Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.
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.
Hart
Elizabeth A
EA
Wellcome Trust Sanger Institute, Wellcome Tust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. eah@sanger.ac.uk
Caccamo
Mario
M
Harrow
Jennifer L
JL
Humphray
Sean J
SJ
Gilbert
James G R
JG
Trevanion
Steve
S
Hubbard
Tim
T
Rogers
Jane
J
Rothschild
Max F
MF
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
D018832:Molecular Chaperones; D033921:Vesicular Transport Proteins; C112806:prefoldin; D003577:Cytochrome P-450 Enzyme System; D054562:Protein Tyrosine Phosphatase, Non-Receptor Type 1
EMBO J. 2001 Jul 16;20(14):3849-60
11447126
Diabetes. 2000 Dec;49(12):2212-6
11118028
Mamm Genome. 2002 Feb;13(2):74-9
11889554
Genes Chromosomes Cancer. 2002 Dec;35(4):311-7
12378525
Genes Chromosomes Cancer. 2002 Dec;35(4):353-8
12378529
Hum Mol Genet. 2003 May 15;12(10):1121-30
12719376
Nucleic Acids Res. 2003 Aug 1;31(15):4663-72
12888528
Genome Biol. 2003;4(10):231
14519192
Trends Endocrinol Metab. 2004 Apr;15(3):129-35
15046742
Genome Res. 2004 May;14(5):934-41
15123589
Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8366-71
15148396
J Anim Sci. 2004 Aug;82(8):2213-28
15318717
BMC Bioinformatics. 2005;6:245
16216129
Peptides. 2006 Feb;27(2):281-90
16434123
Anim Genet. 2006 Jun;37(3):296-7
16734700
J Comput Biol. 2006 Jul-Aug;13(6):1177-96
16901236
Genome Biol. 2006;7 Suppl 1:S4.1-9
16925838
Curr Opin Genet Dev. 2006 Dec;16(6):545-52
17055251
PLoS One. 2007;2(5):e484
17534434
Genome Biol. 2007;8(7):R139
17625002
Diabetes. 2004 Nov;53(11):3007-12
15504984
Cell. 1976 Sep;9(1):91-9
788919
Proc Natl Acad Sci U S A. 1988 Apr;85(7):2081-5
3127824
Genomics. 1988 Apr;2(3):231-9
3294162
Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2156-60
8134364
Cancer Res. 1994 Aug 15;54(16):4257-60
8044767
Nature. 1994 Dec 22-29;372(6508):804-9
7997272
J Biol Chem. 1997 Apr 25;272(17):11657-62
9111083
Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8703-8
9671742
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
9862982
Clin Cancer Res. 2005 Jan 15;11(2 Pt 1):612-20
15701848
BMC Bioinformatics. 2005;6:31
15713233
Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3342-6
10716699
Hum Mol Genet. 2000 Mar 22;9(5):835-41
10749992
Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):7947-50
10859367
Hum Genet. 2000 Aug;107(2):165-75
11030415
Mamm Genome. 2001 Aug;12(8):630-6
11471058