title: Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.
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.
  
  
  CONCLUSIONS
  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.
authors: Wellcome Trust Sanger Institute, Wellcome Tust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. eah@sanger.ac.uk
authors: Elizabeth A
authors: EA
authors: Hart
authors: Mario
authors: M
authors: Caccamo
authors: Jennifer L
authors: JL
authors: Harrow
authors: Sean J
authors: SJ
authors: Humphray
authors: James G R
authors: JG
authors: Gilbert
authors: Steve
authors: S
authors: Trevanion
authors: Tim
authors: T
authors: Hubbard
authors: Jane
authors: J
authors: Rogers
authors: Max F
authors: MF
authors: Rothschild
mesh_terms: D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D033481:Chromosomes, Mammalian / Q000235:genetics; D017124:Conserved Sequence; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D023061:Gene Order; D016678:Genome; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D051379:Mice; D018832:Molecular Chaperones / Q000235:genetics; D008969:Molecular Sequence Data; D054562:Protein Tyrosine Phosphatase, Non-Receptor Type 1 / Q000235:genetics; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics*; D033921:Vesicular Transport Proteins / Q000235:genetics
chemical_list: D018832:Molecular Chaperones; D033921:Vesicular Transport Proteins; C112806:prefoldin; D003577:Cytochrome P-450 Enzyme System; D054562:Protein Tyrosine Phosphatase, Non-Receptor Type 1
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