (20q13.13-q13.33) and mouse (chromosome 2, 167.5 Mb-178.3 Mb), this region was found to be highly conserved with respect to gene order. The most notable difference between the three species is the presence of a large expansion of zinc finger coding genes and pseudogenes on mouse chromosome 2 between Edn3 and Phactr3 that is absent from pig and human. All of our annotation has been made publicly available in the Vertebrate Genome Annotation browser, VEGA. We assessed the impact of coverage on sequence assembly across this region and found, as expected, that increased sequence depth resulted in fewer, longer contigs. One-third of our annotated loci could not be fully re-aligned back to the low coverage version of the sequence, principally because the transcripts are fragmented over several contigs.

Conclusion

We have demonstrated the considerable advantages of sequencing at increased read depths and discuss the implications that lower coverage sequence may have on subsequent comparative and functional studies, particularly those involving complex loci such as GNAS.