Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Wernersson, Rasmus ^a   Schierup, Mikkel H ^b   Jørgensen, Frank G ^b   Gorodkin, Jan ^c   Panitz, Frank ^d   Stærfeldt, Hans Henrik ^a   Christensen, Ole F ^b   Mailund, Thomas ^b   Hornshøj, Henrik ^d   Klein, Ami ^c   Wang, Jun ^b,e   Liu, Bin ^e   Hu, Songnian ^e   Dong, Wei ^e   Li, Wei ^e   Wong, Gane K S ^e   Yu, Jun ^e   Wang, Jian ^e   Bendixen, Christian ^d   Fredholm, Merete ^c   Brunak, Søren ^a   Yang, Huanming ^e   Bolund, Lars ^b,e   more..

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b AARHUS UNIVERSITY   (Denmark)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d DANISH INSTITUTE OF AGRICULTURAL SCIENCES   (Denmark)

^e BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; CONTROLLED STUDY; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC DISTANCE; GENETIC SELECTION; GENOME ANALYSIS; HUMAN GENOME; HUMAN VERSUS NONHUMAN DATA; ISOCHORE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; RNA PURIFICATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SWINE;

ARTIODACTYLA; MAMMALIA; SUS SCROFA;

EID: 23444460778     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-70     Document Type: Article

References (22)

1. Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, Maskeri B, Young AC, Benjamin B, Brooks SY, Coleman BI, Gupta J, Ho SL, Karlins EM, Maduro QL, Stantripop S, Tsurgeon C, Vogt JL, Walker MA, Masiello CA, Guan X, Bouffard GG, Green ED: An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Research 2004, 14:2235-2244.
2. Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green: Comparative analyses of multi-species sequences from targeted genomic regions. Nature 2003, 424:788-793.
3. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, et al. Mouse Genome Sequencing Consortium: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
4. Rat Genome Sequencing project consortium: Genome sequence of the Brown Norway rat yields insight into mammalian evolution. Nature 2004, 428:493-521.
5. The international Chimpanzee Chromosome 22 Consortium: DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 2004, 429:382-388.
6. Springer MS, Murphy WJ, Eizirik E, O'Brien SJ: Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci USA 2003, 100:1056-1061.
7. Jørgensen FG, Hobolth A, Jensen HH, Bendixen C, Fredholm M, Schierup MH: Comparative analysis of protein coding sequences from Human, Mouse and the domesticated Pig. BMC Biology 2005, 3:2.
8. Schwartz SW, Kent J, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-Mouse Alignments with BLASTZ. Genome Res 2003, 13:103-107.
9. Kent WJ, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A, Haussler D: The human genome browser at UCSC. Genome Res 2002, 12:996-1006.
10. Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7:203-214.
11. Morgenstern B: DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15:211-218.
12. Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985, 22:160-174.
13. Yang Z: PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
14. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D: Ultraconserved elementsin the human genome. Science 2004, 304:1321-1325.
15. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
16. Griffiths-Jones S: The miRNA Registry. Nucleic Acids Res 2004:D109-D111.
17. Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877.
18. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 2003, 19:651-652.
19. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T: A uniform system for microRNA annotation. RNA 2003, 9:277-279.
20. Ohta T: An examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci USA 1993, 90:10676-10680.
21. Ohta T: Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 1995, 40:56-63.
22. Belle EM, Duret L, Galtier N, Eyre-Walker A: The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol 2004, 58:653-660.