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The Pig Genome Database (PiGenome): an integrated database for pig genome research

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Abstract

We established the Pig Genome Database (PiGenome) for pig genome research. The PiGenome integrates and analyzes all publicly available genome-wide data on pigs, including UniGenes, sequence tagged sites (STS) markers, quantitative trait loci (QTLs) data, and bacterial artificial chromosome (BAC) contigs. In addition, we produced 69,545 expressed sequence tags (ESTs) from the full-length enriched cDNA libraries of six tissues and 182 BAC contig sequences, which are also included in the database. QTLs, genetic markers, and BAC end-sequencing information were collected from public databases. The full-length enriched EST data were clustered and assembled into unique sequences, contigs, and singletons. The PiGenome provides functional annotation, identification of transcripts, mapping of coding sequences, and SNP information. It also provides an advanced search interface, a disease browser, alternative-splicing events, and a comparative gene map of the pig. A graphical map view and genome browser can map ESTs, contigs, BAC contigs (from the National Institute of Animal Science), Sino-Danish Pig Genome Project transcripts, and UniGene onto pig genome sequences which include our 182 BAC contigs and publically available BAC sequences of the Wellcome Trust Sanger Institute. The PiGenome is accessible at http://pigenome.nabc.go.kr/.

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References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Archibald AL, Haley CS, Brown JF, Couperwhite S, McQueen HA et al (1995) The PiGMaP consortium linkage map of the pig (Sus scrofa). Mamm Genome 6:157–175

    Article  PubMed  CAS  Google Scholar 

  • Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D et al (2003) Strategies and tools for whole-genome alignments. Genome Res 13:73–80

    Article  PubMed  CAS  Google Scholar 

  • de Koning DJ, Janss LL, Rattink AP, van Oers PA, de Vries BJ et al (1999) Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus scrofa). Genetics 152:1679–1690

    PubMed  Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194

    PubMed  CAS  Google Scholar 

  • Fang M, Hu X, Jiang T, Braunschweig M, Hu L et al (2005) The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers. Anim Genet 36:7–13

    Article  PubMed  CAS  Google Scholar 

  • Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8:967–974

    PubMed  CAS  Google Scholar 

  • Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202

    PubMed  CAS  Google Scholar 

  • Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F et al (2007) Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol 8:R45

    Article  PubMed  Google Scholar 

  • Grindflek E, Szyda J, Liu Z, Lien S (2001) Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross. Mamm Genome 12:299–304

    Article  PubMed  CAS  Google Scholar 

  • Hu J, Mungall C, Law A, Papworth R, Nelson JP et al (2001) The ARKdb: genome databases for farmed and other animals. Nucleic Acids Res 29:106–110

    Article  PubMed  CAS  Google Scholar 

  • Hu ZL, Dracheva S, Jang W, Maglott D, Bastiaansen J et al (2005) A QTL resource and comparison tool for pigs: PigQTLDB. Mamm Genome 16:792–800

    Article  PubMed  Google Scholar 

  • Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed  CAS  Google Scholar 

  • Jeon JT, Park EW, Jeon HJ, Kim TH, Lee KT et al (2003) A large-insert porcine library with sevenfold genome coverage: a tool for positional cloning of candidate genes for major quantitative traits. Mol Cells 16:113–116

    PubMed  CAS  Google Scholar 

  • Kim H, Lim D, Han BK, Sung S, Jeon M et al (2006a) ChickGCE: a novel germ cell EST database for studying the early developmental stage in chickens. Genomics 88:252–257

    Article  PubMed  CAS  Google Scholar 

  • Kim TH, Kim NS, Lim D, Lee KT, Oh JH et al (2006b) Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue. BMC Genomics 7:36

    Article  PubMed  Google Scholar 

  • Ovilo C, Perez-Enciso M, Barragan C, Clop A, Rodriquez C et al (2000) A QTL for intramuscular fat and backfat thickness is located on porcine chromosome 6. Mamm Genome 11:344–346

    Article  PubMed  CAS  Google Scholar 

  • Ovilo C, Clop A, Noguera JL, Oliver MA, Barragan C et al (2002) Quantitative trait locus mapping for meat quality traits in an Iberian × Landrace F2 pig population. J Anim Sci 80:2801–2808

    PubMed  CAS  Google Scholar 

  • Rohrer GA, Alexander LJ, Hu Z, Smith TP, Keele JW et al (1996) A comprehensive map of the porcine genome. Genome Res 6:371–391

    Article  PubMed  CAS  Google Scholar 

  • Rothschild MF (2003) From a sow’s ear to a silk purse: real progress in porcine genomics. Cytogenet Genome Res 102:95–99

    Article  PubMed  CAS  Google Scholar 

  • Ruan J, Guo Y, Li H, Hu Y, Song F et al (2007) PigGIS: Pig Genomic Informatics System. Nucleic Acids Res 35:D654–D657

    Article  PubMed  CAS  Google Scholar 

  • Stapleton M, Carlson J, Brokstein P, Yu C, Champe M et al (2002) A Drosophila full-length cDNA resource. Genome Biol 3:RESEARCH0080

    Google Scholar 

  • Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (1997) Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library. Gene 200:149–156

    Article  PubMed  CAS  Google Scholar 

  • Szyda J, Liu Z, Grindflek E, Lien S (2002) Application of a mixed inheritance model to the detection of quantitative trait loci in swine. J Appl Genet 43:69–83

    PubMed  Google Scholar 

  • Uenishi H, Eguchi T, Suzuki K, Sawazaki T, Toki D et al (2004) PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. Nucleic Acids Res 32:D484–D488

    Article  PubMed  Google Scholar 

  • Venter JC, Adams MD, Sutton GG, Kerlavage AR, Smith HO et al (1998) Shotgun sequencing of the human genome. Science 280:1540–1542

    Article  PubMed  CAS  Google Scholar 

  • Vodicka P, Smetana K Jr, Dvorankova B, Emerick T, Xu YZ et al (2005) The miniature pig as an animal model in biomedical research. Ann NY Acad Sci 1049:161–171

    Article  PubMed  Google Scholar 

  • Wall DP, Fraser HB, Hirsh AE (2003) Detecting putative orthologs. Bioinformatics 19:1710–1711

    Article  PubMed  CAS  Google Scholar 

  • Womack JE (2005) Advances in livestock genomics: opening the barn door. Genome Res 15:1699–1705

    Article  PubMed  CAS  Google Scholar 

  • Zhuo D, Zhao WD, Wright FA, Yang HY, Wang JP et al (2001) Assembly, annotation, and integration of UNIGENE clusters into the human genome draft. Genome Res 11:904–918

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by a grant from the National Institute of Animal Science (H. Kim) and from the Biogreen21 Project (20050301034467) of the Korean Rural Development Administration (S.-K. Im).

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Authors and Affiliations

  1. Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University (SNU), Seoul, 151-742, South Korea

    Dajeong Lim, Yeonkyung Kang, Samsun Sung, Jungrye Nam & Heebal Kim

  2. Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Omokchun-dong 564, Kwonsun-gu, South Korea

    Dajeong Lim, Yong-Min Cho, Kyung-Tai Lee, Eung-Woo Park, Sung-Jong Oh & Seok-Ki Im

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  1. Dajeong Lim
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  2. Yong-Min Cho
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  3. Kyung-Tai Lee
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  4. Yeonkyung Kang
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  5. Samsun Sung
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  6. Jungrye Nam
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  7. Eung-Woo Park
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  8. Sung-Jong Oh
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  9. Seok-Ki Im
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  10. Heebal Kim
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Correspondence to Heebal Kim.

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The first three authors should be regarded as joint First Authors.

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Lim, D., Cho, YM., Lee, KT. et al. The Pig Genome Database (PiGenome): an integrated database for pig genome research. Mamm Genome 20, 60–66 (2009). https://doi.org/10.1007/s00335-008-9156-3

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  • DOI: https://doi.org/10.1007/s00335-008-9156-3

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